diff --git a/R/NCA_Server.R b/R/NCA_Server.R index 6052ab8..710159c 100644 --- a/R/NCA_Server.R +++ b/R/NCA_Server.R @@ -3172,7 +3172,7 @@ NCA_Server <- function(id, #'@param id_UD ID string for the upload data module used to save and load app states #'@param id_DW ID string for the data wrangling module used to save and load app states #'@param react_state Variable used within server to handle non-standard reactions (e.g. reacting to plotly) -#'@param react_state Variable passed to server to allow reaction outside of module (\code{NULL}) +#'@param react_internal Variable passed to server to allow reaction outside of module (\code{NULL}) #'@return list containing the current state of the app including default #'values from the yaml file as well as any changes made by the user. The list #'has the following structure: @@ -3809,9 +3809,20 @@ NCA_fetch_state = function(id, input, session, # Saving the caption as well current_ana[["notes"]] = state[["NCA"]][["ui"]][["text_ana_notes"]] + + # If the selected data view is different than the data view being used by + # the current analysis then we need to reset the manual flags + if(current_ana[["ana_dsview"]] != state[["NCA"]][["ui"]][["select_current_view"]]){ + if(nrow(current_ana[["manual_ds_flags"]])){ + notify_text = "Data source change detected: You will need to rerun the analysis. Manual flags reset." + state = FM_set_notification(state, notify_text, "Manual Flags Reset", "warning") } + current_ana[["manual_ds_flags"]] = data.frame() + } # updating the view id current_ana[["ana_dsview"]] = state[["NCA"]][["ui"]][["select_current_view"]] + + # Saving changes to the current analysis state = NCA_set_current_ana(state, current_ana) @@ -4363,6 +4374,8 @@ NCA_append_report = function(state, rpt, rpttype, gen_code_only=FALSE){ ' type = "ggplot",', ' content = list(', notes_str, + paste0(' height = ',state[["MC"]][["reporting"]][["dimensions"]][["figures"]][["height"]],','), + paste0(' width = ',state[["MC"]][["reporting"]][["dimensions"]][["figures"]][["width"]],','), paste0(' image = ', fg_object_name, ','), paste0(' key = "', fig_id, '",'), paste0(' caption_format = "',state[["MC"]][["reporting"]][["text_format"]],'",'), @@ -5033,6 +5046,7 @@ res} #'and reporting. Can be used for manual flagging of data. #'@param DS Dataframe containing the dataset. #'@param flag_map List with flag mapping details. +#'@param col_map List with column mapping details. #'@param ds_flags Dataframe or tibble with a column (key) for dataset row IDs #'("rec_2" for row 2) and a column (flag) for flags mapping can be found. #'@return Dataset with the following columns added for flagging data. @@ -5063,10 +5077,10 @@ flag_nca_ds = function(DS = NULL, dplyr::mutate(rmnt_hlin = NA) |> # By default no inclusions for half-life calculations dplyr::mutate(rmnt_flag = ifelse(.data[[col_conc]] == 0, "blq", - rmnt_flag)) |> # Lastly we flag all the blq values + .data[["rmnt_flag"]])) |> # Lastly we flag all the blq values dplyr::mutate(rmnt_desc = ifelse(.data[[col_conc]] == 0, flag_map[["blq"]][["description"]], - rmnt_desc)) + .data[["rmnt_desc"]])) # Its possible this is being called with no flagging funcions jsut to create # placeholders for the columns above. @@ -6509,22 +6523,22 @@ mk_table_ind_obs = function( all_data[is.na(all_data[["CONC"]]), ][["CONC"]] = not_sampled all_data[all_data[["CONC"]] == "0", ][["CONC"]] = blq all_data = all_data |> - dplyr::mutate(CONC := + dplyr::mutate(CONC = ifelse( - rmnt_flag == "censor", + .data[["rmnt_flag"]] == "censor", paste0(.data[["CONC"]], flag_map[["censor"]][["snmd"]]), .data[["CONC"]])) |> - dplyr::mutate(CONC := + dplyr::mutate(CONC = ifelse( - rmnt_flag == "hlex", + .data[["rmnt_flag"]] == "hlex", paste0(.data[["CONC"]], flag_map[["hlex"]][["snmd"]]), .data[["CONC"]])) |> - dplyr::mutate(CONC := + dplyr::mutate(CONC = ifelse( - rmnt_flag == "hlin", + .data[["rmnt_flag"]] == "hlin", paste0(.data[["CONC"]], flag_map[["hlin"]][["snmd"]]), .data[["CONC"]])) |> - dplyr::select(-rmnt_flag) + dplyr::select(-.data[["rmnt_flag"]]) if(rows_by == "time"){ @@ -6849,10 +6863,16 @@ mk_figure_ind_obs = function( } p = p + ggplot2::xlab(TIME_LAB) p = p + ggplot2::ylab(OBS_LAB) - p = p + ggplot2::labs(color="Data Type") - p = p + ggplot2::theme(legend.position="bottom") + p = p + ggplot2::labs(color="Data Flag", shape="Analyte") + p = p + ggplot2::theme(legend.position="bottom", + legend.box="horizontal") p = p + scale_color_manual(values = fcolors) - + p = p + guides(colour = guide_legend(title.position = "top", ncol=3)) + p = p + guides(shape = guide_legend(title.position = "top", ncol=3)) + p = p + theme(legend.spacing.x = unit(.01, "cm")) + p = p + theme(legend.key.spacing.x = unit(.01, "cm")) + + figures[[fig_key]]$gg = p figures[[fig_key]]$notes = NULL @@ -7013,7 +7033,6 @@ obj} #'@param type Type of table to generate. Can be either \code{"individual"} or \code{"summary"]}. #'@param grouping How to group columns in tables. Can be either \code{"interval"} or \code{"parameter"]}. #'@param flag_map List with flag mapping details. -#'@param not_calc Text string to replace NA values with to indicated values were not calculated. #'@param mult_str Text string to replace * values in units. #'@param infinity Text string to replace infinity in time intervals in column headers. #'@param obnd onbrand reporting object. @@ -7399,7 +7418,7 @@ state} #'\itemize{ #' \item{isgood:} Return status of the function. #' \item{msgs:} Messages to be passed back to the user. -#' \item{dose_rec:} +#' \item{dose_rec:} Tibble with dose records for PKNCA #'} #'@example inst/test_apps/nca_programming_funcs.R dose_records_builder = function( @@ -7412,6 +7431,7 @@ dose_records_builder = function( col_id = col_map[["col_id"]] col_time = col_map[["col_time"]] col_ntime = col_map[["col_ntime"]] + col_evid = col_map[["col_evid"]] col_route = col_map[["col_route"]] col_cycle = col_map[["col_cycle"]] col_dur = col_map[["col_dur"]] diff --git a/docs/articles/noncompartmental_analysis.html b/docs/articles/noncompartmental_analysis.html index 6ce3567..8c88bbd 100644 --- a/docs/articles/noncompartmental_analysis.html +++ b/docs/articles/noncompartmental_analysis.html @@ -290,6 +290,10 @@

Configuration FileConfiguration FileConfiguration FileExamples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -266,13 +266,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 75c19f542448528f50a070072ed90799 -#> → CTS: module checksum updated: eb1f10774687f524e98f2fcc6617d56c +#> → CTS: cohort checksum updated: e47262ff3e2003fbfc10c44a389b8ace +#> → CTS: module checksum updated: 7c4d737accc0fa0175a668028ec34700 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -294,12 +294,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: 28e2207aa4406058581cc1db6c254922 -#> → CTS: module checksum updated: 3e5b409bb78a8269250fc30431a68984 +#> → CTS: cohort checksum updated: d4227893b5f4a45470743252f5fe79b4 +#> → CTS: module checksum updated: 2951b84d38e46c9a0d5b055aae290e6e #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 018b906c957a38b755ba203462eb83d4 -#> → CTS: module checksum updated: f87dc7d6a90ae82e48db9261029337de +#> → CTS: cohort checksum updated: e25e3cf2c09b7e8000eec2ae50676cc2 +#> → CTS: module checksum updated: d79562f73fd76b97358fbc81daf6f29c # } diff --git a/docs/reference/CTS_add_rule.html b/docs/reference/CTS_add_rule.html index 0b99935..a566d5a 100644 --- a/docs/reference/CTS_add_rule.html +++ b/docs/reference/CTS_add_rule.html @@ -236,38 +236,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -281,13 +281,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 75c19f542448528f50a070072ed90799 -#> → CTS: module checksum updated: eb1f10774687f524e98f2fcc6617d56c +#> → CTS: cohort checksum updated: e47262ff3e2003fbfc10c44a389b8ace +#> → CTS: module checksum updated: 7c4d737accc0fa0175a668028ec34700 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -309,12 +309,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: 28e2207aa4406058581cc1db6c254922 -#> → CTS: module checksum updated: 3e5b409bb78a8269250fc30431a68984 +#> → CTS: cohort checksum updated: d4227893b5f4a45470743252f5fe79b4 +#> → CTS: module checksum updated: 2951b84d38e46c9a0d5b055aae290e6e #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 018b906c957a38b755ba203462eb83d4 -#> → CTS: module checksum updated: f87dc7d6a90ae82e48db9261029337de +#> → CTS: cohort checksum updated: e25e3cf2c09b7e8000eec2ae50676cc2 +#> → CTS: module checksum updated: d79562f73fd76b97358fbc81daf6f29c # } diff --git a/docs/reference/CTS_change_source_model.html b/docs/reference/CTS_change_source_model.html index e5214dc..f677a66 100644 --- a/docs/reference/CTS_change_source_model.html +++ b/docs/reference/CTS_change_source_model.html @@ -215,38 +215,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -260,13 +260,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 75c19f542448528f50a070072ed90799 -#> → CTS: module checksum updated: eb1f10774687f524e98f2fcc6617d56c +#> → CTS: cohort checksum updated: e47262ff3e2003fbfc10c44a389b8ace +#> → CTS: module checksum updated: 7c4d737accc0fa0175a668028ec34700 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -288,12 +288,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: 28e2207aa4406058581cc1db6c254922 -#> → CTS: module checksum updated: 3e5b409bb78a8269250fc30431a68984 +#> → CTS: cohort checksum updated: d4227893b5f4a45470743252f5fe79b4 +#> → CTS: module checksum updated: 2951b84d38e46c9a0d5b055aae290e6e #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 018b906c957a38b755ba203462eb83d4 -#> → CTS: module checksum updated: f87dc7d6a90ae82e48db9261029337de +#> → CTS: cohort checksum updated: e25e3cf2c09b7e8000eec2ae50676cc2 +#> → CTS: module checksum updated: d79562f73fd76b97358fbc81daf6f29c # } diff --git a/docs/reference/CTS_del_current_element.html b/docs/reference/CTS_del_current_element.html index 8c32de2..ad749da 100644 --- a/docs/reference/CTS_del_current_element.html +++ b/docs/reference/CTS_del_current_element.html @@ -210,38 +210,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -255,13 +255,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 75c19f542448528f50a070072ed90799 -#> → CTS: module checksum updated: eb1f10774687f524e98f2fcc6617d56c +#> → CTS: cohort checksum updated: e47262ff3e2003fbfc10c44a389b8ace +#> → CTS: module checksum updated: 7c4d737accc0fa0175a668028ec34700 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -283,12 +283,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: 28e2207aa4406058581cc1db6c254922 -#> → CTS: module checksum updated: 3e5b409bb78a8269250fc30431a68984 +#> → CTS: cohort checksum updated: d4227893b5f4a45470743252f5fe79b4 +#> → CTS: module checksum updated: 2951b84d38e46c9a0d5b055aae290e6e #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 018b906c957a38b755ba203462eb83d4 -#> → CTS: module checksum updated: f87dc7d6a90ae82e48db9261029337de +#> → CTS: cohort checksum updated: e25e3cf2c09b7e8000eec2ae50676cc2 +#> → CTS: module checksum updated: d79562f73fd76b97358fbc81daf6f29c # } diff --git a/docs/reference/CTS_fetch_code.html b/docs/reference/CTS_fetch_code.html index 6950617..fed45f7 100644 --- a/docs/reference/CTS_fetch_code.html +++ b/docs/reference/CTS_fetch_code.html @@ -207,38 +207,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -252,13 +252,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 75c19f542448528f50a070072ed90799 -#> → CTS: module checksum updated: eb1f10774687f524e98f2fcc6617d56c +#> → CTS: cohort checksum updated: e47262ff3e2003fbfc10c44a389b8ace +#> → CTS: module checksum updated: 7c4d737accc0fa0175a668028ec34700 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -280,12 +280,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: 28e2207aa4406058581cc1db6c254922 -#> → CTS: module checksum updated: 3e5b409bb78a8269250fc30431a68984 +#> → CTS: cohort checksum updated: d4227893b5f4a45470743252f5fe79b4 +#> → CTS: module checksum updated: 2951b84d38e46c9a0d5b055aae290e6e #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 018b906c957a38b755ba203462eb83d4 -#> → CTS: module checksum updated: f87dc7d6a90ae82e48db9261029337de +#> → CTS: cohort checksum updated: e25e3cf2c09b7e8000eec2ae50676cc2 +#> → CTS: module checksum updated: d79562f73fd76b97358fbc81daf6f29c # } diff --git a/docs/reference/CTS_fetch_current_element.html b/docs/reference/CTS_fetch_current_element.html index c64358e..42f03f5 100644 --- a/docs/reference/CTS_fetch_current_element.html +++ b/docs/reference/CTS_fetch_current_element.html @@ -212,38 +212,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -257,13 +257,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 75c19f542448528f50a070072ed90799 -#> → CTS: module checksum updated: eb1f10774687f524e98f2fcc6617d56c +#> → CTS: cohort checksum updated: e47262ff3e2003fbfc10c44a389b8ace +#> → CTS: module checksum updated: 7c4d737accc0fa0175a668028ec34700 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -285,12 +285,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: 28e2207aa4406058581cc1db6c254922 -#> → CTS: module checksum updated: 3e5b409bb78a8269250fc30431a68984 +#> → CTS: cohort checksum updated: d4227893b5f4a45470743252f5fe79b4 +#> → CTS: module checksum updated: 2951b84d38e46c9a0d5b055aae290e6e #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 018b906c957a38b755ba203462eb83d4 -#> → CTS: module checksum updated: f87dc7d6a90ae82e48db9261029337de +#> → CTS: cohort checksum updated: e25e3cf2c09b7e8000eec2ae50676cc2 +#> → CTS: module checksum updated: d79562f73fd76b97358fbc81daf6f29c # } diff --git a/docs/reference/CTS_fetch_ds.html b/docs/reference/CTS_fetch_ds.html index 05eefc5..d2a3d5f 100644 --- a/docs/reference/CTS_fetch_ds.html +++ b/docs/reference/CTS_fetch_ds.html @@ -223,38 +223,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -268,13 +268,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 75c19f542448528f50a070072ed90799 -#> → CTS: module checksum updated: eb1f10774687f524e98f2fcc6617d56c +#> → CTS: cohort checksum updated: e47262ff3e2003fbfc10c44a389b8ace +#> → CTS: module checksum updated: 7c4d737accc0fa0175a668028ec34700 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -296,12 +296,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: 28e2207aa4406058581cc1db6c254922 -#> → CTS: module checksum updated: 3e5b409bb78a8269250fc30431a68984 +#> → CTS: cohort checksum updated: d4227893b5f4a45470743252f5fe79b4 +#> → CTS: module checksum updated: 2951b84d38e46c9a0d5b055aae290e6e #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 018b906c957a38b755ba203462eb83d4 -#> → CTS: module checksum updated: f87dc7d6a90ae82e48db9261029337de +#> → CTS: cohort checksum updated: e25e3cf2c09b7e8000eec2ae50676cc2 +#> → CTS: module checksum updated: d79562f73fd76b97358fbc81daf6f29c # } diff --git a/docs/reference/CTS_fetch_state.html b/docs/reference/CTS_fetch_state.html index 6529653..fad4903 100644 --- a/docs/reference/CTS_fetch_state.html +++ b/docs/reference/CTS_fetch_state.html @@ -154,38 +154,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE session = sess_res$session @@ -215,8 +215,8 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized diff --git a/docs/reference/CTS_init_state.html b/docs/reference/CTS_init_state.html index 6e1cd6c..bb013ad 100644 --- a/docs/reference/CTS_init_state.html +++ b/docs/reference/CTS_init_state.html @@ -122,38 +122,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE session = sess_res$session @@ -180,8 +180,8 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized state @@ -1827,8 +1827,8 @@

Examples#> 1 One compartment model MB_obj_1_rx MB MB 1 #> 2 PK Biomarker MB_obj_2_rx MB MB 2 #> checksum MDLchecksum -#> 1 69658491058a69f953ae23cd41b20506 f5021a1b0534853463c8561300f61a3f -#> 2 69658491058a69f953ae23cd41b20506 d45ca766892266932518d8cddd760207 +#> 1 0c17af67bc1326ce923c127c21da9701 71118c97a48fbc817ea06d164e658b80 +#> 2 0c17af67bc1326ce923c127c21da9701 3503e24e285b3f919ae901eaf520d871 #> code #> 1 MB_obj_1_fcn = function () \n{\n description <- "One compartment PK model with linear clearance using differential equations"\n ini({\n lka <- 0.45\n label("Absorption rate (Ka)")\n lcl <- 1\n label("Clearance (CL)")\n lvc <- 3.45\n label("Central volume of distribution (V)")\n propSd <- c(0, 0.5)\n label("Proportional residual error (fraction)")\n etalcl ~ 0.1\n etalvc ~ 0.01\n })\n model({\n ka <- exp(lka)\n cl <- exp(lcl + etalcl)\n vc <- exp(lvc + etalvc)\n kel <- cl/vc\n d/dt(depot) <- -ka * depot\n d/dt(central) <- ka * depot - kel * central\n Cc <- central/vc\n Cc ~ prop(propSd)\n })\n}\n\nMB_obj_1_rx = rxode2::rxode2(MB_obj_1_fcn)\n\nMB_obj_1_ts = list(\n system = "weeks",\n details = \n list(months = list(verb = "Months", conv = 4.13359788359788e-07), \n weeks = list(verb = "Weeks", conv = 1.65343915343915e-06), \n days = list(verb = "Days", conv = 1.15740740740741e-05), \n hours = list(verb = "Hours", conv = 0.000277777777777778))\n) #> 2 MB_obj_2_fcn = function () \n{\n ini({\n TV_F1 <- fix(2.22044604925031e-16, 0.744, Inf)\n TV_ka <- c(2.22044604925031e-16, 0.282, Inf)\n TV_CL <- c(-36.0436533891172, -1.6094379124341, 709.782712893384)\n TV_Vc <- c(-36.0436533891172, 1.28370777234479, 709.782712893384)\n TV_Vp <- c(-36.0436533891172, 1.01160091167848, 709.782712893384)\n TV_Q <- c(-36.0436533891172, -0.29169009384932, 709.782712893384)\n TV_MW <- fix(2.22044604925031e-16, 140, Inf)\n TV_BM_IC <- c(2.22044604925031e-16, 1000, Inf)\n TV_kdeg_BM <- fix(2.22044604925031e-16, 0.1, Inf)\n TV_Emax <- c(2.22044604925031e-16, 100, Inf)\n TV_EC50 <- fix(2.22044604925031e-16, 300, Inf)\n prop_err_PK <- c(2.22044604925031e-16, 0.1, Inf)\n add_err_PK <- c(2.22044604925031e-16, 0.1, Inf)\n add_err_BM <- c(2.22044604925031e-16, 0.1, Inf)\n ETAka ~ 0.416\n ETACL ~ 0.09875\n ETAVc ~ c(0.0786, 0.116)\n ETAVp ~ c(0.0619, 0.0377, 0.0789)\n ETAQ ~ 0.699\n ETABM_IC ~ 0.05\n ETAEmax ~ 0.1\n })\n model({\n F1 = TV_F1\n ka = TV_ka * exp(ETAka)\n CL = exp(TV_CL) * exp(ETACL)\n Vc = exp(TV_Vc) * exp(ETAVc)\n Cc = Ac/(Vc)\n Vp = exp(TV_Vp) * exp(ETAVp)\n Q = exp(TV_Q) * exp(ETAQ)\n MW = TV_MW\n BM_IC = TV_BM_IC * exp(ETABM_IC)\n kdeg_BM = TV_kdeg_BM\n Emax = TV_Emax * exp(ETAEmax)\n EC50 = TV_EC50\n Dinf = 0\n WTTV = 70\n CL_IND = CL * (1 + SEX_ID * 0.1) * (1 + SUBTYPE_ID * \n 0.1)\n kel = CL_IND/Vc * ((WT/WTTV))^(-0.35)\n kcp = Q/Vc * ((WT/WTTV))^(-0.35)\n kpc = Q/Vp * ((WT/WTTV))^(-0.35)\n ksyn_BM = kdeg_BM * BM_IC\n STIM = 1 + Emax * Cc/(EC50 + Cc)\n BM(0) = BM_IC\n d/dt(At) = (-ka * At)\n d/dt(Ac) = ((ka * At * F1/Vc - kel * Cc - kcp * Cc + \n kpc * Cp * Vp/Vc + Dinf/Vc)) * Vc\n d/dt(Cp) = (kcp * Cc * Vc/Vp - kpc * Cp)\n d/dt(BM) = ksyn_BM * STIM - (kdeg_BM * BM)\n C_ng_ml = Cc * MW\n C_ng_ml ~ add(add_err_PK) + prop(prop_err_PK)\n BM_obs = BM\n BM_obs ~ add(add_err_BM)\n })\n}\n\nMB_obj_2_rx = rxode2::rxode2(MB_obj_2_fcn)\n\nMB_obj_2_ts = list(\n system = "weeks",\n details = \n list(months = list(verb = "Months", conv = 4.13359788359788e-07), \n weeks = list(verb = "Weeks", conv = 1.65343915343915e-06), \n days = list(verb = "Days", conv = 1.15740740740741e-05), \n hours = list(verb = "Hours", conv = 0.000277777777777778))\n) @@ -1836,7 +1836,7 @@

Examples#> $CTS$MDL$modules #> $CTS$MDL$modules$MB #> $CTS$MDL$modules$MB$MB -#> [1] "69658491058a69f953ae23cd41b20506" +#> [1] "0c17af67bc1326ce923c127c21da9701" #> #> #> @@ -1991,10 +1991,10 @@

Examples#> [1] "MB_obj_1_fcn = function () \n{\n description <- \"One compartment PK model with linear clearance using differential equations\"\n ini({\n lka <- 0.45\n label(\"Absorption rate (Ka)\")\n lcl <- 1\n label(\"Clearance (CL)\")\n lvc <- 3.45\n label(\"Central volume of distribution (V)\")\n propSd <- c(0, 0.5)\n label(\"Proportional residual error (fraction)\")\n etalcl ~ 0.1\n etalvc ~ 0.01\n })\n model({\n ka <- exp(lka)\n cl <- exp(lcl + etalcl)\n vc <- exp(lvc + etalvc)\n kel <- cl/vc\n d/dt(depot) <- -ka * depot\n d/dt(central) <- ka * depot - kel * central\n Cc <- central/vc\n Cc ~ prop(propSd)\n })\n}\n\nMB_obj_1_rx = rxode2::rxode2(MB_obj_1_fcn)\n\nMB_obj_1_ts = list(\n system = \"weeks\",\n details = \n list(months = list(verb = \"Months\", conv = 4.13359788359788e-07), \n weeks = list(verb = \"Weeks\", conv = 1.65343915343915e-06), \n days = list(verb = \"Days\", conv = 1.15740740740741e-05), \n hours = list(verb = \"Hours\", conv = 0.000277777777777778))\n)" #> #> $CTS$MDL$mdl$MB_obj_1_rx$checksum -#> [1] "69658491058a69f953ae23cd41b20506" +#> [1] "0c17af67bc1326ce923c127c21da9701" #> #> $CTS$MDL$mdl$MB_obj_1_rx$MDLchecksum -#> [1] "f5021a1b0534853463c8561300f61a3f" +#> [1] "71118c97a48fbc817ea06d164e658b80" #> #> #> $CTS$MDL$mdl$MB_obj_2_rx @@ -2192,10 +2192,10 @@

Examples#> [1] "MB_obj_2_fcn = function () \n{\n ini({\n TV_F1 <- fix(2.22044604925031e-16, 0.744, Inf)\n TV_ka <- c(2.22044604925031e-16, 0.282, Inf)\n TV_CL <- c(-36.0436533891172, -1.6094379124341, 709.782712893384)\n TV_Vc <- c(-36.0436533891172, 1.28370777234479, 709.782712893384)\n TV_Vp <- c(-36.0436533891172, 1.01160091167848, 709.782712893384)\n TV_Q <- c(-36.0436533891172, -0.29169009384932, 709.782712893384)\n TV_MW <- fix(2.22044604925031e-16, 140, Inf)\n TV_BM_IC <- c(2.22044604925031e-16, 1000, Inf)\n TV_kdeg_BM <- fix(2.22044604925031e-16, 0.1, Inf)\n TV_Emax <- c(2.22044604925031e-16, 100, Inf)\n TV_EC50 <- fix(2.22044604925031e-16, 300, Inf)\n prop_err_PK <- c(2.22044604925031e-16, 0.1, Inf)\n add_err_PK <- c(2.22044604925031e-16, 0.1, Inf)\n add_err_BM <- c(2.22044604925031e-16, 0.1, Inf)\n ETAka ~ 0.416\n ETACL ~ 0.09875\n ETAVc ~ c(0.0786, 0.116)\n ETAVp ~ c(0.0619, 0.0377, 0.0789)\n ETAQ ~ 0.699\n ETABM_IC ~ 0.05\n ETAEmax ~ 0.1\n })\n model({\n F1 = TV_F1\n ka = TV_ka * exp(ETAka)\n CL = exp(TV_CL) * exp(ETACL)\n Vc = exp(TV_Vc) * exp(ETAVc)\n Cc = Ac/(Vc)\n Vp = exp(TV_Vp) * exp(ETAVp)\n Q = exp(TV_Q) * exp(ETAQ)\n MW = TV_MW\n BM_IC = TV_BM_IC * exp(ETABM_IC)\n kdeg_BM = TV_kdeg_BM\n Emax = TV_Emax * exp(ETAEmax)\n EC50 = TV_EC50\n Dinf = 0\n WTTV = 70\n CL_IND = CL * (1 + SEX_ID * 0.1) * (1 + SUBTYPE_ID * \n 0.1)\n kel = CL_IND/Vc * ((WT/WTTV))^(-0.35)\n kcp = Q/Vc * ((WT/WTTV))^(-0.35)\n kpc = Q/Vp * ((WT/WTTV))^(-0.35)\n ksyn_BM = kdeg_BM * BM_IC\n STIM = 1 + Emax * Cc/(EC50 + Cc)\n BM(0) = BM_IC\n d/dt(At) = (-ka * At)\n d/dt(Ac) = ((ka * At * F1/Vc - kel * Cc - kcp * Cc + \n kpc * Cp * Vp/Vc + Dinf/Vc)) * Vc\n d/dt(Cp) = (kcp * Cc * Vc/Vp - kpc * Cp)\n d/dt(BM) = ksyn_BM * STIM - (kdeg_BM * BM)\n C_ng_ml = Cc * MW\n C_ng_ml ~ add(add_err_PK) + prop(prop_err_PK)\n BM_obs = BM\n BM_obs ~ add(add_err_BM)\n })\n}\n\nMB_obj_2_rx = rxode2::rxode2(MB_obj_2_fcn)\n\nMB_obj_2_ts = list(\n system = \"weeks\",\n details = \n list(months = list(verb = \"Months\", conv = 4.13359788359788e-07), \n weeks = list(verb = \"Weeks\", conv = 1.65343915343915e-06), \n days = list(verb = \"Days\", conv = 1.15740740740741e-05), \n hours = list(verb = \"Hours\", conv = 0.000277777777777778))\n)" #> #> $CTS$MDL$mdl$MB_obj_2_rx$checksum -#> [1] "69658491058a69f953ae23cd41b20506" +#> [1] "0c17af67bc1326ce923c127c21da9701" #> #> $CTS$MDL$mdl$MB_obj_2_rx$MDLchecksum -#> [1] "d45ca766892266932518d8cddd760207" +#> [1] "3503e24e285b3f919ae901eaf520d871" #> #> #> @@ -2647,7 +2647,7 @@

Examples#> [1] "One compartment model" #> #> $CTS$elements$element_1$MDLchecksum -#> [1] "f5021a1b0534853463c8561300f61a3f" +#> [1] "71118c97a48fbc817ea06d164e658b80" #> #> $CTS$elements$element_1$SIMchecksum #> [1] "NOTRUN" @@ -2665,7 +2665,7 @@

Examples#> list() #> #> $CTS$elements$element_1$checksum -#> [1] "0f6910a697e293c02aba563866d20888" +#> [1] "c70b0e5527fc578511a069cf6bbed80b" #> #> $CTS$elements$element_1$code #> [1] "library(rxode2)\nlibrary(nonmem2rx)\nlibrary(nlmixr2lib)\nlibrary(ruminate)\n\n# Creating the model\nMB_obj_1_fcn = function () \n{\n description <- \"One compartment PK model with linear clearance using differential equations\"\n ini({\n lka <- 0.45\n label(\"Absorption rate (Ka)\")\n lcl <- 1\n label(\"Clearance (CL)\")\n lvc <- 3.45\n label(\"Central volume of distribution (V)\")\n propSd <- c(0, 0.5)\n label(\"Proportional residual error (fraction)\")\n etalcl ~ 0.1\n etalvc ~ 0.01\n })\n model({\n ka <- exp(lka)\n cl <- exp(lcl + etalcl)\n vc <- exp(lvc + etalvc)\n kel <- cl/vc\n d/dt(depot) <- -ka * depot\n d/dt(central) <- ka * depot - kel * central\n Cc <- central/vc\n Cc ~ prop(propSd)\n })\n}\n\nMB_obj_1_rx = rxode2::rxode2(MB_obj_1_fcn)\n\nMB_obj_1_ts = list(\n system = \"weeks\",\n details = \n list(months = list(verb = \"Months\", conv = 4.13359788359788e-07), \n weeks = list(verb = \"Weeks\", conv = 1.65343915343915e-06), \n days = list(verb = \"Days\", conv = 1.15740740740741e-05), \n hours = list(verb = \"Hours\", conv = 0.000277777777777778))\n)\n\n# Setting the random seeds\nset.seed(5446)\nrxode2::rxSetSeed(5446)\n\n# Define the number of subjects to simulate for this cohort \nCTS_obj_1_nsub = 10\n\n# User defined functions used in the simulations\nCTS_obj_1_preamble = \"\"\n\n# Fetching the system information\nCTS_obj_1_rx_details = fetch_rxinfo(MB_obj_1_rx)\n\n# Defining covariates\nCTS_obj_1_cov = list()\n\n# Generating the subjects\nCTS_obj_1_subs = mk_subjects(object = MB_obj_1_rx,\n nsub = CTS_obj_1_nsub,\n covs = CTS_obj_1_cov)\n\n# Creating rules\nCTS_obj_1_rules = list()\n\n# rxSolve options\nCTS_obj_1_rxopts = list(\n atol = 1e-8,\n rtol = 1e-6,\n sigdig = NULL)\n\n# Output times\nCTS_obj_1_output_times = formods::linspace(0,100,200)\n\n# Running simulation\nCTS_obj_1_simres = \n simulate_rules(object = MB_obj_1_rx,\n subjects = CTS_obj_1_subs[[\"subjects\"]],\n eval_times = c(0),\n output_times = CTS_obj_1_output_times,\n time_scales = MB_obj_1_ts,\n preamble = CTS_obj_1_preamble,\n rules = CTS_obj_1_rules,\n rx_options = CTS_obj_1_rxopts)\n\n# Collecting the simulation and event history values\nCTS_obj_1_sim_tc = CTS_obj_1_simres[[\"simall\"]]\nCTS_obj_1_sim_ev = CTS_obj_1_simres[[\"ev_history\"]]\n\n# Plotting timecourse\nCTS_obj_1_fgtc = \n plot_sr_tc(sro = CTS_obj_1_simres,\n xcol = \"time\", \n xlab_str = \"Time\", \n fncol = 4, \n fnrow = 2, \n dvcols = \"Cc\",\n fpage = 1)\n\n# Plotting events\nCTS_obj_1_fgev = \n plot_sr_ev(sro = CTS_obj_1_simres,\n xcol = \"time\", \n xlab_str = \"Time\", \n fncol = 4, \n fnrow = 2, \n evplot = 1,\n fpage = 1)\n" @@ -2706,7 +2706,7 @@

Examples#> #> #> $CTS$checksum -#> [1] "4ec23ca6de15e261e101be0fac9b385d" +#> [1] "e73a61c31ff660419d7c9562bb6ba2f8" #> #> #> $MOD_TYPE @@ -2722,7 +2722,7 @@

Examples#> [1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/formods/templates/formods.yaml" #> #> $MOD_yaml_file -#> [1] "/private/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T/RtmpGx6vxe/temp_libpathcc545171e30d/ruminate/templates/CTS.yaml" +#> [1] "/private/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T/RtmpGDQNVf/temp_libpath179d1781b4001/ruminate/templates/CTS.yaml" #> #> $shiny_token #> [1] "non_shiny" diff --git a/docs/reference/CTS_mk_preload.html b/docs/reference/CTS_mk_preload.html index c56c87d..ffa00d8 100644 --- a/docs/reference/CTS_mk_preload.html +++ b/docs/reference/CTS_mk_preload.html @@ -107,38 +107,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 650fb8ba7c1ca756d78a9fe0a4e57850 -#> → MB: module checksum updated:ef4fafe0e8213356a97925ccbc6eb820 +#> → MB: model checksum updated: cadea48da8f28a2b94b48d71d5a8c833 +#> → MB: module checksum updated:cd665eab2adb003bbfd8264acea9957d #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 70462a0f7768b2db4dd7e049ff30ac30 -#> → MB: module checksum updated:02fe6299769b465c8d371231cd2bbcbd +#> → MB: model checksum updated: 4903787b494d05b4dff863d1e6887c1c +#> → MB: module checksum updated:e7bc9325bc7e3eaf79cf075783defd36 #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: f5021a1b0534853463c8561300f61a3f -#> → MB: module checksum updated:fc13d346d3cf656e8fe4b70310537a8e +#> → MB: model checksum updated: 71118c97a48fbc817ea06d164e658b80 +#> → MB: module checksum updated:e8471b51d5651c0425fcdc500c4414a2 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: dedf876242a6b49b65c5971ac643aee7 -#> → MB: module checksum updated:a588e805de9b414c032d217f1799f4ef +#> → MB: model checksum updated: 7790f7e2decf60d0ebdab277866b46e3 +#> → MB: module checksum updated:e340d740856c84072ee95771f76ac7ad #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: d45ca766892266932518d8cddd760207 -#> → MB: module checksum updated:69658491058a69f953ae23cd41b20506 +#> → MB: model checksum updated: 3503e24e285b3f919ae901eaf520d871 +#> → MB: module checksum updated:0c17af67bc1326ce923c127c21da9701 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -152,8 +152,8 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 0f6910a697e293c02aba563866d20888 -#> → CTS: module checksum updated: 4ec23ca6de15e261e101be0fac9b385d +#> → CTS: cohort checksum updated: c70b0e5527fc578511a069cf6bbed80b +#> → CTS: module checksum updated: e73a61c31ff660419d7c9562bb6ba2f8 #> → CTS: State initialized #> → CTS: loading element idx: 1 #> → CTS: setting cohort name: Single dose @@ -173,13 +173,13 @@

Examples#> → CTS: - cts_config_seed: 5446 #> → CTS: - cts_config_nsteps: 5 #> → CTS: - cts_config_preamble: -#> → CTS: cohort checksum updated: de0da71da47e0dda4ac4fb75a0e0e41f -#> → CTS: module checksum updated: f55ee91c1ac3689a9eb95dbcbf489c19 +#> → CTS: cohort checksum updated: c409d99638194108456e4016dd84c009 +#> → CTS: module checksum updated: 30300c4815fc7c25a04e19c200e1434e #> → CTS: adding rule: first_dose #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 70b958ddccdfd83348811ff972f23caf -#> → CTS: module checksum updated: 2b3ccec6b236c0088ef2188d50d2a25e +#> → CTS: cohort checksum updated: fa7d9a33cb48b96e86c063041c613022 +#> → CTS: module checksum updated: 0b4e7ecd5c1c974096c9161d5cceb1c6 #> #> #> @@ -190,8 +190,8 @@

Examples#> Warning: multi-subject simulation without without 'omega' #> → CTS: simulation complete #> → CTS: plot complete -#> → CTS: cohort checksum updated: fb2ae2fe4cbb3c0b53239299dd59f000 -#> → CTS: module checksum updated: 14eba49c8e38ee5bc948eab5dc471d5e +#> → CTS: cohort checksum updated: 76e39af0c48499050e3d7de6eb64e2f2 +#> → CTS: module checksum updated: 0189323cdb6ced373a17921c2edc3afa #> → CTS: added element idx: 1 #> → CTS: module isgood: TRUE state = sess_res$state diff --git a/docs/reference/CTS_new_element.html b/docs/reference/CTS_new_element.html index 0236557..72697ee 100644 --- a/docs/reference/CTS_new_element.html +++ b/docs/reference/CTS_new_element.html @@ -212,38 +212,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -257,13 +257,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 1f05a35a13e17be33c5acdabdac048f9 -#> → CTS: module checksum updated: d52c5f2d1640c001c5f163e9b2e253c2 +#> → CTS: cohort checksum updated: 385f73e39375ee52d033dfbba7c5b8a1 +#> → CTS: module checksum updated: 2ab2fbe55900df595938d3a2b74a86ad #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: f29fc3faacde382c657e9c8753bdb72a -#> → CTS: module checksum updated: efd427e2458ef2a481d9c8305776d1db +#> → CTS: cohort checksum updated: d6232be19c07ed09c197fcc8ee1f351d +#> → CTS: module checksum updated: ab4bedc043711cd48a63191649a6a459 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -285,12 +285,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: b3e17838576bac2a0912ee7cca83a1de -#> → CTS: module checksum updated: 05a7581936d50bdc30d9b53f2f8feb80 +#> → CTS: cohort checksum updated: 8ea9a382e5d2666fa60631a40b0bdf69 +#> → CTS: module checksum updated: a9af1c6ddfd64b9e9a2e9a6942e3107b #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 5364f17e98a6308328784427faa75286 -#> → CTS: module checksum updated: c8ac54b1ffcd25bb691c63ccd135fe70 +#> → CTS: cohort checksum updated: 7040112152b5295e5e070546da44b5cd +#> → CTS: module checksum updated: 98828451992422d9ee71a2c9589d5308 # } diff --git a/docs/reference/CTS_plot_element.html b/docs/reference/CTS_plot_element.html index b97dced..26624d3 100644 --- a/docs/reference/CTS_plot_element.html +++ b/docs/reference/CTS_plot_element.html @@ -216,38 +216,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -261,13 +261,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 1f05a35a13e17be33c5acdabdac048f9 -#> → CTS: module checksum updated: d52c5f2d1640c001c5f163e9b2e253c2 +#> → CTS: cohort checksum updated: 385f73e39375ee52d033dfbba7c5b8a1 +#> → CTS: module checksum updated: 2ab2fbe55900df595938d3a2b74a86ad #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: f29fc3faacde382c657e9c8753bdb72a -#> → CTS: module checksum updated: efd427e2458ef2a481d9c8305776d1db +#> → CTS: cohort checksum updated: d6232be19c07ed09c197fcc8ee1f351d +#> → CTS: module checksum updated: ab4bedc043711cd48a63191649a6a459 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -289,12 +289,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: b3e17838576bac2a0912ee7cca83a1de -#> → CTS: module checksum updated: 05a7581936d50bdc30d9b53f2f8feb80 +#> → CTS: cohort checksum updated: 8ea9a382e5d2666fa60631a40b0bdf69 +#> → CTS: module checksum updated: a9af1c6ddfd64b9e9a2e9a6942e3107b #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 5364f17e98a6308328784427faa75286 -#> → CTS: module checksum updated: c8ac54b1ffcd25bb691c63ccd135fe70 +#> → CTS: cohort checksum updated: 7040112152b5295e5e070546da44b5cd +#> → CTS: module checksum updated: 98828451992422d9ee71a2c9589d5308 # } diff --git a/docs/reference/CTS_set_current_element.html b/docs/reference/CTS_set_current_element.html index a047ce4..48409a6 100644 --- a/docs/reference/CTS_set_current_element.html +++ b/docs/reference/CTS_set_current_element.html @@ -215,38 +215,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -260,13 +260,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 1f05a35a13e17be33c5acdabdac048f9 -#> → CTS: module checksum updated: d52c5f2d1640c001c5f163e9b2e253c2 +#> → CTS: cohort checksum updated: 385f73e39375ee52d033dfbba7c5b8a1 +#> → CTS: module checksum updated: 2ab2fbe55900df595938d3a2b74a86ad #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: f29fc3faacde382c657e9c8753bdb72a -#> → CTS: module checksum updated: efd427e2458ef2a481d9c8305776d1db +#> → CTS: cohort checksum updated: d6232be19c07ed09c197fcc8ee1f351d +#> → CTS: module checksum updated: ab4bedc043711cd48a63191649a6a459 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -288,12 +288,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: b3e17838576bac2a0912ee7cca83a1de -#> → CTS: module checksum updated: 05a7581936d50bdc30d9b53f2f8feb80 +#> → CTS: cohort checksum updated: 8ea9a382e5d2666fa60631a40b0bdf69 +#> → CTS: module checksum updated: a9af1c6ddfd64b9e9a2e9a6942e3107b #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 5364f17e98a6308328784427faa75286 -#> → CTS: module checksum updated: c8ac54b1ffcd25bb691c63ccd135fe70 +#> → CTS: cohort checksum updated: 7040112152b5295e5e070546da44b5cd +#> → CTS: module checksum updated: 98828451992422d9ee71a2c9589d5308 # } diff --git a/docs/reference/CTS_simulate_element.html b/docs/reference/CTS_simulate_element.html index 4c07eef..b77c474 100644 --- a/docs/reference/CTS_simulate_element.html +++ b/docs/reference/CTS_simulate_element.html @@ -215,38 +215,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -260,13 +260,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 1f05a35a13e17be33c5acdabdac048f9 -#> → CTS: module checksum updated: d52c5f2d1640c001c5f163e9b2e253c2 +#> → CTS: cohort checksum updated: 385f73e39375ee52d033dfbba7c5b8a1 +#> → CTS: module checksum updated: 2ab2fbe55900df595938d3a2b74a86ad #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: f29fc3faacde382c657e9c8753bdb72a -#> → CTS: module checksum updated: efd427e2458ef2a481d9c8305776d1db +#> → CTS: cohort checksum updated: d6232be19c07ed09c197fcc8ee1f351d +#> → CTS: module checksum updated: ab4bedc043711cd48a63191649a6a459 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -288,12 +288,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: b3e17838576bac2a0912ee7cca83a1de -#> → CTS: module checksum updated: 05a7581936d50bdc30d9b53f2f8feb80 +#> → CTS: cohort checksum updated: 8ea9a382e5d2666fa60631a40b0bdf69 +#> → CTS: module checksum updated: a9af1c6ddfd64b9e9a2e9a6942e3107b #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 5364f17e98a6308328784427faa75286 -#> → CTS: module checksum updated: c8ac54b1ffcd25bb691c63ccd135fe70 +#> → CTS: cohort checksum updated: 7040112152b5295e5e070546da44b5cd +#> → CTS: module checksum updated: 98828451992422d9ee71a2c9589d5308 # } diff --git a/docs/reference/CTS_test_mksession.html b/docs/reference/CTS_test_mksession.html index ac3d0bf..43d9457 100644 --- a/docs/reference/CTS_test_mksession.html +++ b/docs/reference/CTS_test_mksession.html @@ -107,44 +107,44 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 1ab4787b4a3cc920e9421fd2b4ff618c -#> → MB: module checksum updated:1244819553afc28cae24b978f428c09d +#> → MB: model checksum updated: 78dccc66b4dadb5788be091b7954702a +#> → MB: module checksum updated:d866124c0f1f1da62419d5fe8c9480f8 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 1d8b1ac4dfcca5c91aa79aff272578db -#> → MB: module checksum updated:13bd891010b4e421432200a4d1c9fe39 +#> → MB: model checksum updated: 2c0d99199e1469e85095da4b0b8b1e7b +#> → MB: module checksum updated:43f497d2594e7b12d176d38511d257dd #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 5456ffbefa3a247fb95f527f9b88f7a1 -#> → MB: module checksum updated:9e52ab12e0247c4582e8996333c24f04 +#> → MB: model checksum updated: 6dcc3b4c1cee7ef3c0ce87be417f39d4 +#> → MB: module checksum updated:afa6004cb28338791137c0f354ab6c52 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 742f9c912a166efd1cda67ee6a88b2e9 -#> → MB: module checksum updated:2a6279cfc170d54150055d19df1f6005 +#> → MB: model checksum updated: 65e24560103a0f6d89b512581f9c2554 +#> → MB: module checksum updated:ef66b4aee1c2843ea17f6999cd51a2a6 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: a87657f121616d70012e987f05669196 -#> → MB: module checksum updated:ed85e5535a2fde5f1bb1a536c30a0739 +#> → MB: model checksum updated: 77f76cc8ca739d49e0bc4b0a171b97d9 +#> → MB: module checksum updated:aef6ea4735ede44805d4817621af3f8d #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: abd00da81cc9488b427b229f9cf80ade -#> → CTS: module checksum updated: b3c7585c469ea8041f955eebda4e30a7 +#> → CTS: cohort checksum updated: 40da12f649ebaf69d66c0d2e93992485 +#> → CTS: module checksum updated: ae20741e0bc73a97b2bf9e25fd18366d #> → CTS: State initialized #> → CTS: loading element idx: 1 #> → CTS: setting cohort name: Single dose @@ -164,13 +164,13 @@

Examples#> → CTS: - cts_config_seed: 5446 #> → CTS: - cts_config_nsteps: 5 #> → CTS: - cts_config_preamble: -#> → CTS: cohort checksum updated: 2583da3bdfd84ee90b22eab328aa3ea0 -#> → CTS: module checksum updated: be47d199841d00ae74f09ab3d0505f0c +#> → CTS: cohort checksum updated: 682e7bb93fa05ce9adddcf2d47746b10 +#> → CTS: module checksum updated: db0a51e1523ba421b2c0083cefdad94e #> → CTS: adding rule: first_dose #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: 5165ec78419a9dbc87ac36ba856eb595 -#> → CTS: module checksum updated: f1996876ec6e6d7d329e23131ee354e2 +#> → CTS: cohort checksum updated: 18be167e1e9415e6b3444db1475bc266 +#> → CTS: module checksum updated: f150d2afb63249165723484ce26d9beb #> #> #> @@ -181,8 +181,8 @@

Examples#> Warning: multi-subject simulation without without 'omega' #> → CTS: simulation complete #> → CTS: plot complete -#> → CTS: cohort checksum updated: 71ed329c297882bede354f50abc064fe -#> → CTS: module checksum updated: e5800336a98ac568b86a286e079e4e7b +#> → CTS: cohort checksum updated: 2beeb656ca3818a044b589035b9f60b9 +#> → CTS: module checksum updated: ce3b773f4c497ddedb3ce7ca6a0daece #> → CTS: added element idx: 1 #> → CTS: module isgood: TRUE # } diff --git a/docs/reference/CTS_update_checksum.html b/docs/reference/CTS_update_checksum.html index dcfd2ab..4a2659b 100644 --- a/docs/reference/CTS_update_checksum.html +++ b/docs/reference/CTS_update_checksum.html @@ -210,38 +210,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> → CTS: including file @@ -255,13 +255,13 @@

Examples#> → CTS: dest: file.path("config","report.yaml") #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 1f05a35a13e17be33c5acdabdac048f9 -#> → CTS: module checksum updated: d52c5f2d1640c001c5f163e9b2e253c2 +#> → CTS: cohort checksum updated: 385f73e39375ee52d033dfbba7c5b8a1 +#> → CTS: module checksum updated: 2ab2fbe55900df595938d3a2b74a86ad #> → CTS: State initialized #> → CTS: add rule success #> → CTS: rule added -#> → CTS: cohort checksum updated: f29fc3faacde382c657e9c8753bdb72a -#> → CTS: module checksum updated: efd427e2458ef2a481d9c8305776d1db +#> → CTS: cohort checksum updated: d6232be19c07ed09c197fcc8ee1f351d +#> → CTS: module checksum updated: ab4bedc043711cd48a63191649a6a459 #> → CTS: CTS_plot_element() #> → CTS: # Plotting timecourse #> → CTS: CTS_obj_1_fgtc = @@ -283,12 +283,12 @@

Examples#> → CTS: evplot = 1, #> → CTS: fpage = 1) #> → CTS: No simulation available, you need to run the simulation first. -#> → CTS: cohort checksum updated: b3e17838576bac2a0912ee7cca83a1de -#> → CTS: module checksum updated: 05a7581936d50bdc30d9b53f2f8feb80 +#> → CTS: cohort checksum updated: 8ea9a382e5d2666fa60631a40b0bdf69 +#> → CTS: module checksum updated: a9af1c6ddfd64b9e9a2e9a6942e3107b #> → CTS: source model change detected #> → CTS: > covariates reset -#> → CTS: cohort checksum updated: 5364f17e98a6308328784427faa75286 -#> → CTS: module checksum updated: c8ac54b1ffcd25bb691c63ccd135fe70 +#> → CTS: cohort checksum updated: 7040112152b5295e5e070546da44b5cd +#> → CTS: module checksum updated: 98828451992422d9ee71a2c9589d5308 # } diff --git a/docs/reference/MB_build_code.html b/docs/reference/MB_build_code.html index 0f3b546..9cb1295 100644 --- a/docs/reference/MB_build_code.html +++ b/docs/reference/MB_build_code.html @@ -236,38 +236,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -283,8 +283,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_del_current_element.html b/docs/reference/MB_del_current_element.html index e051e1d..02309ff 100644 --- a/docs/reference/MB_del_current_element.html +++ b/docs/reference/MB_del_current_element.html @@ -197,38 +197,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -244,8 +244,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_fetch_appends.html b/docs/reference/MB_fetch_appends.html index 9967751..7e665b3 100644 --- a/docs/reference/MB_fetch_appends.html +++ b/docs/reference/MB_fetch_appends.html @@ -202,38 +202,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -249,8 +249,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_fetch_catalog.html b/docs/reference/MB_fetch_catalog.html index 904d733..b6253ca 100644 --- a/docs/reference/MB_fetch_catalog.html +++ b/docs/reference/MB_fetch_catalog.html @@ -202,38 +202,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -249,8 +249,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_fetch_code.html b/docs/reference/MB_fetch_code.html index 7dc2abc..64e2c79 100644 --- a/docs/reference/MB_fetch_code.html +++ b/docs/reference/MB_fetch_code.html @@ -194,38 +194,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -241,8 +241,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_fetch_component.html b/docs/reference/MB_fetch_component.html index 50f8dd4..42181fb 100644 --- a/docs/reference/MB_fetch_component.html +++ b/docs/reference/MB_fetch_component.html @@ -210,38 +210,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -257,8 +257,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_fetch_current_element.html b/docs/reference/MB_fetch_current_element.html index 253f66f..08bee4b 100644 --- a/docs/reference/MB_fetch_current_element.html +++ b/docs/reference/MB_fetch_current_element.html @@ -199,38 +199,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -246,8 +246,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_fetch_mdl.html b/docs/reference/MB_fetch_mdl.html index 276ce61..3550180 100644 --- a/docs/reference/MB_fetch_mdl.html +++ b/docs/reference/MB_fetch_mdl.html @@ -121,38 +121,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE state = sess_res$state diff --git a/docs/reference/MB_fetch_state.html b/docs/reference/MB_fetch_state.html index 8c08422..fa0f964 100644 --- a/docs/reference/MB_fetch_state.html +++ b/docs/reference/MB_fetch_state.html @@ -149,38 +149,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE session = sess_res$session diff --git a/docs/reference/MB_init_state.html b/docs/reference/MB_init_state.html index d8f6a81..44bd330 100644 --- a/docs/reference/MB_init_state.html +++ b/docs/reference/MB_init_state.html @@ -118,38 +118,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE session = sess_res$session @@ -1841,7 +1841,7 @@

Examples#> [1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/formods/templates/formods.yaml" #> #> $MOD_yaml_file -#> [1] "/private/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T/RtmpGx6vxe/temp_libpathcc545171e30d/ruminate/templates/MB.yaml" +#> [1] "/private/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T/RtmpGDQNVf/temp_libpath179d1781b4001/ruminate/templates/MB.yaml" #> #> $shiny_token #> [1] "non_shiny" diff --git a/docs/reference/MB_mk_preload.html b/docs/reference/MB_mk_preload.html index 8531e31..a04cea2 100644 --- a/docs/reference/MB_mk_preload.html +++ b/docs/reference/MB_mk_preload.html @@ -106,38 +106,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE state = sess_res$state diff --git a/docs/reference/MB_new_element.html b/docs/reference/MB_new_element.html index c6758bd..48340ea 100644 --- a/docs/reference/MB_new_element.html +++ b/docs/reference/MB_new_element.html @@ -199,38 +199,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -246,8 +246,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_set_current_element.html b/docs/reference/MB_set_current_element.html index c6caaec..963109f 100644 --- a/docs/reference/MB_set_current_element.html +++ b/docs/reference/MB_set_current_element.html @@ -202,38 +202,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -249,8 +249,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_test_catalog.html b/docs/reference/MB_test_catalog.html index bf1d5e2..fa6c1a5 100644 --- a/docs/reference/MB_test_catalog.html +++ b/docs/reference/MB_test_catalog.html @@ -204,38 +204,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -251,8 +251,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/MB_test_mksession.html b/docs/reference/MB_test_mksession.html index e894b0d..eda0a38 100644 --- a/docs/reference/MB_test_mksession.html +++ b/docs/reference/MB_test_mksession.html @@ -101,38 +101,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 1ab4787b4a3cc920e9421fd2b4ff618c -#> → MB: module checksum updated:1244819553afc28cae24b978f428c09d +#> → MB: model checksum updated: 78dccc66b4dadb5788be091b7954702a +#> → MB: module checksum updated:d866124c0f1f1da62419d5fe8c9480f8 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 1d8b1ac4dfcca5c91aa79aff272578db -#> → MB: module checksum updated:13bd891010b4e421432200a4d1c9fe39 +#> → MB: model checksum updated: 2c0d99199e1469e85095da4b0b8b1e7b +#> → MB: module checksum updated:43f497d2594e7b12d176d38511d257dd #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 5456ffbefa3a247fb95f527f9b88f7a1 -#> → MB: module checksum updated:9e52ab12e0247c4582e8996333c24f04 +#> → MB: model checksum updated: 6dcc3b4c1cee7ef3c0ce87be417f39d4 +#> → MB: module checksum updated:afa6004cb28338791137c0f354ab6c52 #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 742f9c912a166efd1cda67ee6a88b2e9 -#> → MB: module checksum updated:2a6279cfc170d54150055d19df1f6005 +#> → MB: model checksum updated: 65e24560103a0f6d89b512581f9c2554 +#> → MB: module checksum updated:ef66b4aee1c2843ea17f6999cd51a2a6 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: a87657f121616d70012e987f05669196 -#> → MB: module checksum updated:ed85e5535a2fde5f1bb1a536c30a0739 +#> → MB: model checksum updated: 77f76cc8ca739d49e0bc4b0a171b97d9 +#> → MB: module checksum updated:aef6ea4735ede44805d4817621af3f8d #> → MB: added element idx: 2 #> → MB: module isgood: TRUE diff --git a/docs/reference/MB_update_checksum.html b/docs/reference/MB_update_checksum.html index 28292a3..747a8ad 100644 --- a/docs/reference/MB_update_checksum.html +++ b/docs/reference/MB_update_checksum.html @@ -109,38 +109,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE session = sess_res$session diff --git a/docs/reference/MB_update_model.html b/docs/reference/MB_update_model.html index fed1908..9010d35 100644 --- a/docs/reference/MB_update_model.html +++ b/docs/reference/MB_update_model.html @@ -218,38 +218,38 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: e7a2168462c020e7bdb1357dd57c6a8d -#> → MB: module checksum updated:8e3a530a1e7a6d5bbbc92522c3bc5f20 +#> → MB: model checksum updated: 75bebd8998ed90f37af975a8ad9618f4 +#> → MB: module checksum updated:ea85a45c7abbc26f62191e3b138eb0c3 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: ce07889e8eabac328bb3df998173aea1 -#> → MB: module checksum updated:43cb9bc99d622b0cda8fdc756ecb74e4 +#> → MB: model checksum updated: bf9dae07a6048abe37b2915d7dea9674 +#> → MB: module checksum updated:f83e339a3730eb4165dea639164faabb #> → MB: -> setting name: One compartment model #> → MB: -> setting time scale: hours #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: b4d7aabb37f58f0b13cf66bb3fb6c1cf -#> → MB: module checksum updated:49492559d0264fdc6912c7f280306102 +#> → MB: model checksum updated: f665fb4754434b96e9061c07af34ef20 +#> → MB: module checksum updated:3341a85b1e287c05fe5a8194037e5d7e #> → MB: added element idx: 1 #> → MB: loading model idx: 2 #> #> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 18317e807f8a2def8433052fe0d6af25 -#> → MB: module checksum updated:85695fd4e9bd44ef2a90b9d547958d64 +#> → MB: model checksum updated: 0e8522b959c05d59397f4d4080c25c30 +#> → MB: module checksum updated:f5c100d87e8cc10e0132a4009cffc0a4 #> → MB: -> setting name: PK Biomarker #> → MB: -> setting time scale: days #> → MB: -> setting base from: user #> → MB: -> setting catalog selection: #> → MB: -> setting base model id: manual #> → MB: -> setting base model name: manual -#> → MB: model checksum updated: 1542e861f9ecb403b680c77f75a57cd8 -#> → MB: module checksum updated:e24ec7d3dfe1ee668b2284708e20c3b4 +#> → MB: model checksum updated: 8714d1dd6f800b6789212b7f8fedefd2 +#> → MB: module checksum updated:25f08c5839afcd7dcd83b979cbfe63d2 #> → MB: added element idx: 2 #> → MB: module isgood: TRUE #> ! MB: User-defined model: /Users/jmh/projects/ruminate/github/ruminate/docs/reference/user_model.R not found (skipping) @@ -265,8 +265,8 @@

Examples#> #> ℹ parameter labels from comments are typically ignored in non-interactive mode #> ℹ Need to run with the source intact to parse comments -#> → MB: model checksum updated: 9a6515098c0859fec337b35418d84c5b -#> → MB: module checksum updated:ef304271d1149f6da883f46a39347198 +#> → MB: model checksum updated: 8d553bc3bc1e0676626e8665ce9c3d6c +#> → MB: module checksum updated:83d73bacc2661586d897a6241b5cd33a #> my_fcn_obj = function () #> { #> description <- "One compartment PK model with linear clearance" diff --git a/docs/reference/NCA_fetch_current_obj-1.png b/docs/reference/NCA_fetch_current_obj-1.png index 9b2565f..4c113a0 100644 Binary files a/docs/reference/NCA_fetch_current_obj-1.png and b/docs/reference/NCA_fetch_current_obj-1.png differ diff --git a/docs/reference/NCA_fetch_current_obj.html b/docs/reference/NCA_fetch_current_obj.html index 006b8e4..b24d8a0 100644 --- a/docs/reference/NCA_fetch_current_obj.html +++ b/docs/reference/NCA_fetch_current_obj.html @@ -207,7 +207,7 @@

Examples# Current active table: res = NCA_fetch_current_obj(state, "table") res$ft -

Time

Concentration (ng/mL) by ID

(day)

1

2

3

4

5

6

7

0

BLQ

BLQ

BLQ

BLQ

BLQ

BLQ

BLQ

1

690

750

670

638

855

611

554

2

588

577

576

517

668

521

476

3

506

508

501

438

549

456

425

4

438

476

441

384

472

409

390

7

303

425

320

300

360

325

332

21

123

274

139

173

228

194

210

28

95.5

220

104

135

188

155

169

35

75.8

177

77.8

105

156

125

136

42

60.6

142

58.6

82.2

128

100

109

+

Time

Concentration (ng/mL) by ID

(day)

1

2

3

4

5

6

7

0

BLQ

BLQ

BLQ

BLQ

BLQ

BLQ

BLQ

1

690

750

670

638

855

611

554

2

588

577

576

517

668

521

476

3

506

508

501

438

549

456

425

4

438

476

441

384

472

409

390

7

303

425

320

300

360

325

332

21

123

274

139

173

228

194

210

28

95.5

220

104

135

188

155

169

35

75.8

177

77.8

105

156

125

136

42

60.6

142

58.6

82.2

128

100

109

# Current active figure: res = NCA_fetch_current_obj(state, "figure") res$ggplot diff --git a/docs/reference/NCA_fetch_state.html b/docs/reference/NCA_fetch_state.html index ee29c66..3d5baeb 100644 --- a/docs/reference/NCA_fetch_state.html +++ b/docs/reference/NCA_fetch_state.html @@ -103,6 +103,10 @@

Argumentsreact_state +

Variable used within server to handle non-standard reactions (e.g. reacting to plotly)

+ + +
react_internal

Variable passed to server to allow reaction outside of module (NULL)

diff --git a/docs/reference/apply_route_map-1.png b/docs/reference/apply_route_map-1.png new file mode 100644 index 0000000..ec54ca1 Binary files /dev/null and b/docs/reference/apply_route_map-1.png differ diff --git a/docs/reference/apply_route_map.html b/docs/reference/apply_route_map.html index 8f455fc..2368aeb 100644 --- a/docs/reference/apply_route_map.html +++ b/docs/reference/apply_route_map.html @@ -297,7 +297,6 @@

Examples nfcols = 4, log_scale = TRUE) - figure_ind_obs$figures$Figure_1$gg # Generating tables of the concentration data table_ind_obs = mk_table_ind_obs( @@ -306,7 +305,6 @@

Examples flag_map = flag_map, digits = 3) - table_ind_obs$tables[["Table 1"]]$ft # Generating tables of individual parameters table_ind_params = mk_table_nca_params( @@ -317,11 +315,15 @@

Examples text_format = "md", digits = 3) + print(figure_ind_obs$figures$Figure_1$gg) + table_ind_params$tables[["Table 1"]]$ft + table_ind_obs$tables[["Table 1"]]$ft } #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_se #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_df -

ID

CMT

AUClast

Cmax

AUCinf,obs

thalf

day*ng/mL

ng/mL

day*ng/mL

day

[0,21]

[0,inf]

1

C_ng_ml

5,900

690

9,590

21.3

2

C_ng_ml

8,240

750

17,000

22.2

3

C_ng_ml

6,140

670

9,520

17.0

+ +

Time

Analyte

Concentration (ng/mL) by ID

(day)

1

2

3

0

C_ng_ml

BLQ

BLQ

BLQ

1

C_ng_ml

690

750

670

2

C_ng_ml

588C

577

576

3

C_ng_ml

506

508

501

4

C_ng_ml

438

476

441

7

C_ng_ml

303

425

320

21

C_ng_ml

123HX

274

139

28

C_ng_ml

95.5

220

104

35

C_ng_ml

75.8

177

77.8

42

C_ng_ml

60.6

142

58.6

diff --git a/docs/reference/dose_records_builder-1.png b/docs/reference/dose_records_builder-1.png new file mode 100644 index 0000000..ec54ca1 Binary files /dev/null and b/docs/reference/dose_records_builder-1.png differ diff --git a/docs/reference/dose_records_builder.html b/docs/reference/dose_records_builder.html index ebb2891..dc1d66d 100644 --- a/docs/reference/dose_records_builder.html +++ b/docs/reference/dose_records_builder.html @@ -285,7 +285,6 @@

Examples nfcols = 4, log_scale = TRUE) - figure_ind_obs$figures$Figure_1$gg # Generating tables of the concentration data table_ind_obs = mk_table_ind_obs( @@ -294,7 +293,6 @@

Examples flag_map = flag_map, digits = 3) - table_ind_obs$tables[["Table 1"]]$ft # Generating tables of individual parameters table_ind_params = mk_table_nca_params( @@ -305,11 +303,15 @@

Examples text_format = "md", digits = 3) + print(figure_ind_obs$figures$Figure_1$gg) + table_ind_params$tables[["Table 1"]]$ft + table_ind_obs$tables[["Table 1"]]$ft } #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_se #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_df -

ID

CMT

AUClast

Cmax

AUCinf,obs

thalf

day*ng/mL

ng/mL

day*ng/mL

day

[0,21]

[0,inf]

1

C_ng_ml

5,900

690

9,590

21.3

2

C_ng_ml

8,240

750

17,000

22.2

3

C_ng_ml

6,140

670

9,520

17.0

+ +

Time

Analyte

Concentration (ng/mL) by ID

(day)

1

2

3

0

C_ng_ml

BLQ

BLQ

BLQ

1

C_ng_ml

690

750

670

2

C_ng_ml

588C

577

576

3

C_ng_ml

506

508

501

4

C_ng_ml

438

476

441

7

C_ng_ml

303

425

320

21

C_ng_ml

123HX

274

139

28

C_ng_ml

95.5

220

104

35

C_ng_ml

75.8

177

77.8

42

C_ng_ml

60.6

142

58.6

diff --git a/docs/reference/flag_nca_ds-1.png b/docs/reference/flag_nca_ds-1.png new file mode 100644 index 0000000..ec54ca1 Binary files /dev/null and b/docs/reference/flag_nca_ds-1.png differ diff --git a/docs/reference/flag_nca_ds.html b/docs/reference/flag_nca_ds.html index ea052a6..a1251e3 100644 --- a/docs/reference/flag_nca_ds.html +++ b/docs/reference/flag_nca_ds.html @@ -75,6 +75,10 @@

Argumentscol_map +

List with column mapping details.

+ +
ds_flags

Dataframe or tibble with a column (key) for dataset row IDs ("rec_2" for row 2) and a column (flag) for flags mapping can be found.

@@ -294,7 +298,6 @@

Examples nfcols = 4, log_scale = TRUE) - figure_ind_obs$figures$Figure_1$gg # Generating tables of the concentration data table_ind_obs = mk_table_ind_obs( @@ -303,7 +306,6 @@

Examples flag_map = flag_map, digits = 3) - table_ind_obs$tables[["Table 1"]]$ft # Generating tables of individual parameters table_ind_params = mk_table_nca_params( @@ -314,11 +316,15 @@

Examples text_format = "md", digits = 3) + print(figure_ind_obs$figures$Figure_1$gg) + table_ind_params$tables[["Table 1"]]$ft + table_ind_obs$tables[["Table 1"]]$ft } #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_se #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_df -

ID

CMT

AUClast

Cmax

AUCinf,obs

thalf

day*ng/mL

ng/mL

day*ng/mL

day

[0,21]

[0,inf]

1

C_ng_ml

5,900

690

9,590

21.3

2

C_ng_ml

8,240

750

17,000

22.2

3

C_ng_ml

6,140

670

9,520

17.0

+ +

Time

Analyte

Concentration (ng/mL) by ID

(day)

1

2

3

0

C_ng_ml

BLQ

BLQ

BLQ

1

C_ng_ml

690

750

670

2

C_ng_ml

588C

577

576

3

C_ng_ml

506

508

501

4

C_ng_ml

438

476

441

7

C_ng_ml

303

425

320

21

C_ng_ml

123HX

274

139

28

C_ng_ml

95.5

220

104

35

C_ng_ml

75.8

177

77.8

42

C_ng_ml

60.6

142

58.6

diff --git a/docs/reference/mk_figure_ind_obs-1.png b/docs/reference/mk_figure_ind_obs-1.png index 9d168d1..ec54ca1 100644 Binary files a/docs/reference/mk_figure_ind_obs-1.png and b/docs/reference/mk_figure_ind_obs-1.png differ diff --git a/docs/reference/mk_figure_ind_obs.html b/docs/reference/mk_figure_ind_obs.html index afeb476..0008237 100644 --- a/docs/reference/mk_figure_ind_obs.html +++ b/docs/reference/mk_figure_ind_obs.html @@ -335,7 +335,6 @@

Examples nfcols = 4, log_scale = TRUE) - figure_ind_obs$figures$Figure_1$gg # Generating tables of the concentration data table_ind_obs = mk_table_ind_obs( @@ -344,7 +343,6 @@

Examples flag_map = flag_map, digits = 3) - table_ind_obs$tables[["Table 1"]]$ft # Generating tables of individual parameters table_ind_params = mk_table_nca_params( @@ -355,11 +353,15 @@

Examples text_format = "md", digits = 3) + print(figure_ind_obs$figures$Figure_1$gg) + table_ind_params$tables[["Table 1"]]$ft + table_ind_obs$tables[["Table 1"]]$ft } #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_se #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_df -

ID

CMT

AUClast

Cmax

AUCinf,obs

thalf

day*ng/mL

ng/mL

day*ng/mL

day

[0,21]

[0,inf]

1

C_ng_ml

5,900

690

9,590

21.3

2

C_ng_ml

8,240

750

17,000

22.2

3

C_ng_ml

6,140

670

9,520

17.0

+ +

Time

Analyte

Concentration (ng/mL) by ID

(day)

1

2

3

0

C_ng_ml

BLQ

BLQ

BLQ

1

C_ng_ml

690

750

670

2

C_ng_ml

588C

577

576

3

C_ng_ml

506

508

501

4

C_ng_ml

438

476

441

7

C_ng_ml

303

425

320

21

C_ng_ml

123HX

274

139

28

C_ng_ml

95.5

220

104

35

C_ng_ml

75.8

177

77.8

42

C_ng_ml

60.6

142

58.6

diff --git a/docs/reference/mk_rx_obj.html b/docs/reference/mk_rx_obj.html index ba15182..3357d25 100644 --- a/docs/reference/mk_rx_obj.html +++ b/docs/reference/mk_rx_obj.html @@ -144,7 +144,7 @@

Examples#> cp ~ prop(propSd) #> }) #> } -#> <environment: 0x139189ff0> +#> <environment: 0x160219660> # rxode2 object rx_res[["capture"]][["rx_obj"]] diff --git a/docs/reference/mk_table_ind_obs-1.png b/docs/reference/mk_table_ind_obs-1.png new file mode 100644 index 0000000..ec54ca1 Binary files /dev/null and b/docs/reference/mk_table_ind_obs-1.png differ diff --git a/docs/reference/mk_table_ind_obs.html b/docs/reference/mk_table_ind_obs.html index 578ac1d..ebda6fc 100644 --- a/docs/reference/mk_table_ind_obs.html +++ b/docs/reference/mk_table_ind_obs.html @@ -340,7 +340,6 @@

Examples nfcols = 4, log_scale = TRUE) - figure_ind_obs$figures$Figure_1$gg # Generating tables of the concentration data table_ind_obs = mk_table_ind_obs( @@ -349,7 +348,6 @@

Examples flag_map = flag_map, digits = 3) - table_ind_obs$tables[["Table 1"]]$ft # Generating tables of individual parameters table_ind_params = mk_table_nca_params( @@ -360,11 +358,15 @@

Examples text_format = "md", digits = 3) + print(figure_ind_obs$figures$Figure_1$gg) + table_ind_params$tables[["Table 1"]]$ft + table_ind_obs$tables[["Table 1"]]$ft } #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_se #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_df -

ID

CMT

AUClast

Cmax

AUCinf,obs

thalf

day*ng/mL

ng/mL

day*ng/mL

day

[0,21]

[0,inf]

1

C_ng_ml

5,900

690

9,590

21.3

2

C_ng_ml

8,240

750

17,000

22.2

3

C_ng_ml

6,140

670

9,520

17.0

+ +

Time

Analyte

Concentration (ng/mL) by ID

(day)

1

2

3

0

C_ng_ml

BLQ

BLQ

BLQ

1

C_ng_ml

690

750

670

2

C_ng_ml

588C

577

576

3

C_ng_ml

506

508

501

4

C_ng_ml

438

476

441

7

C_ng_ml

303

425

320

21

C_ng_ml

123HX

274

139

28

C_ng_ml

95.5

220

104

35

C_ng_ml

75.8

177

77.8

42

C_ng_ml

60.6

142

58.6

diff --git a/docs/reference/mk_table_nca_params-1.png b/docs/reference/mk_table_nca_params-1.png new file mode 100644 index 0000000..ec54ca1 Binary files /dev/null and b/docs/reference/mk_table_nca_params-1.png differ diff --git a/docs/reference/mk_table_nca_params.html b/docs/reference/mk_table_nca_params.html index 13d7317..1f07217 100644 --- a/docs/reference/mk_table_nca_params.html +++ b/docs/reference/mk_table_nca_params.html @@ -142,10 +142,6 @@

Argumentsmax_col

Maximum number of columns to have on a page. Spillover will be wrapped to multiple pages.

- -
not_calc
-

Text string to replace NA values with to indicated values were not calculated.

-

Value

@@ -363,7 +359,6 @@

Examples nfcols = 4, log_scale = TRUE) - figure_ind_obs$figures$Figure_1$gg # Generating tables of the concentration data table_ind_obs = mk_table_ind_obs( @@ -372,7 +367,6 @@

Examples flag_map = flag_map, digits = 3) - table_ind_obs$tables[["Table 1"]]$ft # Generating tables of individual parameters table_ind_params = mk_table_nca_params( @@ -383,11 +377,15 @@

Examples text_format = "md", digits = 3) + print(figure_ind_obs$figures$Figure_1$gg) + table_ind_params$tables[["Table 1"]]$ft + table_ind_obs$tables[["Table 1"]]$ft } #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_se #> ! NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_df -

ID

CMT

AUClast

Cmax

AUCinf,obs

thalf

day*ng/mL

ng/mL

day*ng/mL

day

[0,21]

[0,inf]

1

C_ng_ml

5,900

690

9,590

21.3

2

C_ng_ml

8,240

750

17,000

22.2

3

C_ng_ml

6,140

670

9,520

17.0

+ +

Time

Analyte

Concentration (ng/mL) by ID

(day)

1

2

3

0

C_ng_ml

BLQ

BLQ

BLQ

1

C_ng_ml

690

750

670

2

C_ng_ml

588C

577

576

3

C_ng_ml

506

508

501

4

C_ng_ml

438

476

441

7

C_ng_ml

303

425

320

21

C_ng_ml

123HX

274

139

28

C_ng_ml

95.5

220

104

35

C_ng_ml

75.8

177

77.8

42

C_ng_ml

60.6

142

58.6

diff --git a/docs/reference/run_nca_components.html b/docs/reference/run_nca_components.html index 0fef58d..1028012 100644 --- a/docs/reference/run_nca_components.html +++ b/docs/reference/run_nca_components.html @@ -205,7 +205,7 @@

Examplesstate = sess_res$state state = run_nca_components(state, components="tb_ind_params") -#> → NCA: module checksum updated:0e8fc5aabb37c96b3201ef5a09550b74 +#> → NCA: module checksum updated:33b7295a4a7947b45def40574a2684a1