From e90ee1965361cbeb990b43f4762625379d5fa7ce Mon Sep 17 00:00:00 2001 From: catalamarti Date: Tue, 15 Oct 2024 15:20:43 +0100 Subject: [PATCH 1/6] update authors --- DESCRIPTION | 16 ++++++++++++++-- man/OmopViewer-package.Rd | 10 +++++++++- 2 files changed, 23 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index db94213..3f7c5ea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,8 +7,20 @@ Authors@R: c( "Martí", "Català", , "marti.catalasabate@ndorms.ox.ac.uk", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3308-9905")), person( - "Yuchen", "Guo", , "yuchen.guo@ndorms.ox.ac.uk", role = c("aut"), - comment = c(ORCID = "0000-0002-0847-4855")) + "Yuchen", "Guo", , "yuchen.guo@ndorms.ox.ac.uk", role = "aut", + comment = c(ORCID = "0000-0002-0847-4855")), + person( + "Edward", "Burn", , "edward.burn@ndorms.ox.ac.uk", role = "ctb", + comment = c(ORCID = "0000-0002-9286-1128")), + person( + "Nuria", "Mercade-Besora", , "nuria.mercadebesora@ndorms.ox.ac.uk", + role = "ctb", comment = c(ORCID = "0009-0006-7948-3747")), + person( + "Elin", "Rowlands", , "elin.rowlands@ndorms.ox.ac.uk", + role = "ctb", comment = c(ORCID = "0009-0005-5166-0417")), + person( + "Cecilia", "Campanile", , "cecilia.campanile@ndorms.ox.ac.uk", + role = "ctb") ) Maintainer: Martí Català Description: Visualise results obtained from analysing data mapped to the diff --git a/man/OmopViewer-package.Rd b/man/OmopViewer-package.Rd index 4ec77d2..837e618 100644 --- a/man/OmopViewer-package.Rd +++ b/man/OmopViewer-package.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/OmopViewer-package.R +% Please edit documentation in R/omopViewer-package.R \docType{package} \name{OmopViewer-package} \alias{OmopViewer} @@ -23,5 +23,13 @@ Authors: \item Yuchen Guo \email{yuchen.guo@ndorms.ox.ac.uk} (\href{https://orcid.org/0000-0002-0847-4855}{ORCID}) } +Other contributors: +\itemize{ + \item Edward Burn \email{edward.burn@ndorms.ox.ac.uk} (\href{https://orcid.org/0000-0002-9286-1128}{ORCID}) [contributor] + \item Nuria Mercade-Besora \email{nuria.mercadebesora@ndorms.ox.ac.uk} (\href{https://orcid.org/0009-0006-7948-3747}{ORCID}) [contributor] + \item Elin Rowlands \email{elin.rowlands@ndorms.ox.ac.uk} (\href{https://orcid.org/0009-0005-5166-0417}{ORCID}) [contributor] + \item Cecilia Campanile \email{cecilia.campanile@ndorms.ox.ac.uk} [contributor] +} + } \keyword{internal} From 8842c3de6fae2c4314bf2867d87545b11b0087d8 Mon Sep 17 00:00:00 2001 From: catalamarti Date: Tue, 15 Oct 2024 15:23:28 +0100 Subject: [PATCH 2/6] prepare cran --- .Rbuildignore | 1 + DESCRIPTION | 2 +- cran-comments.md | 5 +++++ 3 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 cran-comments.md diff --git a/.Rbuildignore b/.Rbuildignore index b4f7f73..e9adc80 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -13,3 +13,4 @@ ^doc$ ^Meta$ ^vignettes/articles$ +^cran-comments\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index 3f7c5ea..4cf6f3f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: OmopViewer Type: Package Title: Visualise OMOP Results in a Shiny App -Version: 0.0.0.900 +Version: 0.1.0 Authors@R: c( person( "Martí", "Català", , "marti.catalasabate@ndorms.ox.ac.uk", diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..2d8133a --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,5 @@ +## R CMD check results + +0 errors | 0 warnings | 1 note + +* This is a new release. We do not cide any reference. From cfddda7c2bfcf364e561e4b7a3898979c1ac71dd Mon Sep 17 00:00:00 2001 From: catalamarti Date: Tue, 15 Oct 2024 15:33:50 +0100 Subject: [PATCH 3/6] Update DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4cf6f3f..369d471 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,7 +20,7 @@ Authors@R: c( role = "ctb", comment = c(ORCID = "0009-0005-5166-0417")), person( "Cecilia", "Campanile", , "cecilia.campanile@ndorms.ox.ac.uk", - role = "ctb") + role = "ctb", comment = c(ORCID = "0009-0007-6629-4661")) ) Maintainer: Martí Català Description: Visualise results obtained from analysing data mapped to the From 8987667af27873da23a626273c1a2f2f31be327d Mon Sep 17 00:00:00 2001 From: catalamarti Date: Tue, 15 Oct 2024 15:34:01 +0100 Subject: [PATCH 4/6] Update OmopViewer-package.Rd --- man/OmopViewer-package.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/OmopViewer-package.Rd b/man/OmopViewer-package.Rd index 837e618..7f84626 100644 --- a/man/OmopViewer-package.Rd +++ b/man/OmopViewer-package.Rd @@ -28,7 +28,7 @@ Other contributors: \item Edward Burn \email{edward.burn@ndorms.ox.ac.uk} (\href{https://orcid.org/0000-0002-9286-1128}{ORCID}) [contributor] \item Nuria Mercade-Besora \email{nuria.mercadebesora@ndorms.ox.ac.uk} (\href{https://orcid.org/0009-0006-7948-3747}{ORCID}) [contributor] \item Elin Rowlands \email{elin.rowlands@ndorms.ox.ac.uk} (\href{https://orcid.org/0009-0005-5166-0417}{ORCID}) [contributor] - \item Cecilia Campanile \email{cecilia.campanile@ndorms.ox.ac.uk} [contributor] + \item Cecilia Campanile \email{cecilia.campanile@ndorms.ox.ac.uk} (\href{https://orcid.org/0009-0007-6629-4661}{ORCID}) [contributor] } } From e70abace862fde5f734d7aec1a51bed545162522 Mon Sep 17 00:00:00 2001 From: catalamarti Date: Tue, 15 Oct 2024 16:35:17 +0100 Subject: [PATCH 5/6] new version in snapshots --- R/buttons.R | 45 ------------------- R/panelTidy.R | 18 ++++++-- tests/testthat/_snaps/appStatic.md | 20 ++++----- tests/testthat/_snaps/packagesSupported.md | 52 +++++++++++----------- 4 files changed, 51 insertions(+), 84 deletions(-) diff --git a/R/buttons.R b/R/buttons.R index b3dc13c..91ac5ab 100644 --- a/R/buttons.R +++ b/R/buttons.R @@ -45,48 +45,3 @@ selector <- function(id, lab, cho, sel, mult) { glue::glue() |> as.character() } -downloadTable <- function(id, lab, type = NULL) { - if (is.null(type)) { - type <- "" - } else { - type <- paste0('{selector("', id, '_type", "File", {cast(type)}, {cast("docx")}, FALSE)},') |> glue::glue() - } - - 'bslib::card_header( - bslib::popover( - shiny::icon("download"), - {type} - shiny::downloadButton(outputId = "{id}", label = "{lab}") - ), - class = "text-end" - )' |> - glue::glue() |> - as.character() -} -downloadPlot <- function(outputId, id) { - output <- omopViewerPlots$output[omopViewerPlots$plot_id == id] - buttons <- switch( - output, - "ggplot2" = 'shiny::numericInput(inputId = "{outputId}_width", label = "Width", value = 15), - shiny::numericInput(inputId = "{outputId}_height", label = "Height", value = 10), - {selector("{outputId}_units", "Units", {cast(c("px", "cm", "inch"))}, {cast("cm")}, FALSE)}, - shiny::numericInput(inputId = "{outputId}_dpi", label = "dpi", value = 300)' |> - glue::glue() |> - glue::glue(), - "grViz" = 'shiny::numericInput(inputId = "{outputId}_width", label = "Width (px)", value = 15), - shiny::numericInput(inputId = "{outputId}_height", label = "Height (px)", value = 10)' |> - glue::glue() |> - glue::glue() - ) - - 'bslib::card_header( - bslib::popover( - shiny::icon("download"), - {buttons}, - shiny::downloadButton(outputId = "{outputId}", label = "Download png") - ), - class = "text-end" - )' |> - glue::glue() |> - as.character() -} diff --git a/R/panelTidy.R b/R/panelTidy.R index 9740419..1213e1c 100644 --- a/R/panelTidy.R +++ b/R/panelTidy.R @@ -5,10 +5,23 @@ tidyUi <- function(tab) { title = "Tidy", bslib::card( full_screen = TRUE, - {downloadTable("{tab}_tidy_download", "Download csv")}, + bslib::card_header( + bslib::popover( + shiny::icon("download"), + shiny::downloadButton(outputId = "{tab}_tidy_download", label = "Download csv") + ), + class = "text-end" + ), bslib::layout_sidebar( sidebar = bslib::sidebar( - {selector("{tab}_tidy_columns", "Columns", "NULL", "NULL", TRUE)}, + shiny::selectizeInput( + inputId = "{tab}_tidy_columns", + label = "Columns", + choices = NULL, + selected = NULL, + multiple = TRUE, + options = list(plugins = "remove_button") + ), shiny::radioButtons( inputId = "{tab}_tidy_pivot", label = "Pivot estimates/variables", @@ -21,7 +34,6 @@ tidyUi <- function(tab) { ) ) )' |> - glue::glue() |> glue::glue() |> as.character() } diff --git a/tests/testthat/_snaps/appStatic.md b/tests/testthat/_snaps/appStatic.md index 67f3e82..762ea81 100644 --- a/tests/testthat/_snaps/appStatic.md +++ b/tests/testthat/_snaps/appStatic.md @@ -47,7 +47,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -93,7 +93,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -119,7 +119,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -171,7 +171,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -182,7 +182,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -853,7 +853,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -864,7 +864,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -1535,7 +1535,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -1546,7 +1546,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -2221,7 +2221,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) diff --git a/tests/testthat/_snaps/packagesSupported.md b/tests/testthat/_snaps/packagesSupported.md index b58d50f..3b858ca 100644 --- a/tests/testthat/_snaps/packagesSupported.md +++ b/tests/testthat/_snaps/packagesSupported.md @@ -3,7 +3,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -1207,7 +1207,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -1218,7 +1218,7 @@ Code cat(server, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file server <- function(input, output, session) { @@ -1571,7 +1571,7 @@ Code cat(global, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file library(DT) @@ -1595,7 +1595,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -2794,7 +2794,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -2805,7 +2805,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -3846,7 +3846,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -3857,7 +3857,7 @@ Code cat(server, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file server <- function(input, output, session) { @@ -4368,7 +4368,7 @@ Code cat(global, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file library(DT) @@ -4391,7 +4391,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -5427,7 +5427,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -5438,7 +5438,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -6766,7 +6766,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -6777,7 +6777,7 @@ Code cat(server, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file server <- function(input, output, session) { @@ -7346,7 +7346,7 @@ Code cat(global, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file library(CohortCharacteristics) @@ -7371,7 +7371,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -8694,7 +8694,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -8705,7 +8705,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -9051,7 +9051,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -9062,7 +9062,7 @@ Code cat(server, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file server <- function(input, output, session) { @@ -9246,7 +9246,7 @@ Code cat(global, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file library(DT) @@ -9269,7 +9269,7 @@ Code cat(ui, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file ui <- bslib::page_navbar( @@ -10012,7 +10012,7 @@ href = "https://github.com/OHDSI/OmopViewer", target = "_blank" ), - shiny::strong("v0.0.0.900") + shiny::strong("v0.1.0") ) ), bslib::nav_item(bslib::input_dark_mode(id = "dark_mode", mode = "light")) @@ -10023,7 +10023,7 @@ Code cat(server, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file server <- function(input, output, session) { @@ -10317,7 +10317,7 @@ Code cat(global, sep = "\n") Output - # Generated by OmopViewer 0.0.0.900 + # Generated by OmopViewer 0.1.0 # Be careful editing this file library(CodelistGenerator) From 56eb94da724c02bb00552564871c935183a8a3fd Mon Sep 17 00:00:00 2001 From: catalamarti Date: Tue, 15 Oct 2024 16:38:02 +0100 Subject: [PATCH 6/6] Update cran-comments.md --- cran-comments.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 2d8133a..432bde6 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,4 +2,4 @@ 0 errors | 0 warnings | 1 note -* This is a new release. We do not cide any reference. +* This is a new release. We do not cite any reference.