Merge pull request #84 from istallworthy/run-through

clean up

.gitignore

@@ -6,4 +6,4 @@ docs
 .Rdata
 .httr-oauth
 .DS_Store
-!Archive/*
+Archive/*

DESCRIPTION

@@ -2,25 +2,33 @@ Package: devMSMs
 Type: Package
 Title: Tools for Conducting Marginal Structural Models with Developmental Data
 Version: 0.0.0.9000
-Authors: Isabella Stallworthy
+Authors@R: c(person("Isabella", "Stallworthy",
+            email = "[email protected]",
+            role = c("aut", "cre")),
+            person("Meriah", "DeJoseph",
+            email = "[email protected]",
+            role = c("aut")),
+            person("Emily", "Padrutt",
+            email = "[email protected]",
+            role = c("aut")),
+            person("Noah", "Greifer",
+            email = "[email protected]",
+            role = c("aut")),
+            person("Daniel", "Berry",
+            email = "[email protected]",
+            role = c("aut")))
 Description: Functions for preparing, assessing, and implementing MSMS.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.2
 Imports:
-    readr,
-    readxl,
     tidyr,
     dplyr,
     WeightIt,
-    MatchThem,
     marginaleffects,
-    ranger,
-    data.table,
     tidyr,
-    Hmisc,
     stats,
     ggplot2,
     matrixStats,
@@ -33,12 +41,13 @@ Imports:
     doRNG,
     foreach,
     mice,
-    sjPlot,
     stargazer,
     gtools,
-    RColorBrewer,
     cobalt,
-    dbarts
+    purrr,
+    stringr,
+    missMethods,
+    tibble
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -54,6 +54,7 @@ importFrom(mice,complete)
 importFrom(mice,ibind)
 importFrom(mice,mice)
 importFrom(mice,pool)
+importFrom(missMethods,delete_MAR_1_to_x)
 importFrom(parallel,detectCores)
 importFrom(purrr,map_dfr)
 importFrom(stargazer,stargazer)

R/fitModel.R

@@ -324,8 +324,8 @@ fitModel <- function(home_dir, data, weights, exposure, exposure_time_pts, outco
     }
 
     if (save.out){
-      require(officer) #is there another way to do this? required for writing to word
-      require(flextable) # " "
+      requireNamespace(officer) #is there another way to do this? required for writing to word
+      requireNamespace(flextable) # " "
       suppressWarnings(jtools::export_summs(fits, to.file = "docx", statistics = c(N = "nobs", AIC = "AIC", R2 = "r.squared"),
                                             file.name = file.path(home_dir, "models", paste0(exposure, "-", outcome, "_", model,
                                                                                              "_table_mod_ev.docx"))))

R/getModel.R

@@ -21,6 +21,7 @@
 #' @param covariates list of characters reflecting variable names of covariates
 #'   for covariate models
 #' @param verbose TRUE or FALSE indicator for user output (default is TRUE)
+#' @importFrom survey svyglm
 #' @return list of fitted model(s)
 #' @export
 #' @examples
@@ -86,7 +87,6 @@ getModel <- function(d, exposure, exposure_time_pts, outcome, epochs, exp_epochs
         #finds data from each time point in each epoch, horizontally aligns all exposure values within the epoch for averaging
         for (l in seq_len(length(as.numeric(unlist(epochs[e, 2]))))){
           level <- as.numeric(unlist(epochs[e, 2]))[l]
-          # z  <- d[, which(grepl(paste0(exposure, ".", level), names(d)))]
           z <- d[, names(d)[grepl(exposure, names(d))]] #finds exposure vars
           z <- as.numeric(as.character(unlist(z[, sapply(strsplit(names(z), "\\."), "[", 2) == as.character(level)])))
           temp <- cbind(temp, z)

R/imputeData.R

@@ -16,6 +16,7 @@
 #' @importFrom purrr map_dfr
 #' @importFrom foreach getDoParWorkers
 #' @importFrom foreach getDoParName
+#' @importFrom missMethods delete_MAR_1_to_x
 #' @seealso {[mice::mice()],
 #'   <https://cran.r-project.org/web/packages/mice/index.html>}
 #' @param data data in wide format
@@ -29,7 +30,7 @@
 #'   using multiple cores to speed up process (default = TRUE)
 #' @param save.out (optional) TRUE or FALSE indicator to save output and
 #'   intermediary output locally (default is TRUE)
-#' @param read_in_from_file (optional) "yes" or "no" indicatorto read in weights
+#' @param read_imps_from_file (optional) "yes" or "no" indicatorto read in weights
 #'   that have been previously run and saved locally (default is "no")
 #' @return mice object of m imputed datasets
 #' @examples
@@ -45,7 +46,8 @@
 #' test[, c("A.1", "A.2", "A.3")] <- lapply(test[, c("A.1", "A.2", "A.3")], as.numeric)
 #'
 #' test_miss <- missMethods::delete_MAR_1_to_x(as.data.frame(test), p = 0.20,
-#'                                             cols_mis = c("A.1", "B.2", "C"), cols_ctrl = c("B.1", "B.1", "B.1"), 3)
+#'                                             cols_mis = c("A.1", "B.2", "C"),
+#'                                             cols_ctrl = c("B.1", "B.1", "B.1"), 3)
 #' test_i <- imputeData(data = test_miss,
 #'                      m = 3,
 #'                      method = "rf",

R/inspectData.R

@@ -15,10 +15,10 @@
 #' @param hi_lo_cut (optional) list of two numbers indicating quantile values
 #'   that reflect high and low values, respectively, for continuous exposure
 #'   (default is median split)
-#' @param (optional) reference string of "-"-separated "l" and "h" values
+#' @param reference (optional)string of "-"-separated "l" and "h" values
 #'   indicative of a reference exposure history to which to compare comparison,
 #'   required if comparison is specified
-#' @param (optional) comparison list of one or more strings of "-"-separated "l"
+#' @param comparison (optional)list of one or more strings of "-"-separated "l"
 #'   and "h" values indicative of comparison history/histories to compare to
 #'   reference, required if reference is specified
 #' @param verbose (optional) TRUE or FALSE indicator for user output (default is

R/make_love_plot.R

@@ -15,6 +15,8 @@
 #' @param weights_method method character string of WeightItMSM() balancing
 #'   method abbreviation
 #' @param imp_conf list of variable names reflecting important confounders
+#' @param verbose TRUE or FALSE indicator for user output (default is
+#'   TRUE)
 #' @param save.out TRUE or FALSE indicator to save output and intermediary
 #'   output locally
 #' @return none

R/trimWeights.R

@@ -4,8 +4,9 @@
 #' Trims IPTW balancing weights with heavy right tails by populating all weight
 #' values above a given quantile with the weight value of that quantile.
 #'
-#' @seealso {[WeightIt::trim()],
-#'   <https://search.r-project.org/CRAN/refmans/WeightIt/html/trim.html>}
+#' @seealso [WeightIt::trim()],
+#'   <https://search.r-project.org/CRAN/refmans/WeightIt/html/trim.html> which
+#'   this function wraps
 #' @param home_dir path to home directory
 #' @param exposure name of exposure variable
 #' @param outcome name of outcome variable with ".timepoint" suffix

examplePipelineRevised.Rmd

@@ -51,6 +51,8 @@ library(devMSMs)
 # remove.packages("devMSMs")
 #prior to re-installing using the code above. Sorry, this is annoying!
 
+#conducting package checks & tests from documentation
+devtools::check()
 ```