changes in text and prettify code remove unnecessary files and imports

DESCRIPTION

@@ -1,43 +1,37 @@
 Package: gmoTree
 Title: Get and Modify 'oTree' Data
-Version: 1.2.0-9003
-Date: 2024-09-20
+Version: 1.2.0
+Date: 2024-09-30
 Authors@R: 
-    person("Patricia F.", "Zauchner", , "patricia.zauchner@gmx.at", role = c("aut", "trl", "cre", "cph"),
-           comment = c(ORCID = "https://orcid.org/0000-0002-5938-1683"))
+    person(given = "Patricia F.", family = "Zauchner",
+    role = c("aut", "trl", "cre", "cph"),
+    email = "patricia.zauchner@gmx.at",
+    comment = c("https://orcid.org/0000-0002-5938-1683", "University of Bremen"))
 Description: Efficiently manage and process data from 'oTree' experiments.
     Import 'oTree' data and clean them by using 
-    functions to deal with messy data, dropouts,
-    and other problematic cases. Create IDs, calculate the time, transfer
+    functions that handle messy data, dropouts, and other problematic cases.
+    Create IDs, calculate the time, transfer
     variables between app data frames, and delete sensitive information.
-    You can also check your experimental data before running the
-    experiment and automatically make a codebook for your oTree code.
+    Review your experimental data prior to running 
+    the experiment and automatically generate a detailed summary 
+    of the variables used in your 'oTree' code.
     Information on 'oTree' is found in Chen, D. L., Schonger, M., &
     Wickens, C. (2016) <doi:10.1016/j.jbef.2015.12.001>.
 License: GPL (>= 3)
-URL: https://zauchnerp.github.io/gmoTree/, https://github.com/ZauchnerP/gmoTree/, https://github.com/ZauchnerP/gmoTree
+URL: https://zauchnerp.github.io/gmoTree/,
+        https://github.com/ZauchnerP/gmoTree/,
+        https://github.com/ZauchnerP/gmoTree
 BugReports: https://github.com/ZauchnerP/gmoTree/issues
-Depends: 
-    R (>= 4.4.0)
-Imports: 
-    data.table (>= 1.15.4),
-    dplyr (>= 1.1.4),
-    knitr (>= 1.47),
-    openxlsx (>= 4.2.5.2),
-    pander (>= 0.6.5),
-    plyr (>= 1.8.9),
-    rlang (>= 1.1.4),
-    rlist (>= 0.4.6.2),
-    rmarkdown (>= 2.27),
-    stats (>= 4.4.0),
-    stringr (>= 1.5.1)
-Suggests: 
-    testthat (>= 3.2.1),
-    withr (>= 3.0.0)
-VignetteBuilder: 
-    knitr
+Depends: R (>= 4.4.0)
+Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4), knitr (>= 1.47),
+        openxlsx (>= 4.2.5.2), pander (>= 0.6.5), plyr (>= 1.8.9),
+        rlang (>= 1.1.4), rlist (>= 0.4.6.2), rmarkdown (>= 2.27),
+        stringr (>= 1.5.1)
+Suggests: testthat (>= 3.2.1), withr (>= 3.0.0)
+VignetteBuilder: knitr
 BuildVignettes: true
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
+NeedsCompilation: no

NAMESPACE

@@ -20,6 +20,5 @@ export(show_dropouts)
 import(knitr)
 import(pander)
 import(rmarkdown)
-import(stats)
 import(stringr)
 import(utils)

NEWS.md

@@ -17,7 +17,7 @@
 * Minor changes in tests.R
 * Minor changes in website, new logo
 
-# gmoTree 1.0.1 (available also on CRAN)
+# gmoTree 1.0.1
 
 * Minor changes in examples and DESCRIPTION file. 
 * Changes in functions: NONE

R/apptime.R

@@ -743,7 +743,7 @@ apptime <- function(oTree,
                               message_vector,
                               firststageproblemparticipants,
                               warningparticipants) {
-    if (nrow(singledurations) > 0) {
+    if (nrow(singledurations) > 0L) {
       output[[appname]][["mean_duration"]] <-
         ifelse(rounded,
                round(
@@ -787,7 +787,7 @@ apptime <- function(oTree,
 
       output[[appname]]$first_app_one_page <- firststageproblemparticipants
 
-      if (length(warningparticipants) > 0) {
+      if (length(warningparticipants) > 0L) {
         output[[appname]]$warnings <- unique(warningparticipants)
       }
     } # Else:
@@ -802,7 +802,7 @@ apptime <- function(oTree,
                                            firststageproblemparticipants,
                                            warningparticipants) {
     # Output for all participants or several
-    if (length(apps) == 1) {
+    if (length(apps) == 1L) {
       return(output_oneapp(
         singledurations,
         message_vector,

R/codebook.R

@@ -97,7 +97,6 @@
 #' @import knitr
 #' @import pander
 #' @import rmarkdown
-#' @import stats
 #' @import stringr
 #' @import utils
 #' @returns
@@ -209,7 +208,7 @@ codebook <- function(path = ".",
                      settings_replace = "global",
                      user_settings = NULL,
                      include_cons = TRUE,
-                     preamb = TRUE,
+                     preamb = FALSE,
                      encoding = "UTF-8",
                      title = "Codebook",
                      subtitle = "created with gmoTree",
@@ -236,7 +235,7 @@ codebook <- function(path = ".",
       }
 
       # Check if fsource is valid
-      if (length(fsource) > 1) {
+      if (length(fsource) > 1L) {
         stop("Please enter only one fsource!")
       }
 
@@ -250,7 +249,7 @@ codebook <- function(path = ".",
     # Others  ####
     # Check output format
     if (!is.character(output) ||
-        length(output) != 1 ||
+        length(output) != 1L ||
         !(output %in% c("list", "both", "file"))) {
       stop("Output should be \"list\", \"both\", or \"file\"!")
     }
@@ -330,11 +329,11 @@ codebook <- function(path = ".",
 
     # Check if app(s) exist(s)
     if (!is.null(app)) {
-      if (length(app) == 1) {
-        if (!(app %in% basename(dirname(files)))) {  # TODO
+      if (length(app) == 1L) {
+        if (!(app %in% basename(dirname(files)))) {
           stop("App \"", app, "\"is not in oTree code!")
         }
-      } else if (length(app) > 1) {
+      } else if (length(app) > 1L) {
         for (app_i in seq_along(app)) {
 
           if (!(app[app_i] %in% basename(dirname(files)))) {
@@ -351,7 +350,7 @@ codebook <- function(path = ".",
                          "odt_document", "rtf_document", "md_document")
 
     if (is.null(output_format) ||
-        length(output_format) > 1 ||
+        length(output_format) > 1L ||
         !(output_format %in% allowed_formats)) {
       stop("Output format should be one of the following: ",
            paste0(allowed_formats, collapse = ", "), "!")
@@ -393,12 +392,6 @@ codebook <- function(path = ".",
           stop("Please don't use relative paths in output_dir!")
         }
 
-        # If dir is combined with a relative output_file path
-        # if (!is.null(output_file) && grepl("^\\.", x = output_file)) {
-        #   stop("Please don't use relative paths in output_file ",
-        #        "if output_dir is not empty!")
-        # }  # TODO das ist doch quatsch oder?
-
         # If dir is not there
         if (!dir.exists(output_dir)) {
 

R/delete_dropouts.R

@@ -172,7 +172,7 @@ delete_dropouts <- function(oTree,
 
       inconsistent <- readLines(
         con = getOption("mypkg.connection"),
-        n = 1)
+        n = 1L)
     }
 
     # Stop if user requests it

R/make_ids.R

@@ -123,10 +123,10 @@ make_ids <- function(oTree,
 
     } else if (from_app == "all_apps_wide") {
       if (is.null(oTree[[from_app]][[from_var]])) {
-        stop(paste0("from_var \"",
+        stop("from_var \"",
                     from_var,
                     "\" not found. ",
-                    "Please select another one."))
+                    "Please select another one.")
       }
     }
 
@@ -181,19 +181,19 @@ make_ids <- function(oTree,
   }
 
   # Check for NAs in the relevant variables
-  if (any(is.na(oTree[[from_app]]$participant.code))) {
+  if (anyNA(oTree[[from_app]]$participant.code)) {
     stop("There are NAs in your participant.code variable in your ",
                 "from_app! Clean your data or assign ",
                 "participant.code values by hand ",
                 "before running this function!")
   }
 
-  if (any(is.na(oTree$Chats$participant_code))) {
+  if (anyNA(oTree$Chats$participant_code)) {
     stop("There are NAs in your participant_code variable in ",
          "the oTree$Chats data frame.")
   }
 
-  if (any(is.na(oTree$Chats$participant__code))) {
+  if (anyNA(oTree$Chats$participant__code)) {
     stop("There are NAs in your participant__code variable in ",
          "the oTree$Chats data frame.")
   }
@@ -400,7 +400,7 @@ make_ids <- function(oTree,
 
     if (length(
       unique(oTree[[from_app]][, grep("group.id_in_subsession",
-                                      colnames(oTree[[from_app]]))])) == 1) {
+                                      colnames(oTree[[from_app]]))])) == 1L) {
 
       my_warnings <<- c(my_warnings, paste0(
         "The group variable values are constant. ",
@@ -549,7 +549,7 @@ make_ids <- function(oTree,
     } else {
       # This part is usually called if session.code is NA
       # This does not happen with cleaned data
-      if (any(is.na(oTree[[from_app]]$session.code))) {
+      if (anyNA(oTree[[from_app]]$session.code)) {
         my_warnings <-
           c(my_warnings,
             (paste0("At least one of your session.codes in your from_app is ",
@@ -671,7 +671,7 @@ make_ids <- function(oTree,
           !(oTree[[i]]$participant.code %in%
               oTree[[from_app]]$participant.code)])
 
-        if (length(participants_more) > 0) {
+        if (length(participants_more) > 0L) {
           my_warnings <- c(my_warnings,
                            paste0("Data frame \"",
                                   names(oTree)[[i]],
@@ -740,7 +740,7 @@ make_ids <- function(oTree,
         j <- j + 1
       }
       oTree[[i]] <-
-        oTree[[i]][ , c(c((ncol(oTree[[i]]) - j):ncol(oTree[[i]])),
+        oTree[[i]][, c(c((ncol(oTree[[i]]) - j):ncol(oTree[[i]])),
                         c(1L:(ncol(oTree[[i]]) - j - 1L)))
       ] # Again -1 because otherwise a number is there twice
 

R/messy_chat.R

@@ -146,7 +146,7 @@ messy_chat <- function(oTree,
     stop(paste(stop_messages, collapse  = "\n"))
   }
 
-  if (info == TRUE && length(warning_messages) > 0L) {
+  if (info && length(warning_messages) > 0L) {
     # This is printed as a warning because other functions catch the message
     warning(paste(warning_messages, collapse = "\n"))
   }

README.md

@@ -11,7 +11,7 @@ status](https://www.r-pkg.org/badges/version/gmoTree)](https://cran.r-project.or
 
 gmoTree is an R package developed for importing, merging, and
 efficiently managing data obtained from running
-<a href="https://www.otree.org/" target="_blank">oTree</a> experiments.
+<a href="https://www.otree.org/" target="_blank">oTree</a> (Chen et al., 2016) experiments.
 It’s particularly valuable when dealing with complex experimental
 designs that span multiple sessions and generate a large number of files
 that need to be integrated.[^1]
@@ -89,15 +89,20 @@ apps.
 
 - `pagesec()`: Calculates the time spent on each page.
 
-# Transferring variables between the apps
+## Transferring variables between the apps
 
 - `assignv()`: Copies a variable from the all_apps_wide data frame to the data frames
 of all other apps.
 
 - `assignv_to_aaw()`: Copies a variable from one of your data frames to the `all_apps_wide` data
 frame.
 
-# Before running the experiment
+## Before running the experiment
 
 - `show_constant()`: Shows constant variables.
 - `codebook()`: Creates a codebook based on the oTree code. See also the vignette <a href="https://zauchnerp.github.io/gmoTree/articles/codebook.html" target="_blank">"gmoTree Codebooks."</a>
+
+
+# References
+
+Chen, D. L., Schonger, M., & Wickens, C. (2016). oTree—An open-source platform for laboratory, online, and field experiments. Journal of Behavioral and Experimental Finance, 9, 88–97. https://doi.org/10.1016/j.jbef.2015.12.001