CRAN peparation

jakub-jedrusiak · Aug 8, 2023 · 9496aae · 9496aae
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,3 +9,5 @@
 ^\.lintr$
 ^\.covrignore$
 ^\.vscode$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 1.0.0
+Date: 2023-08-07 12:57:06 UTC
+SHA: 49620267b928e590dd5e1dbda7bb4a97d03d1f0d
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,17 @@
 Package: mtscr
 Type: Package
-Title: Multidimentional Top Scoring for Creativity Research
-Version: 0.1.0
+Title: Multidimensional Top Scoring for Creativity Research
+Version: 1.0.0
 Authors@R: c(
+    person(
+      "Jakub", "Jędrusiak",
+      email = "kuba23031999@gmail.com",
+      role = c("aut", "cre", "cph"),
+      comment = c(
+        ORCID = "0000-0002-6481-8210",
+        affiliation = "University of Wrocław"
+        )
+      ),
     person(
       "Boris", "Forthmann",
       email = "boris.forthmann@uni-muenster.de",
@@ -12,15 +21,6 @@ Authors@R: c(
         affiliation = "University of Münster"
       )
     ),
-    person(
-      "Maciej", "Karwowski",
-      email = "maciej.karwowski@uwr.edu.pl",
-      role = "aut",
-      comment = c(
-        ORCID = "0000-0001-6974-1673",
-        affiliation = "University of Wrocław"
-      )
-    ),
     person(
       c("Roger", "E."), "Beaty",
       email = "rebeaty@psu.edu",
@@ -31,17 +31,17 @@ Authors@R: c(
         )
       ),
     person(
-      "Jakub", "Jędrusiak",
-      email = "kuba23031999@gmail.com",
-      role = c("aut", "cre"),
+      "Maciej", "Karwowski",
+      email = "maciej.karwowski@uwr.edu.pl",
+      role = "aut",
       comment = c(
-        ORCID = "0000-0002-6481-8210",
+        ORCID = "0000-0001-6974-1673",
         affiliation = "University of Wrocław"
-        )
       )
     )
-Description: R implementation of Multidimentional Top Scoring
-    method for creativity assesment. Proposed by Forthmann,
+  )
+Description: Implementation of Multidimensional Top Scoring
+    method for creativity assessment proposed by Forthmann,
     Karwowski and Beaty (2023).
 License: MIT + file LICENSE
 Encoding: UTF-8
@@ -60,10 +60,10 @@ Imports:
     purrr,
     readr,
     rlang (>= 0.4.11),
-    shiny,
     stringr,
     tibble
 Suggests: 
+    shiny,
     covr,
     datamods,
     DT,

diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,3 @@
+# mtscr 1.0.0
+
+* Initial CRAN submission.
diff --git a/R/data.R b/R/data.R
@@ -1,6 +1,6 @@
 #' Creativity assessment through semantic distance dataset
 #'
-#' A dataset from Forthmann, Karwowski & Beaty ([2023](https://doi.org/10.1037/aca0000571)) paper.
+#' A dataset from Forthmann, Karwowski & Beaty (2023) paper.
 #' It contains a set of responses in Alternative Uses Task for different items with their
 #' semantic distance assessment.
 #'
@@ -15,6 +15,7 @@
 #' }
 #'
 #' @source <https://osf.io/7rgsp/>
+#' @references \doi{10.1037/aca0000571}
 "mtscr_creativity"
 
 #' @rdname mtscr_self_rank
@@ -31,4 +32,7 @@
 #'   \item{avr}{average judges' raiting}
 #'   \item{top_two}{indicator of self-chosen two best answer; 1 if chosen, 0 if not}
 #' }
+#'
+#' @source <https://osf.io/7rgsp/>
+#' @references \doi{10.1037/aca0000571}
 "mtscr_self_rank"
diff --git a/R/mtscr_app.R b/R/mtscr_app.R
@@ -4,9 +4,6 @@
 #'
 #' @return Runs the app. No explicit return value.
 #'
-#' @param debug_mode Integer. If 0, app runs normally. If 1, `needed_packages` are
-#'     returned. If 2, an invalid package is added to `needed_packages` and an error
-#'    is thrown.
 #' @export
 #'
 #' @details
@@ -38,18 +35,14 @@
 #'   Forthmann, B., Karwowski, M., & Beaty, R. E. (2023).
 #'     Don’t throw the “bad” ideas away!
 #'     Multidimensional top scoring increases reliability of divergent thinking tasks.
-#'     Psychology of Aesthetics, Creativity, and the Arts. [https://doi.org/10.1037/aca0000571](https://doi.org/10.1037/aca0000571)
+#'     Psychology of Aesthetics, Creativity, and the Arts. \doi{10.1037/aca0000571}
 #'
 #' @examples
 #' \dontrun{
 #' mtscr_app()
 #' }
-mtscr_app <- function(debug_mode = 0) {
-  needed_packages <- if (debug_mode == 2) {
-    c("DT", "datamods", "writexl", "shinyWidgets", "INVALID_PACKAGE")
-  } else {
-    c("DT", "datamods", "writexl", "shinyWidgets")
-  }
+mtscr_app <- function() {
+  needed_packages <- c("shiny", "DT", "datamods", "writexl", "shinyWidgets")
 
   needed_packages <- sapply(needed_packages, \(x) {
     if (system.file(package = x) != "") {
@@ -79,9 +72,6 @@ mtscr_app <- function(debug_mode = 0) {
       )
     )
   }
-  if (debug_mode %in% 1:2) {
-    return(needed_packages)
-  } else {
-    shiny::runApp(app_dir, display.mode = "normal")
-  }
+
+  shiny::runApp(app_dir, display.mode = "normal")
 }
diff --git a/R/mtscr_model.R b/R/mtscr_model.R
@@ -17,6 +17,9 @@
 #' @examples
 #' data("mtscr_creativity", package = "mtscr")
 #'
+#' mtscr_creativity <- mtscr_creativity |>
+#'   dplyr::slice_sample(n = 300) # for performance, ignore
+#'
 #' mtscr_model(mtscr_creativity, id, item, SemDis_MEAN) |>
 #'   summary()
 #'
@@ -29,7 +32,7 @@
 #' mtscr_model(data, id, item, SemDis_MEAN, prepared = TRUE)
 #'
 #' # extract effects for creativity score by hand
-#' model <- mtscr_model(mtscr_creativity, id, item, SemDis_MEAN, top = 2)
+#' model <- mtscr_model(mtscr_creativity, id, item, SemDis_MEAN, top = 1)
 #' creativity_score <- glmmTMB::ranef(model)$cond$id[, 1]
 mtscr_model <- function(df, id_column, item_column = NULL, score_column, top = 1, prepared = FALSE, ties_method = c("random", "average"), normalise = TRUE, self_ranking = NULL) {
   id_column <- rlang::ensym(id_column)

diff --git a/README.Rmd b/README.Rmd
@@ -13,31 +13,35 @@ knitr::opts_chunk$set(
 )
 ```
 
-# Multidimensional Top Scoring for Creativity Research <img src="./man/figures/mtscr-hex.svg" width="200" align="right"/> {#multidimentional-top-scoring-for-creativity-research}
+# Multidimensional Top Scoring for Creativity Research <img src="./man/figures/mtscr-hex.svg" width="200" align="right"/> {#multidimensional-top-scoring-for-creativity-research}
 
 <!-- badges: start -->
 
-[![codecov](https://codecov.io/gh/jakub-jedrusiak/mtscr/branch/main/graph/badge.svg?token=N3UGHFK5QN)](https://codecov.io/gh/jakub-jedrusiak/mtscr) [![R-CMD-check](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml)
-[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![codecov](https://codecov.io/gh/jakub-jedrusiak/mtscr/branch/main/graph/badge.svg?token=N3UGHFK5QN)](https://app.codecov.io/gh/jakub-jedrusiak/mtscr) [![R-CMD-check](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![CRAN status](https://www.r-pkg.org/badges/version/mtscr)](https://CRAN.R-project.org/package=mtscr)
 <!-- badges: end -->
 
 An R adaptation of Multidimensional Top Scoring method presented by Forthmann, Karwowski and Beaty ([2023](https://doi.org/10.1037/aca0000571)) using the code from the [OSF database](https://osf.io/7rgsp/). The code was adapted to use the [tidyverse](https://www.tidyverse.org/) framework for greater flexibility.
 
 ## Installation {#installation}
 
+Install mtscr with:
+
+``` r
+install.packages("mtscr")
+```
+
 You can install the development version of mtscr from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
 devtools::install_github("jakub-jedrusiak/mtscr")
 ```
 
-The mtscr package is not on CRAN yet.
-
 ## Usage {#usage}
 
-Basic usage involves scoring participants' responses to a divergent thinking task. The package includes a sample dataset `mtscr_creativity` with 4652 responses to the [Alternative Uses Task](https://en.wikipedia.org/wiki/Alternative_uses_test) with semantic distance scored. The dataset comes from the original paper (Forthmann, Karwowski and Beaty, [2023](https://doi.org/10.1037/aca0000571)).
+Basic usage involves scoring participants' responses to a divergent thinking task. The package includes a sample dataset `mtscr_creativity` with 4652 responses to the [Alternative Uses Task](https://en.wikipedia.org/wiki/Guilford%27s_Alternate_Uses) with semantic distance scored. The dataset comes from the original paper (Forthmann, Karwowski and Beaty, [2023](https://doi.org/10.1037/aca0000571)).
 
 The main function is `mtscr_scores()` which returns a dataframe with scored responses. It takes a dataframe with responses, an ID column, an item column and a score column as arguments. The score column should contain semantic distance scores for each response. The function adds columns with scores for each person. The number of creativity scores is based on a given number of top answers provided by the `top` argument.
 

diff --git a/README.md b/README.md
@@ -5,10 +5,10 @@
 
 <!-- badges: start -->
 
-[![codecov](https://codecov.io/gh/jakub-jedrusiak/mtscr/branch/main/graph/badge.svg?token=N3UGHFK5QN)](https://codecov.io/gh/jakub-jedrusiak/mtscr)
+[![codecov](https://codecov.io/gh/jakub-jedrusiak/mtscr/branch/main/graph/badge.svg?token=N3UGHFK5QN)](https://app.codecov.io/gh/jakub-jedrusiak/mtscr)
 [![R-CMD-check](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml)
 [![Lifecycle:
-experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/mtscr)](https://CRAN.R-project.org/package=mtscr)
 <!-- badges: end -->
@@ -22,6 +22,12 @@ flexibility.
 
 ## Installation
 
+Install mtscr with:
+
+``` r
+install.packages("mtscr")
+```
+
 You can install the development version of mtscr from
 [GitHub](https://github.com/) with:
 
@@ -30,16 +36,15 @@ You can install the development version of mtscr from
 devtools::install_github("jakub-jedrusiak/mtscr")
 ```
 
-The mtscr package is not on CRAN yet.
-
 ## Usage
 
 Basic usage involves scoring participants’ responses to a divergent
 thinking task. The package includes a sample dataset `mtscr_creativity`
 with 4652 responses to the [Alternative Uses
-Task](https://en.wikipedia.org/wiki/Alternative_uses_test) with semantic
-distance scored. The dataset comes from the original paper (Forthmann,
-Karwowski and Beaty, [2023](https://doi.org/10.1037/aca0000571)).
+Task](https://en.wikipedia.org/wiki/Guilford%27s_Alternate_Uses) with
+semantic distance scored. The dataset comes from the original paper
+(Forthmann, Karwowski and Beaty,
+[2023](https://doi.org/10.1037/aca0000571)).
 
 The main function is `mtscr_scores()` which returns a dataframe with
 scored responses. It takes a dataframe with responses, an ID column, an
@@ -56,14 +61,14 @@ mtscr_score(mtscr_creativity, id, item, SemDis_MEAN, top = 1:2)
 #> # A tibble: 149 × 3
 #>    id    .creativity_score_top1 .creativity_score_top2
 #>    <chr>                  <dbl>                  <dbl>
-#>  1 84176                 0.142                  0.0696
-#>  2 84177                -0.509                 -0.494 
-#>  3 84178                -0.0737                -0.0990
-#>  4 84188                 0.530                  0.527 
+#>  1 84176                 0.142                  0.0681
+#>  2 84177                -0.508                 -0.494 
+#>  3 84178                -0.0733                -0.0995
+#>  4 84188                 0.529                  0.527 
 #>  5 84193                -0.299                 -0.350 
-#>  6 84206                -0.310                 -0.301 
-#>  7 84211                -0.0462                 0.0360
-#>  8 84226                 0.239                  0.211 
+#>  6 84206                -0.312                 -0.301 
+#>  7 84211                -0.0464                 0.0356
+#>  8 84226                 0.238                  0.210 
 #>  9 84228                 0.137                  0.139 
 #> 10 84236                 0.459                  0.422 
 #> # ℹ 139 more rows
@@ -83,9 +88,9 @@ mtscr_model(mtscr_creativity, id, item, SemDis_MEAN, top = 1:3) |>
 #> # A tibble: 3 × 9
 #>   model  nobs sigma logLik    AIC    BIC df.residual emp_rel   FDI
 #>   <chr> <int> <dbl>  <dbl>  <dbl>  <dbl>       <int>   <dbl> <dbl>
-#> 1 top1   4621 0.735 -5335. 10730. 10923.        4591   0.845 0.919
-#> 2 top2   4621 0.767 -5511. 11082. 11275.        4591   0.869 0.932
-#> 3 top3   4621 0.825 -5823. 11705. 11898.        4591   0.877 0.936
+#> 1 top1   4585 0.736 -5298. 10657. 10850.        4555   0.877 0.936
+#> 2 top2   4585 0.767 -5472. 11003. 11196.        4555   0.892 0.944
+#> 3 top3   4585 0.825 -5777. 11613. 11806.        4555   0.896 0.947
 ```
 
 ### Graphical User Interface

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,12 +1,11 @@
-citHeader("To cite mtscr in publications use:")
-
-citEntry(
-  entry    = "Manual",
+bibentry(
+  mheader  = "To cite mtscr in publications use:",
+  bibtype  = "Manual",
   title    = "Multidimensional Top Scoring for Creativity Research",
-  author   = "Boris Forthmann, Maciej Karwowski, Roger E. Beaty, Jakub Jędrusiak",
+  author   = "Jakub Jędrusiak, Boris Forthmann, Roger E. Beaty, Maciej Karwowski",
   year     = "2023",
   url      = "https://github.com/jakub-jedrusiak/mtscr",
   textVersion = paste(
-"Forthmann, B., Karwowski, M., Beaty, R. E., Jędrusiak, J. (2023). Multidimensional Top Scoring for Creativity Research. Retrieved from: https://github.com/jakub-jedrusiak/mtscr"
+"Jędrusiak, J., Forthmann, B., Beaty, R. E., Karwowski, M. (2023). Multidimensional Top Scoring for Creativity Research. Retrieved from: https://github.com/jakub-jedrusiak/mtscr"
   )
 )
diff --git a/inst/GUI/rsconnect/shinyapps.io/jakub-jedrusiak/mtscr_GUI.dcf b/inst/GUI/rsconnect/shinyapps.io/jakub-jedrusiak/mtscr_GUI.dcf
@@ -5,9 +5,9 @@ account: jakub-jedrusiak
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 9014241
-bundleId: 7325206
+bundleId: 7383306
 url: https://jakub-jedrusiak.shinyapps.io/mtscr_GUI/
-when: 1686322197.11898
-lastSyncTime: 1686322197.119
+when: 1687616453.90466
+lastSyncTime: 1687616453.90468
 asMultiple: FALSE
 asStatic: FALSE
diff --git a/man/mtscr-package.Rd b/man/mtscr-package.Rd
diff --git a/man/mtscr_app.Rd b/man/mtscr_app.Rd
diff --git a/man/mtscr_creativity.Rd b/man/mtscr_creativity.Rd