small fixes before CRAN submission

.Rbuildignore

@@ -10,3 +10,4 @@
 ^doc$
 ^Meta$
 ^CITATION\.cff$
+^cran-comments\.md$

DESCRIPTION

@@ -1,22 +1,26 @@
 Package: neuroUp
 Type: Package
-Title: Plan Sample Size for fMRI Regions of Interest research using Bayesian updating
+Title: Plan Sample Size for Task fMRI Research using Bayesian Updating
 Version: 0.2.0
 Authors@R: c(person(  "Eduard", "Klapwijk",
                 email = "[email protected]",
-                role = c("aut", "cre"),
+                role = c("aut", "cre", "cph"),
                 comment = c(ORCID = "0000-0002-8936-0365")), 
           person( "Herbert", "Hoijtink", 
-                role = c("aut"),
+                role = c("aut", "cph"),
                 comment = c(ORCID = "0000-0001-8509-1973")),
           person( "Joran", "Jongerling", 
-                role = c("aut"),
+                role = c("aut", "cph"),
                 comment = c(ORCID = "0000-0001-5697-1381")))
-Description: The package calculates the precision in mean differences (raw or Cohen's D) and correation coefficients for different sample sizes using permutations of the collected data.
+Description: Calculate the precision in mean differences (raw or Cohen's D) and 
+    correlation coefficients for different sample sizes. Uses permutations of the
+    collected functional magnetic resonance imaging (fMRI) region of interest data.
+    Method described in Klapwijk, Jongerling, Hoijtink and Crone (2024) 
+    <doi:10.31234/osf.io/cz32t>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 NeedsCompilation: no
 Imports: 
     dplyr,
@@ -37,4 +41,5 @@ Depends:
     R (>= 2.10)
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
-URL: https://eduardklap.github.io/neuroUp/
+URL: https://eduardklap.github.io/neuroUp/, https://github.com/eduardklap/neuroUp
+BugReports: https://github.com/eduardklap/neuroUp/issues

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2022
+YEAR: 2024
 COPYRIGHT HOLDER: neuroUp authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022 neuroUp authors
+Copyright (c) 2024 neuroUp authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

R/data.R

@@ -39,7 +39,7 @@
 #'   \item{lnacc_self_winvsloss}{parameter estimates for the left nucleas accumbens for
 #'   the contrast winning versus losing (-2.60-4.47)}
 #' }
-#' @source {Schreuders, E., Braams, B. R., Blankenstein, N. E., Peper, J. S., Güroğlu, B., & 
+#' @source {Schreuders, E., Braams, B. R., Blankenstein, N. E., Peper, J. S., Guroglu, B., & 
 #'  Crone, E. A. (2018). Contributions of reward sensitivity to ventral striatum activity across 
 #'  adolescence and early adulthood. Child development, 89(3), 797-810.}
 #'  \doi{10.1111/cdev.13056}
@@ -48,7 +48,7 @@
 #' Self-evaluations task fMRI region of interest data
 #'
 #' A dataset containing the parameter estimates of the
-#'  left medial prefrontal cortex (x = −6, y = 50, z = 4),
+#'  left medial prefrontal cortex (x = -6, y = 50, z = 4),
 #'  with one value for the mean activation during self-evaluation 
 #'  and one value for the mean activation during the control condition for all participants.
 #'
@@ -71,7 +71,7 @@
 #'
 #' A dataset containing the parameter estimates from
 #'  the anatomical mask of the left nucleus accumbens (Harvard-Oxford subcortical atlas; 
-#'  thresholded at 40%; center-of-mass coordinates x = −10, y = 12, z = −7; 28 voxels included),
+#'  thresholded at 40%; center-of-mass coordinates x = -10, y = 12, z = -7; 28 voxels included),
 #'  with one value for the mean activation during gaining for self and one value for the mean 
 #'  activation during no-gain for self and charity for all participants.
 #'
@@ -86,6 +86,6 @@
 #' }
 #' @source {Spaans, J., Peters, S., Becht, A., van der Cruijsen, R., van de Groep, S., 
 #'  & Crone, E. A. (2023). Longitudinal neural and behavioral trajectories of charity 
-#'  contributions across adolescence. Journal of Research on Adolescence, 33(2), 480–495.}
+#'  contributions across adolescence. Journal of Research on Adolescence, 33(2), 480-495.}
 #'  \doi{10.1111/jora.12820}
 "vicar_char"

R/estim_corr.R

@@ -12,7 +12,7 @@
 #' @param name The title of the dataset or variables to be displayed with the
 #'   figure. Defaults to `""`
 #' @returns
-#' * `tbl_select` returns a [tibble::tibble()] containing estimates of the Pearson’s
+#' * `tbl_select` returns a [tibble::tibble()] containing estimates of the Pearson
 #' correlation between two correlated variables with associated SD, SE, 95% CI,
 #' and width of the 95% CI (lower, upper) for five different sample sizes
 #' (starting with the minimum sample size, then 1/5th parts of the total
@@ -23,7 +23,7 @@
 #' for each sample size are plotted in orange
 #' * `fig_corr_nozero` returns a barplot where for each of the five sample sizes
 #' the proportion of permutations not containing zero is displayed
-#' * `tbl_total` returns a [tibble::tibble()] containing estimates of the Pearson’s
+#' * `tbl_total` returns a [tibble::tibble()] containing estimates of the Pearson
 #' correlation between two correlated variables with associated SD, SE, 95% CI,
 #' and width of the 95% CI (lower, upper) for all sample sizes, including the
 #' permutation number.

R/sample_corr.R

@@ -3,7 +3,7 @@
 #' @param data Dataframe with the data to be analyzed
 #' @param vars_of_interest Vector containing the names of the variables to be compared on their means
 #' @param sample_size The range of sample size to be used
-#' @return list with correlations and credible intervals for given sample_size
+#' @returns list with correlations and credible intervals for given sample_size
 #' @noRd
 
 sample_corr <- function(data, vars_of_interest, sample_size){

R/sample_diff.R

@@ -4,7 +4,7 @@
 #' @param vars_of_interest Vector containing the names of the variables to be
 #'   compared on their means
 #' @param sample_size The range of sample size to be used
-#' @return list with estimate, variance, stdev, sterror, lower, upper values for
+#' @returns list with estimate, variance, stdev, sterror, lower, upper values for
 #'   unstandardized differences as well as Cohen's d for given sample_size
 #' @noRd
 

README.Rmd

@@ -29,13 +29,25 @@ Klapwijk, E. T., Jongerling, J., Hoijtink, H., & Crone, E. (2024, July 9). Sampl
 
 ## Installation
 
-You can install the development version of neuroUp from [GitHub](https://github.com/) with:
+Run the following in R:
+
+```r
+install.packages("neuroUp")
+```
+
+Or you can install the latest development version of neuroUp from [GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
+install.packages("devtools")
 devtools::install_github("eduardklap/neuroUp")
 ```
 
+Then run the following to get started:
+
+```r
+library(neuroUp)
+```
+
 ## Citation
 
 To cite package neuroUp in publications use:

README.md

@@ -24,14 +24,26 @@ Bayesian updating. <https://doi.org/10.31234/osf.io/cz32t>
 
 ## Installation
 
-You can install the development version of neuroUp from
+Run the following in R:
+
+``` r
+install.packages("neuroUp")
+```
+
+Or you can install the latest development version of neuroUp from
 [GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
+install.packages("devtools")
 devtools::install_github("eduardklap/neuroUp")
 ```
 
+Then run the following to get started:
+
+``` r
+library(neuroUp)
+```
+
 ## Citation
 
 To cite package neuroUp in publications use:

cran-comments.md

@@ -0,0 +1,72 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.
+
+### Additional notes
+
+#### Notes returned after running `devtools::check(remote = TRUE, manual = TRUE)`:
+
+❯ checking CRAN incoming feasibility ... [5s/18s] NOTE
+  Maintainer: ‘Eduard Klapwijk <[email protected]>’
+
+  New submission
+
+❯ checking examples ... [14s/14s] NOTE
+  Examples with CPU (user + system) or elapsed time > 5s
+               user system elapsed
+  estim_diff 10.222  0.424  10.657
+
+❯ checking HTML version of manual ... NOTE
+  Found the following HTML validation problems:
+  estim_corr.html:4:1 (estim_corr.Rd:5): Warning: <link> inserting "type" attribute
+  estim_corr.html:12:1 (estim_corr.Rd:5): Warning: <script> proprietary attribute "onload"
+  estim_corr.html:12:1 (estim_corr.Rd:5): Warning: <script> inserting "type" attribute
+  estim_corr.html:17:1 (estim_corr.Rd:5): Warning: <table> lacks "summary" attribute
+  estim_corr.html:36:1 (estim_corr.Rd:10): Warning: <table> lacks "summary" attribute
+  estim_diff.html:4:1 (estim_diff.Rd:5): Warning: <link> inserting "type" attribute
+  estim_diff.html:12:1 (estim_diff.Rd:5): Warning: <script> proprietary attribute "onload"
+  estim_diff.html:12:1 (estim_diff.Rd:5): Warning: <script> inserting "type" attribute
+  estim_diff.html:17:1 (estim_diff.Rd:5): Warning: <table> lacks "summary" attribute
+  estim_diff.html:37:1 (estim_diff.Rd:10): Warning: <table> lacks "summary" attribute
+  feedback.html:4:1 (feedback.Rd:6): Warning: <link> inserting "type" attribute
+  feedback.html:12:1 (feedback.Rd:6): Warning: <script> proprietary attribute "onload"
+  feedback.html:12:1 (feedback.Rd:6): Warning: <script> inserting "type" attribute
+  feedback.html:17:1 (feedback.Rd:6): Warning: <table> lacks "summary" attribute
+  gambling.html:4:1 (gambling.Rd:6): Warning: <link> inserting "type" attribute
+  gambling.html:12:1 (gambling.Rd:6): Warning: <script> proprietary attribute "onload"
+  gambling.html:12:1 (gambling.Rd:6): Warning: <script> inserting "type" attribute
+  gambling.html:17:1 (gambling.Rd:6): Warning: <table> lacks "summary" attribute
+  pipe.html:4:1 (pipe.Rd:5): Warning: <link> inserting "type" attribute
+  pipe.html:12:1 (pipe.Rd:5): Warning: <script> proprietary attribute "onload"
+  pipe.html:12:1 (pipe.Rd:5): Warning: <script> inserting "type" attribute
+  pipe.html:17:1 (pipe.Rd:5): Warning: <table> lacks "summary" attribute
+  pipe.html:19:1 (pipe.Rd:5): Warning: <h2> attribute "id" has invalid value "+25+26gt+3B+25"
+  pipe.html:35:1 (pipe.Rd:10): Warning: <table> lacks "summary" attribute
+  pipe.html:36:14 (pipe.Rd:10): Warning: <code> attribute "id" has invalid value "+25+26gt+3B+25_:_lhs"
+  pipe.html:40:14 (pipe.Rd:12): Warning: <code> attribute "id" has invalid value "+25+26gt+3B+25_:_rhs"
+  self_eval.html:4:1 (self_eval.Rd:6): Warning: <link> inserting "type" attribute
+  self_eval.html:12:1 (self_eval.Rd:6): Warning: <script> proprietary attribute "onload"
+  self_eval.html:12:1 (self_eval.Rd:6): Warning: <script> inserting "type" attribute
+  self_eval.html:17:1 (self_eval.Rd:6): Warning: <table> lacks "summary" attribute
+  vicar_char.html:4:1 (vicar_char.Rd:6): Warning: <link> inserting "type" attribute
+  vicar_char.html:12:1 (vicar_char.Rd:6): Warning: <script> proprietary attribute "onload"
+  vicar_char.html:12:1 (vicar_char.Rd:6): Warning: <script> inserting "type" attribute
+  vicar_char.html:17:1 (vicar_char.Rd:6): Warning: <table> lacks "summary" attribute
+
+0 errors ✔ | 0 warnings ✔ | 3 notes ✖
+
+*Author note on HTML validation problems:* Seems to be a problem on my local MacOS system (which was not fixed by updating roxygen2), not encountered on remote system checks.
+
+#### Notes returned after running `devtools::check_win_devel()`:
+
+* checking CRAN incoming feasibility ... [10s] NOTE
+Maintainer: 'Eduard Klapwijk <[email protected]>'
+
+New submission
+
+* checking examples ... [26s] NOTE
+Examples with CPU (user + system) or elapsed time > 10s
+            user system elapsed
+estim_diff 19.04   2.04    21.1