update example files

Author: maRce10

R/add_to_gitignore.R

@@ -35,8 +35,6 @@ add_to_gitignore <- function(add.to.gitignore = FALSE, cutoff = NULL, extension
   # ensure the path is in the correct format for your system
   path <- normalizePath(path)
 
-  print("asasd")
-
   if (is.null(cutoff) & is.null(extension))
     .stop("'cutoff' and/or 'extension' must be supplied")
 

R/make_compendium.R

@@ -7,7 +7,7 @@
 #' @param name character string: the research compendium directory name. No special characters should be used. Default is "research_compendium".
 #' @param path Path to put the project directory in. Default is current directory.
 #' @param force Logical controlling whether existing folders with the same name are used for setting the folder structure. The function will never overwrite existing files or folders.
-#' @param format A character vector of length 1 with the name of the built-in compendiums available in the example object `compendiums` (see \code{\link{compendiums}} for available formats). Default is 'basic'. Alternatively, it can be a character vector with 2 or more elements with the names of the folders and subfolders to be included.
+#' @param format A character vector of length 1 with the name of the built-in compendiums available in the example object `compendiums` (see \code{\link{compendiums}} for available formats). Default is 'basic'. Alternatively, it can be a character vector with 2 or more elements with the names of the folders and subfolders to be included (e.g. \code{c("folder_1", "folder_1/subfolder_1", "folder_1/subfolder_2")}).
 #' @param packrat Logical to control if packrat is initialized (\code{packrat::init()}) when creating the compendium. Default is \code{FALSE}.
 #' @param git Logical to control if a git repository is initialized (\code{git2r::init()}) when creating the compendium. Default is \code{FALSE}.
 #' @param clone Path to a directory containing a folder structure to be cloned. Default is \code{NULL}. If provided 'format' is ignored. Folders starting with \code{^\\.git|^\.Rproj.user|^\\.\\.Rcheck} will be ignored.
@@ -21,8 +21,14 @@
 #' @examples {
 #' data(compendiums)
 #'
-#'make_compendium(name = "mycompendium", path = tempdir(), format = "basic",
+#' # default format
+#' make_compendium(name = "mycompendium", path = tempdir(), format = "basic",
 #' force = TRUE)
+#'
+#' # custom format
+#' make_compendium(name = "my_second_compendium", path = tempdir(),
+#'  format = c("folder_1", "folder_1/subfolder_1", "folder_1/subfolder_2"),
+#'  force = TRUE)
 #' }
 #'
 #' @author Marcelo Araya-Salas (\email{marcelo.araya@@ucr.ac.cr})
@@ -190,10 +196,13 @@ make_compendium <-
           ignore.case = TRUE,
           value = TRUE
         )[1],
-        "analysis_template.Rmd"
-      )))
+        "analysis_template_rmarkdown.Rmd"
+      ))){
+        rmarkdown_template <- internal_files$analysis_template_rmarkdown
+        rmarkdown_template[3] <- paste("subtitle:", name)
+
         writeLines(
-          internal_files$analysis_template,
+          rmarkdown_template,
           file.path(
             path,
             name,
@@ -203,9 +212,10 @@ make_compendium <-
               ignore.case = TRUE,
               value = TRUE
             )[1],
-            "analysis_template.Rmd"
+            "analysis_template_rmarkdown.Rmd"
           )
         )
+        }
 
       # save analysis template in quarto format
       if (!file.exists(file.path(
@@ -218,9 +228,13 @@ make_compendium <-
           value = TRUE
         )[1],
         "analysis_template_quarto.qmd"
-      )))
+      ))){
+        # change subtitle
+        quarto_template <- internal_files$analysis_template_quarto
+        quarto_template[3] <- paste("subtitle:", name)
+
         writeLines(
-          internal_files$analysis_template_quarto,
+          quarto_template,
           file.path(
             path,
             name,
@@ -233,7 +247,7 @@ make_compendium <-
             "analysis_template_quarto.qmd"
           )
         )
-
+}
       # save rmd.css
       if (!file.exists(file.path(
         path,

R/print_skeleton.R

@@ -22,7 +22,6 @@
 #' @references {
 #' Araya-Salas, M., Arriaga, A. (2023), sketchy: research compendiums for data analysis in R. R package version 1.0.3.
 #' }
-#last modification on dec-26-2019 (MAS)
 
 print_skeleton <- function(path = ".", comments = NULL, folders = NULL)
   {

R/sysdata.rda

@@ -0,0 +1 @@
+/.quarto/

examples/.gitignore

@@ -4,7 +4,7 @@ subtitle: A very fancy project
 author: <a href="http://researcher.website.com/">Researcher name</a>
 date: "`r Sys.Date()`"
 toc: true
-toc-depth: 2
+toc-depth: 3
 toc-location: left
 number-sections: true
 highlight-style: pygments
@@ -14,6 +14,8 @@ format:
     code-fold: show
     code-tools: true
     css: qmd.css
+editor_options: 
+  chunk_output_type: console
 ---
 
 ```{r set root directory}
@@ -28,12 +30,14 @@ knitr::opts_knit$set(root.dir =  "..")
 ```{r add link to github repo}
 #| eval: true
 #| output: asis
+#| echo: false
 
 # print link to github repo if any
 if (file.exists("./.git/config")){
   config <- readLines("./.git/config")
   url <- grep("url",  config, value = TRUE)
   url <- gsub("\\turl = |.git$", "", url)
+  if (nchar(url) > 1)
   cat("\nSource code and data found at [", url, "](", url, ")", sep = "")
   }
 
@@ -52,37 +56,33 @@ knitr::opts_chunk$set(
 
 ```
 
-
 <!-- skyblue box -->
 
 ::: {.alert .alert-info}
-
 # Purpose {.unnumbered .unlisted}
 
-- The first goal of this report
-
-- The second goal of this report
+-   The first goal of this report
 
+-   The second goal of this report
 :::
 
-&nbsp; 
-
+ 
 
 <!-- light brown box -->
-::: {.alert .alert-warning}
 
+::: {.alert .alert-warning}
 # Report overview {.unnumbered .unlisted}
 
-- You can have the sections listed here, for instance:
-
-  - [Lorem ipsum](#lorem-ipsum)
-  - [Takeaways](#takeaways)
+-   You can have the sections listed here, for instance:
 
+    -   [Lorem ipsum](#lorem-ipsum)
+    -   [Takeaways](#takeaways)
 :::
 
-&nbsp;
+ 
 
 # Analysis flowchart {.unnumbered .unlisted}
+
 ```{mermaid}
 
 flowchart
@@ -91,14 +91,13 @@ flowchart
   C --> D(Statistical analysis)
   D --> E(Model summary) 
 
-style A fill:#44015466
-style B fill:#3E4A894D
-style C fill:#26828E4D
-style D fill:#6DCD594D
+style A fill:#382A5433
+style B fill:#395D9C33
+style C fill:#3497A933
+style D fill:#60CEAC33
 
 ```
 
-
 # Load packages {.unnumbered .unlisted}
 
 ```{r load packages}
@@ -119,9 +118,9 @@ a <- 1
 b <- 2
 ```
 
-# Lorem ipsum
+# Lorem ipsum {#lorem-ipsum}
 
-Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum in felis ut mauris consectetur sodales. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Suspendisse nec ex neque. Nunc ultricies et ante ac feugiat. Nulla quam ex, viverra eget mollis non, porttitor nec ante. Donec non felis a nisi elementum consectetur tempor in mauris. Curabitur leo nunc, posuere in erat sit amet, varius aliquam mi. Nullam lacinia odio neque, et semper erat fermentum ut. Praesent mi massa, convallis in vehicula mattis, condimentum ac risus. In eget metus eget nunc pulvinar finibus. Proin nec tellus sed lorem malesuada aliquet sed laoreet augue. 
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum in felis ut mauris consectetur sodales. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Suspendisse nec ex neque. Nunc ultricies et ante ac feugiat. Nulla quam ex, viverra eget mollis non, porttitor nec ante. Donec non felis a nisi elementum consectetur tempor in mauris. Curabitur leo nunc, posuere in erat sit amet, varius aliquam mi. Nullam lacinia odio neque, et semper erat fermentum ut. Praesent mi massa, convallis in vehicula mattis, condimentum ac risus. In eget metus eget nunc pulvinar finibus. Proin nec tellus sed lorem malesuada aliquet sed laoreet augue.
 
 ```{r example external image}
 #| eval: true
@@ -137,32 +136,37 @@ knitr::include_graphics("https://www.r-project.org/logo/Rlogo.svg")
 
 <!-- '&nbsp;' adds blank space -->
 
-
-
 <!-- light green box -->
 
 ::: {.alert .alert-success}
-
-# Takeaways {.unnumbered .unlisted}
+# Takeaways {#takeaways .unnumbered .unlisted}
 
 Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum in felis ut mauris consectetur sodales. Lorem ipsum dolor sit amet, consectetur adipiscing elit.
+:::
 
-::: 
-
-&nbsp;
+ 
 
 <!-- '---' adds a gray vertical line -->
 
----
+------------------------------------------------------------------------
+
+ 
+
+<!-- add packages used, system details and versions  -->
 
-&nbsp; 
- 
- <!-- add packages used, system details and versions  -->
- 
 # Session information {.unnumbered .unlisted}
 
-```{r session info, echo=F}
+<details>
+  <summary>Click to see</summary>
+```{r session info}
+#| echo: false
 
-sessionInfo()
+# if devtools is installed use devtools::session_info()
+if (requireNamespace("devtools", quietly = TRUE)) {
+  devtools::session_info()
+} else {
+  sessionInfo()
+}
 
 ```
+</details>