Merge pull request #127 from jhollway/develop

Fixed CRAN issues with errors related to API rate limits (patch fix)

DESCRIPTION

@@ -10,8 +10,8 @@ Description: A set of tools for writing documents
     The package includes additional functions for institutional color palettes,
     an institutional 'ggplot' theme, a function for counting manuscript words,
     and a bibliographical analysis toolkit.
-Date: 2022-05-12
-Version: 0.9.3
+Date: 2022-09-20
+Version: 0.9.4
 Authors@R: 
     c(person(given = "James",
            family = "Hollway",
@@ -20,9 +20,13 @@ Authors@R:
            comment = c(ORCID = "0000-0002-8361-9647")),
       person(given = "Bernhard",
            family = "Bieri",
-           role = c("ctb"),
+           role = "ctb",
            email = "bernhard.bieri@graduateinstitute.ch",
-           comment = c(ORCID = "0000-0001-5943-9059"))
+           comment = c(ORCID = "0000-0001-5943-9059")),
+      person(given = "Henrique",
+           family = "Sposito",
+           role = "ctb",
+           comment = c(ORCID = "0000-0003-3420-6085"))
     )
 URL: https://github.com/jhollway/iheiddown
 BugReports: https://github.com/jhollway/iheiddown/issues
@@ -51,7 +55,7 @@ Imports:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Suggests: 
     testthat,
     kableExtra,

NEWS.md

@@ -1,3 +1,14 @@
+# iheiddown 0.9.4
+
+## Package updates:
+
+- Closed #126 by adding more informative message for when `percent_female()` reaches API rate limits
+- Skipped `bibstats` functions tests on linux
+
+## Thesis
+
+- Added packages to 'thesis_pdf' template to improve rendering
+
 # iheiddown 0.9.3
 
 ## Package updates:
@@ -51,7 +62,7 @@ presentation template
 
 # iheiddown 0.8.6
 
-# Minor fix
+## Minor fix
 
 - Re-rendered README.md manually following CRAN comments about a potentially invalid URL
 

R/bibfix.R

@@ -23,7 +23,6 @@
 #   bib2df::df2bib(bib, bib_file)
 # }
 
-
 get_used_bib <- function(bib_file, rmd_file) {
   if (missing(bib_file)) bib_file <- find_bib()
   if (missing(rmd_file)) rmd_file <- rstudioapi::getSourceEditorContext()$path

R/bibstats.R

@@ -28,7 +28,6 @@
 #' @importFrom bib2df bib2df
 #' @importFrom utils install.packages
 #' @return Prints a summary statistic (e.g. mean or proportion)
-#' 
 NULL
 
 #' @rdname bibstats
@@ -40,30 +39,36 @@ percent_female <- function(bib_file,
   if (missing(bib_file)) bib_file <- find_bib()
   if (missing(rmd_file)) rmd_file <- rstudioapi::getSourceEditorContext()$path
   by <- match.arg(by, c("author", "publication"))
-
   # if (!requireNamespace("genderdata", quietly = TRUE)) {
   #   if (!requireNamespace("remotes", quietly = TRUE)) {
   #     utils::install.packages("remotes")
   #   }
   #   remotes::install_github("lmullen/genderdata")
   # }
-
   bib <- suppressWarnings(bib2df::bib2df(bib_file))
   if (!missing(rmd_file)) {
     used <- get_used_bib(bib_file, rmd_file)
     bib <- dplyr::filter(bib, .data$BIBTEXKEY %in% used)
   }
   authors <- bib$AUTHOR
+  gender <- NULL
   # Total percentage of women
   if (by == "author") {
     authors <- unlist(authors)
     authors <- stringr::str_remove(authors, "^.+, \\{")
     authors <- stringr::str_remove(authors, "\\}")
     authors <- stringr::str_remove(authors, ".*,[:blank:]")
     authors <- stringr::str_remove(authors, "\\s.*")
-    gender <- table(gender::gender(authors, method = "genderize")$gender)
-    paste0((1 - round(gender[2] / sum(gender), 2)) * 100,
-                 "% female authors")
+    gender <- tryCatch({
+      table(gender::gender(authors, method = "genderize")$gender)
+    },
+    message = "Rate limit for the `{gender}` R package has been reached due to the amount of download requests.
+    Please wait a few hours and try again later."
+    )
+    if (!is.null(gender)) {
+      paste0((1 - round(gender[2] / sum(gender), 2)) * 100,
+             "% female authors") 
+    }
   } else if (by == "publication") {
     # Percentage of papers written by at least one women
     for (i in seq_len(length(authors))) {
@@ -76,10 +81,17 @@ percent_female <- function(bib_file,
                                                  ".*,[:blank:]")
       }
     }
-    gender <- sapply(authors,
-                     function(x) any(gender::gender(x, method = "genderize")$gender == "female"))
-    paste0(round(sum(gender) / length(gender), 2) * 100,
-                 "% female authors")
+    gender <- tryCatch({
+      sapply(authors, function(x)
+        any(gender::gender(x, method = "genderize")$gender == "female"))
+      },
+      message = "Rate limit for the `{gender}` R package has been reached due to the amount of download requests.
+      Please wait a few hours and try again later."
+      )
+    if (!is.null(gender)) {
+      paste0(round(sum(gender) / length(gender), 2) * 100,
+             "% female authors") 
+    }
   }
 }
 

R/poster_html.R

@@ -4,8 +4,11 @@
 #' templates with a little IHEID twist to them. All exports are in HTML format.
 #' You can save them by printing them to PDF via a modern browser.
 #'
-#' @inheritParams pagedown::poster_relaxed
 #' @param ... Additional arguments to `rmarkdown::html_document`
+#' @param template Additional argument passed to `pagedown::poster_relaxed`.
+#' IHEID poster templates by default.
+#' @param css Additional argument passed to `pagedown::poster_relaxed`.
+#' NULL by default.
 #' @source [`{Posterdown}`](https://github.com/brentthorne/posterdown)
 #' @return R Markdown output format to pass to
 #'   [rmarkdown::render()]
@@ -15,7 +18,10 @@
 #' file <- file.path(tempdir(),"foo.rmd")
 #' rmarkdown::draft(file, template="iheiddown_poster", package="iheiddown")
 #' }
-#' @rdname posterdown_html
+#' @name posterdown_html
+NULL
+
+#' @rdname posterdown_html 
 #' @export
 iheiddown_poster <- function(...,
 	template = system.file("rmarkdown",

R/theme.R

@@ -213,4 +213,4 @@ theme_iheid <- function(base_family="sans", base_size = 11.5,
                            color = iheid_palette("IHEID")["IHEIDGrey"]))
     ret <- ret + theme(plot.margin = plot_margin)
     ret
-  }
+}

cran-comments.md

@@ -9,5 +9,4 @@
 
 0 errors | 0 warnings | 0 notes
 
-- Fixed issue relating to tests on Linux
-
+- Added informative message for when rate limits are reached with `percent_female()`

inst/rmarkdown/templates/thesis_pdf/resources/template.tex

@@ -30,6 +30,8 @@
 
 \fancypagestyle{plain}{\fancyhf{}\fancyfoot[C]{\emph{\thepage}}}
 
+\fancyfoot[C]{\emph{\thepage}}
+
 % This adds a "DRAFT" footer to every normal page.  (The first page of each chapter is not a "normal" page.) Page numbers are also printed on the right side.
 $if(draft)$
 \fancyfoot[C]{\emph{DRAFT: \today}}
@@ -275,18 +277,25 @@
 \newlist{abbrv}{itemize}{1}
 \setlist[abbrv,1]{label=,labelwidth=1in,align=parleft,itemsep=0.1\baselineskip,leftmargin=!}
 
+% Packages used to display math
 \usepackage{nicefrac}
 \usepackage{amsmath}
 \usepackage{amssymb}
+\usepackage{mathtools}
 \usepackage{textcomp}
+\usepackage{adjustbox} % adjust things to page width
+
 
 \usepackage{longtable} 
 	% Allows tables to span multiple pages (this package must be called before hyperref)
 
+\usepackage{colortbl, xcolor}
+  % Allows cells to be colored. Required by kableExtra
+
 \usepackage[font=small,labelfont=bf]{caption} 
 	% Nicer captions
 
-\usepackage{multicol,multirow,array} 
+\usepackage{multicol,multirow,array,xparse,pdflscape} 
 	% Used to make multiple columns for the indices and for creating columns that span multiple rows in tables
 
 \usepackage{rotating} 
@@ -301,7 +310,10 @@
 \usepackage{graphicx}
 \graphicspath{{figures/}{_bookdown_files/}}
 
-\usepackage{xfrac}
+\usepackage{float} % Use the 'float' package for table and figure alignment
+\floatplacement{figure}{H} % Make every figure with caption = h
+
+\usepackage{blkarray} % Adding annotations to border for matrices
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% ACTUAL DOCUMENT HERE  %%
@@ -321,7 +333,9 @@
 
 \vspace*{1cm}
 
+$if(phd)$
 \sffamily{Thesis No. $thesisno$}
+$endif$
 
 \vspace*{1cm}
 \sffamily\textbf{Supervisor: $supervisor$}\\

tests/testthat/test-bibstats.R

@@ -1,22 +1,22 @@
 test_that("Bibstats works properly", {
+  testthat::skip_on_os("linux")
   rmarkdown::draft(file = "test", template = "syllabus",
                    package = "iheiddown", create_dir = TRUE, edit = FALSE)
   expect_equal(percent_female(bib_file = "test/references.bib",
-                         rmd_file = "test/test.Rmd",
-                         by = "author"),
+                              rmd_file = "test/test.Rmd", by = "author"),
                "33% female authors")
   expect_equal(percent_female(bib_file = "test/references.bib",
                               rmd_file = "test/test.Rmd",
                               by = "publication"),
                "50% female authors")
   expect_equal(mean_year(bib_file = "test/references.bib",
-                              rmd_file = "test/test.Rmd"),
+                         rmd_file = "test/test.Rmd"),
                "Average date of publication: 1934")
   expect_equal(total_pages(bib_file = "test/references.bib",
-                         rmd_file = "test/test.Rmd"),
+                           rmd_file = "test/test.Rmd"),
                "Total number of pages: 7")
   expect_equal(mean_pages(bib_file = "test/references.bib",
-                           rmd_file = "test/test.Rmd"),
+                          rmd_file = "test/test.Rmd"),
                "Average number of pages: 7")
   unlink("test", recursive = TRUE)
 })