fix minor errors and roxygenise

DESCRIPTION

@@ -12,7 +12,6 @@ Description: Facilitates citation of R packages used in analysis projects.
 Depends: R (>= 3.0.0)
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 Imports:
   renv,
   rmarkdown,

NAMESPACE

@@ -1,8 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export(cite_packages)
-export(create_rmd)
 export(get_citations)
 export(get_csl)
+export(get_pkgs_info)
 export(nocite_references)
 export(scan_packages)

R/cite_packages.R

@@ -26,7 +26,7 @@
 #' bibliography file in the YAML header of the Rmarkdown document.
 #'
 #' Finally, you can use \code{output = "citekeys"} to obtain a vector of citation keys,
-#' and then call \code{\link{nocite_references()}} within an Rmarkdown document
+#' and then call \code{\link{nocite_references}} within an Rmarkdown document
 #' to cite these packages in the reference list without mentioning them in the text.
 #'
 #'
@@ -38,7 +38,7 @@
 #'   references are put into the text manually, they may need to be updated
 #'   periodically.
 #'
-#' @param output. Either "file" to generate a separate document with formatted citations
+#' @param output Either "file" to generate a separate document with formatted citations
 #' for all packages; "paragraph" to return a paragraph with in-text citations of
 #' used packages, suitable to be used within an Rmarkdown document;
 #' or "citekeys" to return a vector with citation keys.
@@ -145,7 +145,7 @@ cite_packages <- function(output = c("file", "paragraph", "citekeys"),
   }
 
   if (output == "citekeys") {
-    return(citekeys)
+    return(unlist(pkgs.df$citekeys))
   }
 
 }

R/create_rmd.R

@@ -9,6 +9,7 @@
 #' @param out.format Output format. One of: "docx" (Word), "pdf", "html", "Rmd", or "md" (markdown).
 #' @param Rmd.file Name of the Rmarkdown file to be created.
 #' @param out.dir Directory to save the output document. Default is the working directory.
+#' @param ... Further arguments for \code{\link{render_citations}}.
 #'
 #' @return An Rmarkdown file, if out.format = "Rmd", or a rendered document otherwise.
 #' @noRd
@@ -23,7 +24,8 @@ create_rmd <- function(pkgs.df = NULL,
                        csl = NULL,
                        Rmd.file = "grateful-report.Rmd",
                        out.format = "html",
-                       out.dir = getwd()) {
+                       out.dir = getwd(),
+                       ...) {
 
   use.csl <- ifelse(is.null(csl), "#csl: null", "csl: ")
 
@@ -64,7 +66,7 @@ create_rmd <- function(pkgs.df = NULL,
   if (tolower(out.format) == "rmd") {
     return(Rmd.file)
   } else {
-    render_citations(Rmd.file, out.format = out.format, out.dir = out.dir)
+    render_citations(Rmd.file, out.format = out.format, out.dir = out.dir, ...)
     file.remove(Rmd.file)
   }
 

R/get_citations.R

@@ -28,7 +28,7 @@ get_citations <- function(pkgs,
 
   if (include.RStudio == TRUE) {
     # Put an RStudio citation on the end
-    if (!require(rstudioapi)) {
+    if (!requireNamespace("rstudioapi")) {
       stop("Please install the {rstudioapi} package to cite RStudio.")
     } else {
       rstudio_cit <- tryCatch(rstudioapi::versionInfo()$citation,

R/get_pkgs_info.R

@@ -27,7 +27,7 @@ get_pkgs_info <- function(all.pkgs = TRUE,
 
   citekeys <- get_citations(pkgs.df$pkg,
                             out.dir = out.dir,
-                            bibfile = bib.file,
+                            bib.file = bib.file,
                             include.RStudio = include.RStudio)
 
   # Group all citations from same package

R/scan_packages.R

@@ -27,7 +27,7 @@ scan_packages <- function(all.pkgs = TRUE, ...) {
   pkgs <- sort(pkgs)
 
   # Get package versions
-  pkgVersion <- Vectorize(packageVersion, SIMPLIFY = FALSE)
+  pkgVersion <- Vectorize(utils::packageVersion, SIMPLIFY = FALSE)
   versions <- pkgVersion(pkgs)
   versions <- unlist(lapply(versions, as.character))