Merge pull request #70 from usa-npn/docs-and-linting

Non-code changes

DESCRIPTION

@@ -1,46 +1,49 @@
 Package: rnpn
 Title: Interface to the National 'Phenology' Network 'API'
-Description: Programmatic interface to the
-    Web Service methods provided by the National 'Phenology' Network
-    (<https://usanpn.org/>), which includes data on various life history
-    events that occur at specific times.
 Version: 1.2.9.9000
-License: MIT + file LICENSE
 Authors@R: c(
-    person("Jeff", "Switzer", role = c("aut", "cre"), email = "jeff@usanpn.org"),
+    person("Jeff", "Switzer", , "jeff@usanpn.org", role = c("aut", "cre")),
     person("Scott", "Chamberlain", role = "aut"),
-    person("Lee", "Marsh", role= "aut"),
+    person("Lee", "Marsh", role = "aut"),
     person("Kevin", "Wong", role = "aut"),
     person("David", "LeBauer", role = "ctb"),
     person("Eric R", "Scott", role = "ctb")
-    )
-Depends: R (>= 3.5.0)
+  )
+Description: Programmatic interface to the Web Service methods provided by
+    the National 'Phenology' Network (<https://usanpn.org/>), which
+    includes data on various life history events that occur at specific
+    times.
+License: MIT + file LICENSE
+URL: https://github.com/usa-npn/rnpn, http://usa-npn.github.io/rnpn/
+BugReports: https://github.com/usa-npn/rnpn/issues
+Depends: 
+    R (>= 3.5.0)
 Imports:
-    httr (>= 1.1.0),
-    jsonlite (>= 0.9.19),
-    data.table (>= 1.9.6),
-    tibble,
     curl,
-    xml2,
-    httr2,
+    data.table (>= 1.9.6),
     dplyr,
+    httr (>= 1.1.0),
+    httr2,
+    jsonlite (>= 0.9.19),
+    magrittr,
     rlang,
-    magrittr
+    tibble,
+    xml2
 Suggests:
-    ggplot2,
-    testthat (>= 3.0.0),
     covr,
+    ggplot2,
     knitr,
     markdown,
-    rmarkdown,
     RColorBrewer,
-    vcr,
-    withr,
+    rmarkdown,
     sf,
-    terra
-RoxygenNote: 7.3.2
-Encoding: UTF-8
-VignetteBuilder: knitr
-URL: https://github.com/usa-npn/rnpn, http://usa-npn.github.io/rnpn/
-BugReports: https://github.com/usa-npn/rnpn/issues
+    terra,
+    testthat (>= 3.0.0),
+    vcr,
+    withr
+VignetteBuilder: 
+    knitr
 Config/testthat/edition: 3
+Encoding: UTF-8
+RoxygenNote: 7.3.2
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -36,7 +36,7 @@ export(npn_stations_by_state)
 export(npn_stations_with_spp)
 export(npn_stationsbystate)
 export(npn_stationswithspp)
-importFrom(httr2,"%>%")
+importFrom(magrittr,"%>%")
 importFrom(utils,URLencode)
 importFrom(utils,download.file)
 importFrom(utils,write.table)

R/defunct.R

@@ -58,12 +58,12 @@ npn_stationswithspp <- function (...){
 #' Defunct functions in rnpn
 #'
 #' \itemize{
-#'  \item \code{\link{npn_obsspbyday}}: Removed.
-#'  \item \code{\link{npn_allobssp}}: Removed.
-#'  \item \code{\link{npn_indspatstations}}: Removed.
-#'  \item \code{\link{npn_indsatstations}}: Removed.
-#'  \item \code{\link{npn_stationsbystate}}: Removed.
-#'  \item \code{\link{npn_stationswithspp}}: Removed.
+#'  \item [npn_obsspbyday()]: Removed.
+#'  \item [npn_allobssp()]: Removed.
+#'  \item [npn_indspatstations()]: Removed.
+#'  \item [npn_indsatstations()]: Removed.
+#'  \item [npn_stationsbystate()]: Removed.
+#'  \item [npn_stationswithspp()]: Removed.
 #' }
 #'
 #' @name rnpn-defunct

R/lookup_names.R

@@ -3,23 +3,23 @@
 #' Look up species IDs by taxonomic or common name
 #'
 #' @export
-#' @param name A scientific or common name
-#' @param type One of common_name, genus, or species
-#' @param fuzzy One of TRUE or FALSE, if FALSE, uses fuzzy search via agrep, if
-#'    FALSE, uses grep.
-#' @return A data frame with species ID numbers based on the name and type parameters.
+#' @param name A scientific or common name.
+#' @param type One of `"common_name"`, `"genus"`, or `"species"`.
+#' @param fuzzy Logical; if `TRUE`, uses fuzzy search via [agrep()], if
+#'   `FALSE`, uses [grep()].
+#' @return A data frame with species ID numbers based on the name and type
+#'   parameters.
 #' @examples \dontrun{
 #' npn_lookup_names(name='Pinus', type='genus')
 #' npn_lookup_names(name='pine', type='common_name')
 #' npn_lookup_names(name='bird', type='common_name', fuzzy=TRUE)
 #' }
 npn_lookup_names <- function(name, type = 'genus', fuzzy = FALSE) {
-
-  if(is.null(pkg.env$species_list)){
-    assign("species_list",npn_species(),envir = pkg.env)
+  if (is.null(pkg.env$species_list)) {
+    assign("species_list", npn_species(), envir = pkg.env)
   }
 
-  type <- match.arg(type, choices = c('common_name','genus','species'))
+  type <- match.arg(type, choices = c('common_name', 'genus', 'species'))
 
   if (fuzzy) {
     pkg.env$species_list[agrep(name, pkg.env$species_list[, type]), ]