Address CRAN note, issue #263

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.2.2
+Date: 2023-03-23 08:31:23 UTC
+SHA: 59f6b3b192cd8a7bb990aab94748f3bc7b044dac

DESCRIPTION

@@ -6,7 +6,7 @@ Description: A programmatic interface to many species occurrence data sources,
     Ocean 'Biogeographic' Information System ('OBIS'), and 
     Atlas of Living Australia ('ALA'). Includes functionality for retrieving
     species occurrence data, and combining those data.
-Version: 1.2.2
+Version: 1.2.3
 License: MIT + file LICENSE
 Authors@R: 
     c(person(given = "Hannah", family = "Owens",
@@ -48,7 +48,7 @@ Suggests:
     testthat,
     taxize,
     vcr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 X-schema.org-applicationCategory: Biodiversity
 X-schema.org-keywords: specimens, API, web-services, occurrences, species, taxonomy, GBIF, INAT, Vertnet, eBird, iDigBio, OBIS, ALA
 X-schema.org-isPartOf: ropensci.org

NAMESPACE

@@ -38,6 +38,12 @@ S3method(as.vertnet,list)
 S3method(as.vertnet,occdat)
 S3method(as.vertnet,occkey)
 S3method(as.vertnet,vertnetkey)
+S3method(handle_geom,LINESTRING)
+S3method(handle_geom,MULTILINESTRING)
+S3method(handle_geom,MULTIPOINT)
+S3method(handle_geom,MULTIPOLYGON)
+S3method(handle_geom,POINT)
+S3method(handle_geom,POLYGON)
 S3method(inspect,data.frame)
 S3method(inspect,occdat)
 S3method(inspect,occkey)
@@ -67,33 +73,7 @@ export(occ_options)
 export(spocc_capwords)
 export(wkt2bbox)
 export(wkt_vis)
-importFrom(data.table,rbindlist)
-importFrom(data.table,setDF)
-importFrom(jsonlite,toJSON)
-importFrom(lubridate,as_date)
-importFrom(lubridate,now)
-importFrom(lubridate,ydm_hm)
-importFrom(lubridate,ymd)
-importFrom(lubridate,ymd_hm)
-importFrom(lubridate,ymd_hms)
-importFrom(rebird,ebirdgeo)
-importFrom(rebird,ebirdregion)
-importFrom(rgbif,name_lookup)
-importFrom(rgbif,occ_data)
-importFrom(rgbif,occ_get)
-importFrom(ridigbio,idig_search_records)
-importFrom(ridigbio,idig_view_records)
-importFrom(rvertnet,vertsearch)
 importFrom(s2,s2_centroid)
-importFrom(tibble,as_tibble)
-importFrom(tibble,tibble)
-importFrom(utils,browseURL)
-importFrom(utils,data)
-importFrom(utils,head)
-importFrom(utils,read.csv)
-importFrom(utils,setTxtProgressBar)
-importFrom(utils,txtProgressBar)
-importFrom(whisker,whisker.render)
 importFrom(wk,wk_bbox)
 importFrom(wk,wk_coords)
 importFrom(wk,wkt)

NEWS.md

@@ -1,3 +1,16 @@
+spocc 1.2.3
+===========
+
+### Documentation
+
+* Documented argument ‘scientificname’ in 'obis_search()' changed to 'scientificName'.
+* Documented argument 'n' in 'spocc_objects()' removed
+
+### DEFUNCT
+
+* `datecollected` field flagged by `ridigbio` maintainers as inappropriate field--should be `eventDate`. See `scrubr::fix_names()` (#263)
+
+
 spocc 1.2.2
 ===========
 

R/handle_sf.R

@@ -21,22 +21,34 @@ handle_geoms <- function(x) {
 handle_geom <- function(x, ...) {
   UseMethod("handle_geom")
 }
+
+#' @export
 handle_geom.POINT <- function(x, ...) {
   if (!is.matrix(x)) x<- matrix(x, nrow = 1L)
   declare(sf2wkt_coords(x), "POINT")
 }
+
+#' @export
 handle_geom.MULTIPOINT <- function(x, ...) {
   declare(sf2wkt_coords(x), "MULTIPOINT")
 }
+
+#' @export
 handle_geom.LINESTRING <- function(x, ...) {
  declare(sf2wkt_coords(x), "LINESTRING")
 }
+
+#' @export
 handle_geom.MULTILINESTRING <- function(x, ...) {
   declare(sf2wkt_polygon(x), "MULTILINESTRING")
 }
+
+#' @export
 handle_geom.POLYGON <- function(x, ...) {
   declare(sf2wkt_polygon(x), "POLYGON")
 }
+
+#' @export
 handle_geom.MULTIPOLYGON <- function(x, ...) {
   declare(paren(paste0(unlist(lapply(unclass(x), sf2wkt_polygon)),
     collapse = ", ")),

R/methods.r

@@ -6,9 +6,6 @@
 #' @param x Input, of class occdatind
 #' @param object Input to summary methods
 #' @param ... Further args to print, plot or summary methods
-#' @param n Number of rows to show. If `NULL`, the default, will print
-#'   all rows if less than option `dplyr.print_max`. Otherwise, will
-#'   print `dplyr.print_min`
 #'
 #' @examples \dontrun{
 #' # occdat object

R/obis_helpers.R

@@ -3,7 +3,7 @@ obis_base <- function() "https://api.obis.org"
 #' OBIS search
 #' @export
 #' @keywords internal
-#' @param scientificname (character) Scientific name. Leave empty to
+#' @param scientificName (character) Scientific name. Leave empty to
 #' include all taxa. This is what we pass your name query to
 #' @param taxonid (character) Taxon AphiaID.
 #' @param datasetid (character) Dataset UUID.

R/occ2df.R

@@ -101,7 +101,7 @@ occ2df.occdat <- function(obj, what = "data") {
 
 datemap <- list(gbif = 'eventDate', inat = 'observed_on',
                 ebird = 'obsDt', vertnet = "eventdate",
-                idigbio = "datecollected", obis = "eventDate",
+                idigbio = "eventDate", obis = "eventDate",
                 ala = "eventDate")
 
 keymap <- list(gbif = "key", inat = "id",

R/spocc-package.R

@@ -1,68 +1,6 @@
-#' @title Interface to many species occurrence data sources
-#' 
-#' @description A programmatic interface to many species occurrence data 
-#' sources, including GBIF, iNaturalist, Berkeley Ecoinformatics 
-#' Engine, eBird, iDigBio, VertNet, OBIS, and ALA. Includes 
-#' functionality for retrieving species occurrence data, and 
-#' combining that data.
-#' 
-#' @section Package API:
-#' 
-#' The main function to use is [occ()] - a single interface to 
-#' many species occurrence databases (see below for a list). 
-#' 
-#' Other functions include:
-#' 
-#' - [occ2df()] - Combine results from `occ` into a 
-#'  data.frame
-#' - [wkt_vis()] - Visualize WKT strings (used to define 
-#'  geometry based searches for some data sources) in an interactive map
-#' 
-#' @section Currently supported species occurrence data sources:
-#'
-#' \tabular{ll}{
-#' Provider \tab Web \cr
-#' GBIF \tab <https://www.gbif.org/> \cr
-#' eBird \tab <http://ebird.org/content/ebird/> \cr
-#' iNaturalist \tab <https://www.inaturalist.org/> \cr
-#' VertNet \tab <http://vertnet.org/> \cr
-#' iDigBio \tab <https://www.idigbio.org/> \cr
-#' OBIS \tab <https://www.iobis.org/> \cr
-#' ALA \tab <https://www.ala.org.au/>
-#' }
-#' 
-#' @section Duplicates:
-#' 
-#' See [spocc_duplicates()] for more.
-#' 
-#' @section Clean data:
-#' 
-#' All data cleaning functionality is in as archived package: `scrubr` 
-#' (<https://github.com/ropensci-archive/scrubr>).
-#' On CRAN: <https://cran.r-project.org/src/contrib/Archive/scrubr/>. 
-#' See also package 
-#' <https://cran.r-project.org/package=CoordinateCleaner>
-#' 
-#' @section Make maps:
-#' 
-#' All mapping functionality is now in a separate package: `mapr``
-#' (<https://github.com/ropensci/mapr>) (formerly known as `spoccutils`).
-#' On CRAN: <https://cran.r-project.org/package=mapr>
-#'
-#' @importFrom jsonlite toJSON
-#' @importFrom utils browseURL head read.csv data setTxtProgressBar 
-#' txtProgressBar
-#' @importFrom data.table rbindlist setDF
-#' @importFrom tibble tibble as_tibble
-#' @importFrom lubridate now ymd_hms ymd_hm ydm_hm ymd as_date
-#' @importFrom rgbif occ_data occ_get name_lookup
-#' @importFrom rebird ebirdregion ebirdgeo
-#' @importFrom rvertnet vertsearch
-#' @importFrom ridigbio idig_search_records idig_view_records
-#' @importFrom whisker whisker.render
-#' @name spocc-package
-#' @aliases spocc
-#' @docType package
-#' @author Scott Chamberlain
-#' @keywords package
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
 NULL

cran-comments.md

@@ -1,6 +1,6 @@
 ## Test environments
 
-* local OS X install, R 4.1.2
+* local OS X install (14.2.1), R 4.3.1
 * ubuntu 16.04 (on GitHub Actions), R 4.0.3
 * win-builder (release/devel)
 * rhub
@@ -15,7 +15,7 @@
 
 --------
 
-This version removes a defunct API, and changes the maintainer to Hannah L. Owens
+This version removes unused arguments from documentation and addresses an update to dependency `ridigbio`.
 
 
 Thanks!