diff --git a/DESCRIPTION b/DESCRIPTION index 9f69dd0..b22697d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: occCite Type: Package -Title: Tools for Querying and Managing Large Biodiversity Occurrence Datasets -Version: 0.2.0 +Title: Querying and Managing Large Biodiversity Occurrence Datasets +Version: 0.3.0 Authors@R: c( person("Hannah L.","Owens", ,"hannah.owens@gmail.com", role=c("aut","cre"), comment = c(ORCID = "0000-0003-0071-1745")), diff --git a/NEWS.md b/NEWS.md index 31659d9..9f32eda 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# occCite 0.3.0 + +*Updated to meet CRAN reviewer guidelines +*Citations now include packages used. + # occCite 0.2.0 * Updated to reflect new object structures returned by searches with update `rgbif`, version 3.1. diff --git a/R/GBIFtableCleanup.R b/R/GBIFtableCleanup.R index 5c4c1a6..a8004e0 100644 --- a/R/GBIFtableCleanup.R +++ b/R/GBIFtableCleanup.R @@ -9,15 +9,6 @@ #' @return A data.frame tidied for compatibility with #' \code{\link{getBIENpoints}} results. #' -#' @examples -#' \dontrun{ -#' ##If you have already created a occCite object, and have not previously -#' temp <- getGBIFpoints(taxon = "Protea cynaroides", GBIFLogin = GBIFLogin, -#' GBIFDownloadDirectory = GBIFDownloadDirectory, -#' checkPreviousGBIFDownload = checkPreviousGBIFDownload) -#' fitForUseTable <- GBIFtableCleanup(temp$OccurrenceTable) -#'} -#' #' @keywords internal GBIFtableCleanup <- function(GBIFtable){ diff --git a/R/gbifRetriever.R b/R/gbifRetriever.R index 58f0623..304ea15 100644 --- a/R/gbifRetriever.R +++ b/R/gbifRetriever.R @@ -13,10 +13,6 @@ #' data; (2) GBIF search metadata for every GBIF download in the #' specified directory. #' -#' @examples -#' \dontrun{ -#' gbifRetriever("Protea cynaroides") -#' } #' @keywords internal gbifRetriever <- function (taxon = NULL){ diff --git a/R/occCite_plotting.R b/R/occCite_plotting.R index e434960..73c5464 100644 --- a/R/occCite_plotting.R +++ b/R/occCite_plotting.R @@ -10,13 +10,6 @@ #' @return A table that can be more easily mapped and used #' for summary plots. #' -#' @examples -#' \dontrun{ -#' data(myOccCiteObject) -#' tableForPlot <- tabulate.occResults(myOccCiteObject@occResults$`Protea cynaroides`, -#' "Protea cynaroides") -#' } -#' #' @keywords internal #' tabulate.occResults <- function(x, sp.name) { diff --git a/R/tabGBIF.R b/R/tabGBIF.R index 2c9527f..e0a405a 100644 --- a/R/tabGBIF.R +++ b/R/tabGBIF.R @@ -13,13 +13,6 @@ #' occurrence data \item GBIF search metadata for every GBIF download in #' the specified directory.} #' -#' @examples -#' \dontrun{ -#' res <- rgbif::as.download(system.file("extdata/Protea_cynaroides", -#' "0012335-190621201848488.zip", -#' package = "occCite")) -#' tabGBIF(GBIFresults = res, taxon = "Protea cynaroides") -#' } #' @keywords internal tabGBIF <- function(GBIFresults, taxon){ diff --git a/man/GBIFtableCleanup.Rd b/man/GBIFtableCleanup.Rd index f5131e6..54b055a 100644 --- a/man/GBIFtableCleanup.Rd +++ b/man/GBIFtableCleanup.Rd @@ -17,15 +17,5 @@ A data.frame tidied for compatibility with \description{ Forces occurrence table columns to a uniform format. This is an internal function for use by \code{\link{occQuery}}. -} -\examples{ -\dontrun{ -##If you have already created a occCite object, and have not previously -temp <- getGBIFpoints(taxon = "Protea cynaroides", GBIFLogin = GBIFLogin, - GBIFDownloadDirectory = GBIFDownloadDirectory, - checkPreviousGBIFDownload = checkPreviousGBIFDownload) -fitForUseTable <- GBIFtableCleanup(temp$OccurrenceTable) -} - } \keyword{internal} diff --git a/man/gbifRetriever.Rd b/man/gbifRetriever.Rd index 1e23aa5..905da33 100644 --- a/man/gbifRetriever.Rd +++ b/man/gbifRetriever.Rd @@ -22,9 +22,4 @@ Searches for the most recent instance of a data set navigated to the folder that contains the download zip files from GBIF. } -\examples{ -\dontrun{ -gbifRetriever("Protea cynaroides") -} -} \keyword{internal} diff --git a/man/tabGBIF.Rd b/man/tabGBIF.Rd index a1e932a..f6c569f 100644 --- a/man/tabGBIF.Rd +++ b/man/tabGBIF.Rd @@ -22,12 +22,4 @@ the specified directory.} Internal function--imports results from `occ_download_get()` and processes them into a table for an `occCiteData` object. } -\examples{ -\dontrun{ -res <- rgbif::as.download(system.file("extdata/Protea_cynaroides", - "0012335-190621201848488.zip", - package = "occCite")) -tabGBIF(GBIFresults = res, taxon = "Protea cynaroides") -} -} \keyword{internal} diff --git a/man/tabulate.occResults.Rd b/man/tabulate.occResults.Rd index bf5982b..e06f82a 100644 --- a/man/tabulate.occResults.Rd +++ b/man/tabulate.occResults.Rd @@ -18,13 +18,5 @@ for summary plots. \description{ This is a helper function that tabulates `occCiteData` objects for use by map.occCite and `sumFig.occCite`. -} -\examples{ -\dontrun{ -data(myOccCiteObject) -tableForPlot <- tabulate.occResults(myOccCiteObject@occResults$`Protea cynaroides`, - "Protea cynaroides") -} - } \keyword{internal}