diff --git a/DESCRIPTION b/DESCRIPTION index ac384e7..99325b6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -48,7 +48,7 @@ Suggests: testthat, taxize, vcr -RoxygenNote: 7.3.0 +RoxygenNote: 7.3.1 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 diff --git a/NAMESPACE b/NAMESPACE index fd161db..dc51be4 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -73,7 +73,33 @@ 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) diff --git a/R/spocc-package.R b/R/spocc-package.R index e6425f1..7fcd4df 100644 --- a/R/spocc-package.R +++ b/R/spocc-package.R @@ -61,8 +61,7 @@ #' @importFrom ridigbio idig_search_records idig_view_records #' @importFrom whisker whisker.render #' @name spocc-package -#' @aliases spocc -#' @docType package +#' @aliases spocc-package #' @author Scott Chamberlain #' @keywords package NULL diff --git a/man/occ.Rd b/man/occ.Rd index 666ebc4..a3a4c9d 100644 --- a/man/occ.Rd +++ b/man/occ.Rd @@ -663,8 +663,8 @@ occ2df(x) } \seealso{ Other queries: -\code{\link{occ_names_options}()}, \code{\link{occ_names}()}, +\code{\link{occ_names_options}()}, \code{\link{occ_options}()}, \code{\link{spocc_objects}} } diff --git a/man/occ_names.Rd b/man/occ_names.Rd index 6b8c498..118d787 100644 --- a/man/occ_names.Rd +++ b/man/occ_names.Rd @@ -54,9 +54,9 @@ head(res$gbif$data[[1]]) } \seealso{ Other queries: +\code{\link{occ}()}, \code{\link{occ_names_options}()}, \code{\link{occ_options}()}, -\code{\link{occ}()}, \code{\link{spocc_objects}} } \concept{queries} diff --git a/man/occ_names_options.Rd b/man/occ_names_options.Rd index ffbeac0..f587e99 100644 --- a/man/occ_names_options.Rd +++ b/man/occ_names_options.Rd @@ -43,9 +43,9 @@ occ_names_options('gbif', 'html') } \seealso{ Other queries: +\code{\link{occ}()}, \code{\link{occ_names}()}, \code{\link{occ_options}()}, -\code{\link{occ}()}, \code{\link{spocc_objects}} } \concept{queries} diff --git a/man/occ_options.Rd b/man/occ_options.Rd index aa33905..311d77d 100644 --- a/man/occ_options.Rd +++ b/man/occ_options.Rd @@ -47,9 +47,9 @@ occ_options('gbif', 'html') } \seealso{ Other queries: -\code{\link{occ_names_options}()}, -\code{\link{occ_names}()}, \code{\link{occ}()}, +\code{\link{occ_names}()}, +\code{\link{occ_names_options}()}, \code{\link{spocc_objects}} } \concept{queries} diff --git a/man/spocc-package.Rd b/man/spocc-package.Rd index e61b46f..5a40493 100644 --- a/man/spocc-package.Rd +++ b/man/spocc-package.Rd @@ -1,39 +1,69 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/spocc-package.R -\docType{package} \name{spocc-package} -\alias{spocc} \alias{spocc-package} -\title{spocc: Interface to Species Occurrence Data Sources} +\title{Interface to many species occurrence data sources} \description{ -\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} - -A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist', 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data. +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. } -\seealso{ -Useful links: +\section{Package API}{ + + +The main function to use is \code{\link[=occ]{occ()}} - a single interface to +many species occurrence databases (see below for a list). + +Other functions include: \itemize{ - \item \url{https://github.com/ropensci/spocc (devel)} - \item \url{https://docs.ropensci.org/spocc/ (user manual)} - \item Report bugs at \url{https://github.com/ropensci/spocc/issues/} +\item \code{\link[=occ2df]{occ2df()}} - Combine results from \code{occ} into a +data.frame +\item \code{\link[=wkt_vis]{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 \url{https://www.gbif.org/} \cr +eBird \tab \url{http://ebird.org/content/ebird/} \cr +iNaturalist \tab \url{https://www.inaturalist.org/} \cr +VertNet \tab \url{http://vertnet.org/} \cr +iDigBio \tab \url{https://www.idigbio.org/} \cr +OBIS \tab \url{https://www.iobis.org/} \cr +ALA \tab \url{https://www.ala.org.au/} +} } -\author{ -\strong{Maintainer}: Hannah Owens \email{hannah.owens@gmail.com} (\href{https://orcid.org/0000-0003-0071-1745}{ORCID}) -Authors: -\itemize{ - \item Vijay Barve (\href{https://orcid.org/0000-0002-4852-2567}{ORCID}) - \item Scott Chamberlain (\href{https://orcid.org/0000-0003-1444-9135}{ORCID}) +\section{Duplicates}{ + + +See \code{\link[=spocc_duplicates]{spocc_duplicates()}} for more. } -Other contributors: -\itemize{ - \item Karthik Ram [contributor] - \item Ted Hart [contributor] - \item rOpenSci (ropensci.org/) [funder] +\section{Clean data}{ + + +All data cleaning functionality is in as archived package: \code{scrubr} +(\url{https://github.com/ropensci-archive/scrubr}). +On CRAN: \url{https://cran.r-project.org/src/contrib/Archive/scrubr/}. +See also package +\url{https://cran.r-project.org/package=CoordinateCleaner} } +\section{Make maps}{ + + +All mapping functionality is now in a separate package: \verb{mapr`` () (formerly known as }spoccutils`). +On CRAN: \url{https://cran.r-project.org/package=mapr} +} + +\author{ +Scott Chamberlain } -\keyword{internal} +\keyword{package} diff --git a/man/spocc_objects.Rd b/man/spocc_objects.Rd index aa1f8d3..099d367 100644 --- a/man/spocc_objects.Rd +++ b/man/spocc_objects.Rd @@ -60,10 +60,10 @@ res$idigbio } \seealso{ Other queries: -\code{\link{occ_names_options}()}, +\code{\link{occ}()}, \code{\link{occ_names}()}, -\code{\link{occ_options}()}, -\code{\link{occ}()} +\code{\link{occ_names_options}()}, +\code{\link{occ_options}()} } \concept{queries} \keyword{internal}