From cb80a64abc0238d3c2de7b89dcf8ddf0b38e7c70 Mon Sep 17 00:00:00 2001 From: hannahlowens Date: Wed, 6 Mar 2024 15:15:24 +0100 Subject: [PATCH] bad obis.org link and update website --- CRAN-SUBMISSION | 6 +-- R/spocc-package.R | 2 +- docs/authors.html | 7 +-- docs/news/index.html | 4 +- docs/pkgdown.yml | 2 +- docs/reference/as.vertnet.html | 4 +- docs/reference/index.html | 4 +- docs/reference/occ.html | 14 +++--- docs/reference/occ_names.html | 2 +- docs/reference/occ_names_options.html | 2 +- docs/reference/occ_options.html | 4 +- docs/reference/spocc-package.html | 72 ++++++++++++++++++++------- docs/reference/spocc_objects.html | 6 +-- man/spocc-package.Rd | 2 +- 14 files changed, 85 insertions(+), 46 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 8466d5a..3f510b9 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 1.2.2 -Date: 2023-03-23 08:31:23 UTC -SHA: 59f6b3b192cd8a7bb990aab94748f3bc7b044dac +Version: 1.2.3 +Date: 2024-03-06 08:04:21 UTC +SHA: f4f5e42216d0a3d6bf2f8b8a07764063d2b8f19f diff --git a/R/spocc-package.R b/R/spocc-package.R index 7fcd4df..caff7fd 100644 --- a/R/spocc-package.R +++ b/R/spocc-package.R @@ -27,7 +27,7 @@ #' iNaturalist \tab \cr #' VertNet \tab \cr #' iDigBio \tab \cr -#' OBIS \tab \cr +#' OBIS \tab \cr #' ALA \tab #' } #' diff --git a/docs/authors.html b/docs/authors.html index 8345481..e6998f1 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -96,15 +96,16 @@

Citation

Owens H, Barve V, Chamberlain S (2024). spocc: Interface to Species Occurrence Data Sources. -https://github.com/ropensci/spocc (devel), -https://docs.ropensci.org/spocc/ (user manual). +R package version 1.2.3, +https://docs.ropensci.org/spocc/ (user manual), https://github.com/ropensci/spocc (devel). 

@Manual{,
   title = {spocc: Interface to Species Occurrence Data Sources},
   author = {Hannah Owens and Vijay Barve and Scott Chamberlain},
   year = {2024},
-  note = {https://github.com/ropensci/spocc (devel),
+  note = {R package version 1.2.3, 
 https://docs.ropensci.org/spocc/ (user manual)},
+  url = {https://github.com/ropensci/spocc (devel)},
 }
diff --git a/docs/news/index.html b/docs/news/index.html index 0a068c2..9cd42b5 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -130,7 +130,7 @@

MINOR IMPROVEMENTSBUG FIXES

  • Fix for ALA data source in occ(): total records found count was always 0 because ALA changed the records found field to totalRecords
    • -
  • Fix for Vertnet data source in occ(): was using an old parameter query passed to rvertnet::searchbyterm() - changed to scientificname instead
    • +
  • Fix for Vertnet data source in occ(): was using an old parameter query passed to rvertnet::searchbyterm() - changed to scientificname instead
@@ -265,7 +265,7 @@

MINOR IMPROVEMENTSMove all is() to inherits(), and namespace all setNames() calls
  • We are now using rgbif::occ_data() instead of rgbif::occ_search()
    • -
  • We are now using rvertnet::searchbyterm() instead of rgbif::vertsearch() +
  • We are now using rvertnet::searchbyterm() instead of rgbif::vertsearch()

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index f43714d..9bf5ecb 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,5 +4,5 @@ pkgdown_sha: ~ articles: fixnames: fixnames.html spocc: spocc.html -last_built: 2024-01-24T15:06Z +last_built: 2024-03-06T14:13Z diff --git a/docs/reference/as.vertnet.html b/docs/reference/as.vertnet.html index 921d9ec..b449bad 100644 --- a/docs/reference/as.vertnet.html +++ b/docs/reference/as.vertnet.html @@ -85,8 +85,8 @@

    Value

    Details

    -

    Internally, we use rvertnet::vert_id(), whereas occ() -uses rvertnet::vertsearch().

    +

    Internally, we use rvertnet::vert_id(), whereas occ() +uses rvertnet::vertsearch().

    See also

    diff --git a/docs/reference/index.html b/docs/reference/index.html index e7feb96..ba229b5 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -64,9 +64,9 @@

    General information

    -

    spocc spocc-package

    +

    spocc-package

    -

    spocc: Interface to Species Occurrence Data Sources

    +

    Interface to many species occurrence data sources

    Queries

    diff --git a/docs/reference/occ.html b/docs/reference/occ.html index d960829..e2e9774 100644 --- a/docs/reference/occ.html +++ b/docs/reference/occ.html @@ -172,7 +172,7 @@

    Arguments

    vertnetopts

    (list) List of named options to pass on to -rvertnet::searchbyterm(). See also occ_options().

    +rvertnet::searchbyterm(). See also occ_options().

    idigbioopts
    @@ -263,7 +263,7 @@

    Using the query parameter

    rebird::ebirdgeo() functions, depending on whether you set method="ebirdregion" or method="ebirdgeo" - API parameters: sci for both rebird::ebirdregion() and rebird::ebirdgeo()

    -

  • rvertnet - taxon in the rvertnet::vertsearch() function - API +

  • rvertnet - taxon in the rvertnet::vertsearch() function - API parameter: q

  • ridigbio - scientificname in the ridigbio::idig_search_records() function - API parameter: scientificname

    • @@ -382,7 +382,7 @@

    Notes on the date parameter

    Notes on some special cases

    • idigbio: We search on the datecollected field. Other date fields can be searched on, but we chose datecollected as it seemed most appropriate.

    • vertnet: If you want more flexible date searches, you can pass various -types of date searches to vertnetopts. See rvertnet::searchbyterm() +types of date searches to vertnetopts. See rvertnet::searchbyterm() for more information

    • ala: There's some issues with the dates returned from ALA. They are returned as time stamps, and some seem to be malformed. So do beware @@ -434,8 +434,8 @@

      BEWARE

      @@ -585,13 +585,13 @@

      Examples

      # taxize integration ## You can pass in taxonomic identifiers library("taxize") -(ids <- get_ids(c("Chironomus riparius","Pinus contorta"), db = c('itis','gbif'))) +(ids <- get_ids(c("Chironomus riparius","Pinus contorta"), db = c('itis','gbif'))) occ(ids = ids, from='gbif', limit=20) -(ids <- get_ids("Chironomus riparius", db = 'gbif')) +(ids <- get_ids("Chironomus riparius", db = 'gbif')) occ(ids = ids, from='gbif', limit=20) -(ids <- get_gbifid("Chironomus riparius")) +(ids <- get_gbifid("Chironomus riparius")) occ(ids = ids, from='gbif', limit=20) ## sf classes diff --git a/docs/reference/occ_names.html b/docs/reference/occ_names.html index 7f479be..7ff7912 100644 --- a/docs/reference/occ_names.html +++ b/docs/reference/occ_names.html @@ -120,9 +120,9 @@

      Details

      See also

      Other queries: +occ(), occ_names_options(), occ_options(), -occ(), spocc_objects

      diff --git a/docs/reference/occ_names_options.html b/docs/reference/occ_names_options.html index 2da9979..b8e70e4 100644 --- a/docs/reference/occ_names_options.html +++ b/docs/reference/occ_names_options.html @@ -100,9 +100,9 @@

      Details

      See also

      Other queries: +occ(), occ_names(), occ_options(), -occ(), spocc_objects

      diff --git a/docs/reference/occ_options.html b/docs/reference/occ_options.html index f474360..cf53b8e 100644 --- a/docs/reference/occ_options.html +++ b/docs/reference/occ_options.html @@ -101,9 +101,9 @@

      Details

      See also

      Other queries: -occ_names_options(), -occ_names(), occ(), +occ_names(), +occ_names_options(), spocc_objects

      diff --git a/docs/reference/spocc-package.html b/docs/reference/spocc-package.html index dc8694c..897ceec 100644 --- a/docs/reference/spocc-package.html +++ b/docs/reference/spocc-package.html @@ -1,6 +1,9 @@ -spocc: Interface to Species Occurrence Data Sources — spocc-package • spoccInterface to many species occurrence data sources — spocc-package • spocc @@ -57,33 +60,68 @@
      -

      spocc: Interface to Species Occurrence Data Sources

      +

      Interface to many species occurrence data sources

      Source: R/spocc-package.R
      -

      -

      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.

      -
      -

      See also

      -

      Useful links:

      diff --git a/man/spocc-package.Rd b/man/spocc-package.Rd index 5a40493..a7cdf9f 100644 --- a/man/spocc-package.Rd +++ b/man/spocc-package.Rd @@ -35,7 +35,7 @@ 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 +OBIS \tab \url{https://www.obis.org/} \cr ALA \tab \url{https://www.ala.org.au/} } }