worrms/0000755000177500001440000000000013036407641012127 5ustar deepayanusersworrms/inst/0000755000177500001440000000000013036237401013077 5ustar deepayanusersworrms/inst/doc/0000755000177500001440000000000013036237401013644 5ustar deepayanusersworrms/inst/doc/worrms_vignette.html0000644000177500001440000453752413036237401020014 0ustar deepayanusers Introduction to the worrms package

worrms introduction

worrms is an R client for the World Register of Marine Species.

Install

Stable version from CRAN

install.packages("worrms")

Development version from GitHub

install.packages("devtools")
devtools::install_github("ropensci/worrms")
library("worrms")

Get records

WoRMS ‘records’ are taxa, not specimen occurrences or something else.

by date

wm_records_date('2016-12-23T05:59:45+00:00')
#> # A tibble: 50 × 25
#>    AphiaID                                                           url
#> *    <int>                                                         <chr>
#> 1   894298 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894298
#> 2   894301 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894301
#> 3   894297 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894297
#> 4   894302 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894302
#> 5   894296 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894296
#> 6   894299 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894299
#> 7   894303 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894303
#> 8   897486 http://www.marinespecies.org/aphia.php?p=taxdetails&id=897486
#> 9   901957 http://www.marinespecies.org/aphia.php?p=taxdetails&id=901957
#> 10  899919 http://www.marinespecies.org/aphia.php?p=taxdetails&id=899919
#> # ... with 40 more rows, and 23 more variables: scientificname <chr>,
#> #   authority <chr>, status <chr>, unacceptreason <lgl>, rank <chr>,
#> #   valid_AphiaID <int>, valid_name <chr>, valid_authority <chr>,
#> #   kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> #   genus <chr>, citation <chr>, lsid <chr>, isMarine <int>,
#> #   isBrackish <lgl>, isFreshwater <lgl>, isTerrestrial <lgl>,
#> #   isExtinct <int>, match_type <chr>, modified <chr>

by a taxonomic name

wm_records_name(name = 'Platanista gangetica')
#> # A tibble: 3 × 25
#>   AphiaID                                                           url
#> *   <int>                                                         <chr>
#> 1  254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967
#> 2  383571 http://www.marinespecies.org/aphia.php?p=taxdetails&id=383571
#> 3  254969 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254969
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <lgl>, rank <chr>, valid_AphiaID <int>,
#> #   valid_name <chr>, valid_authority <chr>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <chr>, citation <chr>,
#> #   lsid <chr>, isMarine <int>, isBrackish <lgl>, isFreshwater <int>,
#> #   isTerrestrial <int>, isExtinct <lgl>, match_type <chr>, modified <chr>

by many names

wm_records_names(name = c('Platanista gangetica', 'Coryphaena'))
#> [[1]]
#> # A tibble: 1 × 25
#>   AphiaID                                                           url
#> *   <int>                                                         <chr>
#> 1  254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <lgl>, rank <chr>, valid_AphiaID <int>,
#> #   valid_name <chr>, valid_authority <chr>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <chr>, citation <chr>,
#> #   lsid <chr>, isMarine <lgl>, isBrackish <lgl>, isFreshwater <int>,
#> #   isTerrestrial <lgl>, isExtinct <lgl>, match_type <chr>, modified <chr>
#> 
#> [[2]]
#> # A tibble: 2 × 25
#>   AphiaID                                                           url
#> *   <int>                                                         <chr>
#> 1  125960 http://www.marinespecies.org/aphia.php?p=taxdetails&id=125960
#> 2  843430                                                          <NA>
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <chr>, rank <chr>, valid_AphiaID <int>,
#> #   valid_name <chr>, valid_authority <chr>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <chr>, citation <chr>,
#> #   lsid <chr>, isMarine <int>, isBrackish <int>, isFreshwater <int>,
#> #   isTerrestrial <lgl>, isExtinct <lgl>, match_type <chr>, modified <chr>

by common name

wm_records_common(name = 'clam')
#> # A tibble: 2 × 25
#>   AphiaID                                                           url
#> *   <int>                                                         <chr>
#> 1  141919 http://www.marinespecies.org/aphia.php?p=taxdetails&id=141919
#> 2  141936 http://www.marinespecies.org/aphia.php?p=taxdetails&id=141936
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <lgl>, rank <chr>, valid_AphiaID <int>,
#> #   valid_name <chr>, valid_authority <chr>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <chr>, citation <chr>,
#> #   lsid <chr>, isMarine <int>, isBrackish <lgl>, isFreshwater <lgl>,
#> #   isTerrestrial <lgl>, isExtinct <lgl>, match_type <chr>, modified <chr>

using the TAXMATCH algorithm

wm_records_taxamatch(name = 'Platanista gangetica')
#> [[1]]
#> # A tibble: 1 × 25
#>   AphiaID                                                           url
#> *   <int>                                                         <chr>
#> 1  254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <lgl>, rank <chr>, valid_AphiaID <int>,
#> #   valid_name <chr>, valid_authority <chr>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <chr>, citation <chr>,
#> #   lsid <chr>, isMarine <lgl>, isBrackish <lgl>, isFreshwater <int>,
#> #   isTerrestrial <lgl>, isExtinct <lgl>, match_type <chr>, modified <chr>

APHIA ID <–> name

wm_name2id(name = "Rhincodon")
#> [1] 105749
wm_id2name(id = 105706)
#> [1] "Rhincodontidae"

Get AphiaID via an external ID

wm_external(id = 1080)
#> [1] 85257
wm_external(id = 105706)
#> [1] 159854

Get vernacular names from an AphiaID

wm_common_id(id = 156806)
#> # A tibble: 2 × 3
#>            vernacular language_code language
#> *               <chr>         <chr>    <chr>
#> 1    gilded wedgeclam           eng  English
#> 2 Turton's wedge clam           eng  English

Children

Get direct taxonomic children for an AphiaID

wm_classification(id = 105706)
#> # A tibble: 11 × 3
#>    AphiaID       rank   scientificname
#> *    <int>      <chr>            <chr>
#> 1        2    Kingdom         Animalia
#> 2     1821     Phylum         Chordata
#> 3   146419  Subphylum       Vertebrata
#> 4     1828 Superclass    Gnathostomata
#> 5    11676 Superclass           Pisces
#> 6    10193      Class   Elasmobranchii
#> 7   368407   Subclass      Neoselachii
#> 8   368408 Infraclass         Selachii
#> 9   368410 Superorder      Galeomorphi
#> 10   10208      Order Orectolobiformes
#> 11  105706     Family   Rhincodontidae

Classification

Get classification for an AphiaID

wm_classification(id = 105706)
#> # A tibble: 11 × 3
#>    AphiaID       rank   scientificname
#> *    <int>      <chr>            <chr>
#> 1        2    Kingdom         Animalia
#> 2     1821     Phylum         Chordata
#> 3   146419  Subphylum       Vertebrata
#> 4     1828 Superclass    Gnathostomata
#> 5    11676 Superclass           Pisces
#> 6    10193      Class   Elasmobranchii
#> 7   368407   Subclass      Neoselachii
#> 8   368408 Infraclass         Selachii
#> 9   368410 Superorder      Galeomorphi
#> 10   10208      Order Orectolobiformes
#> 11  105706     Family   Rhincodontidae

Synonyms

Get synonyms for an AphiaID

wm_synonyms(id = 105706)
#> # A tibble: 1 × 25
#>   AphiaID                                                           url
#> *   <int>                                                         <chr>
#> 1  148832 http://www.marinespecies.org/aphia.php?p=taxdetails&id=148832
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <chr>, rank <chr>, valid_AphiaID <int>,
#> #   valid_name <chr>, valid_authority <chr>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <lgl>, citation <chr>,
#> #   lsid <chr>, isMarine <lgl>, isBrackish <lgl>, isFreshwater <lgl>,
#> #   isTerrestrial <lgl>, isExtinct <lgl>, match_type <chr>, modified <chr>
worrms/inst/doc/worrms_vignette.R0000644000177500001440000000357413036237401017236 0ustar deepayanusers## ----echo=FALSE---------------------------------------------------------- knitr::opts_chunk$set( comment = "#>", collapse = TRUE, warning = FALSE, message = FALSE ) ## ----eval=FALSE---------------------------------------------------------- # install.packages("worrms") ## ----eval=FALSE---------------------------------------------------------- # install.packages("devtools") # devtools::install_github("ropensci/worrms") ## ------------------------------------------------------------------------ library("worrms") ## ------------------------------------------------------------------------ wm_records_date('2016-12-23T05:59:45+00:00') ## ------------------------------------------------------------------------ wm_records_name(name = 'Platanista gangetica') ## ------------------------------------------------------------------------ wm_records_names(name = c('Platanista gangetica', 'Coryphaena')) ## ------------------------------------------------------------------------ wm_records_common(name = 'clam') ## ------------------------------------------------------------------------ wm_records_taxamatch(name = 'Platanista gangetica') ## ------------------------------------------------------------------------ wm_name2id(name = "Rhincodon") ## ------------------------------------------------------------------------ wm_id2name(id = 105706) ## ------------------------------------------------------------------------ wm_external(id = 1080) wm_external(id = 105706) ## ------------------------------------------------------------------------ wm_common_id(id = 156806) ## ------------------------------------------------------------------------ wm_classification(id = 105706) ## ------------------------------------------------------------------------ wm_classification(id = 105706) ## ------------------------------------------------------------------------ wm_synonyms(id = 105706) worrms/inst/doc/worrms_vignette.Rmd0000644000177500001440000000351013036237401017545 0ustar deepayanusers--- title: "Introduction to the worrms package" author: "Scott Chamberlain" date: "`r Sys.Date()`" output: html_document: toc: true toc_float: true theme: readable vignette: > %\VignetteIndexEntry{Introduction to the worrms package} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r echo=FALSE} knitr::opts_chunk$set( comment = "#>", collapse = TRUE, warning = FALSE, message = FALSE ) ``` worrms introduction =================== `worrms` is an R client for the [World Register of Marine Species](http://www.marinespecies.org/). ## Install Stable version from CRAN ```{r eval=FALSE} install.packages("worrms") ``` Development version from GitHub ```{r eval=FALSE} install.packages("devtools") devtools::install_github("ropensci/worrms") ``` ```{r} library("worrms") ``` ## Get records WoRMS 'records' are taxa, not specimen occurrences or something else. by date ```{r} wm_records_date('2016-12-23T05:59:45+00:00') ``` by a taxonomic name ```{r} wm_records_name(name = 'Platanista gangetica') ``` by many names ```{r} wm_records_names(name = c('Platanista gangetica', 'Coryphaena')) ``` by common name ```{r} wm_records_common(name = 'clam') ``` using the TAXMATCH algorithm ```{r} wm_records_taxamatch(name = 'Platanista gangetica') ``` ## APHIA ID <--> name ```{r} wm_name2id(name = "Rhincodon") ``` ```{r} wm_id2name(id = 105706) ``` ## Get AphiaID via an external ID ```{r} wm_external(id = 1080) wm_external(id = 105706) ``` ## Get vernacular names from an AphiaID ```{r} wm_common_id(id = 156806) ``` ## Children Get direct taxonomic children for an AphiaID ```{r} wm_classification(id = 105706) ``` ## Classification Get classification for an AphiaID ```{r} wm_classification(id = 105706) ``` ## Synonyms Get synonyms for an AphiaID ```{r} wm_synonyms(id = 105706) ``` worrms/tests/0000755000177500001440000000000013036237401013264 5ustar deepayanusersworrms/tests/testthat/0000755000177500001440000000000013036237401015124 5ustar deepayanusersworrms/tests/testthat/test-wm_distribution.R0000644000177500001440000000073513033061770021454 0ustar deepayanuserscontext("wm_distribution") test_that("wm_distribution basic usage works", { skip_on_cran() aa <- wm_distribution(id = 156806) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_gt(NROW(aa), 1) }) test_that("wm_distribution fails well", { skip_on_cran() expect_error(wm_distribution(), "argument \"id\" is missing") expect_error(wm_distribution("asdfafasdfs"), "id must be of class") expect_error(wm_distribution(44444), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_records_taxamatch.R0000644000177500001440000000135713027323324022430 0ustar deepayanuserscontext("wm_records_taxamatch") test_that("wm_records_taxamatch basic usage works", { skip_on_cran() aa <- wm_records_taxamatch(name = 'Platanista gangetica') expect_is(aa, "list") expect_equal(length(aa), 1) expect_is(aa[[1]], "tbl_df") expect_is(aa[[1]], "data.frame") expect_equal(NROW(aa[[1]]), 1) }) test_that("wm_records_taxamatch fails well", { skip_on_cran() expect_error(wm_records_taxamatch(), "argument \"name\" is missing") expect_error(wm_records_taxamatch("asdfafasdfs"), "No Content") expect_error(wm_records_taxamatch(5), "name must be of class character") expect_error(wm_records_taxamatch('Platanista gangetica', marine_only = 5), "marine_only must be of class logical") }) worrms/tests/testthat/test-wm_records_names.R0000644000177500001440000000203213035052410021542 0ustar deepayanuserscontext("wm_records_names") test_that("wm_records_names - works", { skip_on_cran() aa <- wm_records_names(name = 'Platanista gangetica') expect_is(aa, "list") expect_is(aa[[1]], "tbl_df") expect_is(aa[[1]], "data.frame") expect_true(all(grepl("Platanista", aa[[1]]$scientificname))) expect_equal(NROW(aa[[1]]), 1) }) test_that("wm_records_names - fuzzy parameter", { skip_on_cran() aa <- wm_records_names(name = 'Platanista gangetica', fuzzy = TRUE) expect_is(aa, "list") expect_is(aa[[1]], "tbl_df") expect_is(aa[[1]], "data.frame") expect_true(all(grepl("Platanista", aa[[1]]$scientificname))) expect_gt(NROW(aa[[1]]), 1) }) test_that("wm_records_names fails well", { skip_on_cran() expect_error(wm_records_names(), "argument \"name\" is missing") expect_error(wm_records_names(55555), "name must be of class character") expect_error(wm_records_names("asdfs", "Adf"), "fuzzy must be of class logical") expect_error(wm_records_names("asdfs", marine_only = 5), "marine_only must be of class logical") }) worrms/tests/testthat/test-wm_name2id.R0000644000177500001440000000066113034574257020264 0ustar deepayanuserscontext("wm_name2id") test_that("wm_name2id - default usage works", { skip_on_cran() aa <- wm_name2id(name = "Rhincodon") expect_type(aa, "integer") expect_equal(aa, 105749) }) test_that("wm_name2id fails well", { skip_on_cran() expect_error(wm_name2id(), "argument \"name\" is missing") expect_error(wm_name2id(44444), "name must be of class") expect_error(wm_name2id("asdfafasdfs"), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_id2name.R0000644000177500001440000000065213034574134020256 0ustar deepayanuserscontext("wm_id2name") test_that("wm_id2name - default usage works", { skip_on_cran() aa <- wm_id2name(id = 1080) expect_type(aa, "character") expect_equal(aa, "Copepoda") }) test_that("wm_id2name fails well", { skip_on_cran() expect_error(wm_id2name(), "argument \"id\" is missing") expect_error(wm_id2name("asdfafasdfs"), "id must be of class") expect_error(wm_id2name(44444), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_common_id.R0000644000177500001440000000102613034561576020705 0ustar deepayanuserscontext("wm_common_id") test_that("wm_common_id basic usage works", { skip_on_cran() aa <- wm_common_id(id = 156806) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_named(aa, c('vernacular', 'language_code', 'language')) expect_match(aa$vernacular, "clam") }) test_that("wm_common_id fails well", { skip_on_cran() expect_error(wm_common_id(), "argument \"id\" is missing") expect_error(wm_common_id("asdfafasdfs"), "id must be of class") expect_error(wm_common_id(44444), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_external.R0000644000177500001440000000112713034574022020553 0ustar deepayanuserscontext("wm_external") test_that("wm_external - default usage works", { skip_on_cran() aa <- wm_external(id = 1080) expect_type(aa, "integer") expect_equal(aa, 85257) }) test_that("wm_external - type: fishbase", { skip_on_cran() aa <- wm_external(id = 278468, type = "fishbase") expect_type(aa, "integer") expect_equal(aa, 8399) }) test_that("wm_external fails well", { skip_on_cran() expect_error(wm_external(), "argument \"id\" is missing") expect_error(wm_external("asdfafasdfs"), "id must be of class") expect_error(wm_external(44444), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_records_common.R0000644000177500001440000000224513035050776021752 0ustar deepayanuserscontext("wm_records_common") test_that("wm_records_common - works", { skip_on_cran() aa <- wm_records_common(name = 'dolphin') expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_true(any(grepl("AphiaID", names(aa)))) expect_equal(aa$kingdom, "Animalia") expect_equal(aa$genus, "Coryphaena") }) test_that("wm_records_common - fuzzy parameter works", { skip_on_cran() aa <- wm_records_common(name = 'dolphin') bb <- wm_records_common(name = 'dolphin', fuzzy = TRUE) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_is(bb, "tbl_df") expect_is(bb, "data.frame") expect_gt(NROW(bb), NROW(aa)) }) test_that("wm_records_common - offset parameter works", { skip_on_cran() aa <- wm_records_common(name = 'dolphin', fuzzy = TRUE) bb <- wm_records_common(name = 'dolphin', fuzzy = TRUE, offset = 10) expect_false(identical(aa$AphiaID, bb$AphiaID)) }) test_that("wm_records_common fails well", { skip_on_cran() expect_error(wm_records_common(), "argument \"name\" is missing") expect_error(wm_records_common(55555), "name must be of class character") expect_error(wm_records_common("asdfafasdfs"), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_record.R0000644000177500001440000000073213034763464020222 0ustar deepayanuserscontext("wm_record") test_that("wm_record - default usage works", { skip_on_cran() aa <- wm_record(id = 105706) expect_type(aa, "list") expect_equal(aa$valid_name, "Rhincodontidae") expect_equal(aa$valid_AphiaID, 105706) }) test_that("wm_record fails well", { skip_on_cran() expect_error(wm_record(), "argument \"id\" is missing") expect_error(wm_record("asdfafasdfs"), "id must be of class") expect_error(wm_record(44444), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_records_name.R0000644000177500001440000000204113035052147021366 0ustar deepayanuserscontext("wm_records_name") test_that("wm_records_name - works", { skip_on_cran() aa <- wm_records_name(name = 'Platanista gangetica') expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_true(all(grepl("Platanista", aa$scientificname))) expect_gt(NROW(aa), 1) }) test_that("wm_records_name - fuzzy parameter", { skip_on_cran() aa <- wm_records_name(name = 'Platanista gangetica', fuzzy = FALSE) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_true(all(grepl("Platanista", aa$scientificname))) expect_equal(NROW(aa), 1) }) test_that("wm_records_name fails well", { skip_on_cran() expect_error(wm_records_name(), "argument \"name\" is missing") expect_error(wm_records_name(55555), "name must be of class character") expect_error(wm_records_name("asdfs", "Adf"), "fuzzy must be of class logical") expect_error(wm_records_name("asdfs", marine_only = 5), "marine_only must be of class logical") expect_error(wm_records_name("asdfs", offset = "foobar"), "offset must be of class numeric, integer") }) worrms/tests/testthat/test-wm_children.R0000644000177500001440000000215413034560417020525 0ustar deepayanuserscontext("wm_children") test_that("wm_children basic usage works", { skip_on_cran() aa <- wm_children(id = 105706) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_gt(NROW(aa), 1) expect_equal(unique(aa$family), "Rhincodontidae") expect_equal(unique(aa$order), "Orectolobiformes") expect_equal(unique(aa$class), "Elasmobranchii") expect_equal(unique(aa$phylum), "Chordata") expect_equal(unique(aa$kingdom), "Animalia") }) test_that("wm_children - marine_only usage works", { skip_on_cran() expect_is(wm_children(id = 105706, FALSE), "tbl_df") expect_is(wm_children(id = 105706, TRUE), "tbl_df") }) test_that("wm_children - offset parameter works", { skip_on_cran() off1 <- wm_children(id = 105706, offset = 1) off2 <- wm_children(id = 105706, offset = 2) expect_equal(off1$AphiaID[1], 297110) expect_equal(off2$AphiaID[1], 398065) }) test_that("wm_children fails well", { skip_on_cran() expect_error(wm_children(), "argument \"id\" is missing") expect_error(wm_children("asdfafasdfs"), "id must be of class") expect_error(wm_children(44444), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_classification.R0000644000177500001440000000104713035240313021717 0ustar deepayanuserscontext("wm_classification") test_that("wm_classification works", { skip_on_cran() aa <- wm_classification(id = 105706) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_named(aa, c('AphiaID', 'rank', 'scientificname')) }) test_that("wm_classification fails well", { skip_on_cran() expect_error(wm_classification(), "argument \"id\" is missing") expect_error(wm_classification("asdfafasdfs"), "id must be of class") bb <- wm_classification(23424234) expect_equal(NROW(bb), 0) expect_equal(length(names(bb)), 0) }) worrms/tests/testthat/test-wm_synonyms.R0000644000177500001440000000120113035053115020615 0ustar deepayanuserscontext("wm_synonyms") test_that("wm_synonyms - works", { skip_on_cran() aa <- wm_synonyms(id = 105706) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_equal(NROW(aa), 1) expect_true(any(grepl("scientificname", names(aa)))) expect_true(any(grepl("AphiaID", names(aa)))) expect_true(any(grepl("valid_AphiaID", names(aa)))) expect_true(any(grepl("valid_name", names(aa)))) expect_true(any(grepl("valid_authority", names(aa)))) }) test_that("wm_synonyms fails well", { skip_on_cran() expect_error(wm_synonyms(), "argument \"id\" is missing") expect_error(wm_synonyms(55555), "\\(204\\) No Content") }) worrms/tests/testthat/test-wm_record_by_external.R0000644000177500001440000000167613035043204022606 0ustar deepayanuserscontext("wm_record_by_external") test_that("wm_record_by_external - default - by id type tsn", { skip_on_cran() # tsn tsn <- wm_record_by_external(id = 85257) expect_type(tsn, "list") expect_equal(tsn$valid_name, "Copepoda") expect_equal(tsn$valid_AphiaID, 1080) # ncbi ncbi <- wm_record_by_external(id = 6830, type = "ncbi") expect_type(ncbi, "list") expect_equal(ncbi$valid_name, "Copepoda") expect_equal(ncbi$valid_AphiaID, 1080) # they're equivvalent expect_identical(tsn, ncbi) # fishbase fishbase <- wm_record_by_external(id = 8399, type = "fishbase") expect_type(fishbase, "list") expect_equal(fishbase$valid_name, "Callorhinchus callorynchus") expect_equal(fishbase$valid_AphiaID, 278468) }) test_that("wm_record_by_external fails well", { skip_on_cran() expect_error(wm_record_by_external(), "argument \"id\" is missing") expect_error(wm_record_by_external("asdfafasdfs"), "id must be of class") }) worrms/tests/testthat/test-wm_records_date.R0000644000177500001440000000076613035051347021400 0ustar deepayanuserscontext("wm_records_date") test_that("wm_records_date - works", { skip_on_cran() a_date <- format(Sys.Date() - 1, "%Y-%m-%dT%H:%M:%S+00:00") aa <- wm_records_date(a_date) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_true(all(grepl("2017", aa$modified))) }) test_that("wm_records_date fails well", { skip_on_cran() expect_error(wm_records_date(), "argument \"start_date\" is missing") expect_error(wm_records_date(55555), "start_date must be of class character") }) worrms/tests/testthat/test-wm_sources.R0000644000177500001440000000101613035052745020415 0ustar deepayanuserscontext("wm_sources") test_that("wm_sources - works", { skip_on_cran() aa <- wm_sources(id = 105706) expect_is(aa, "tbl_df") expect_is(aa, "data.frame") expect_true(any(grepl("use", names(aa)))) expect_true(any(grepl("reference", names(aa)))) expect_true(any(grepl("page", names(aa)))) expect_true(any(grepl("url", names(aa)))) }) test_that("wm_sources fails well", { skip_on_cran() expect_error(wm_sources(), "argument \"id\" is missing") expect_error(wm_sources(55555), "\\(204\\) No Content") }) worrms/tests/test-all.R0000644000177500001440000000005113027321070015124 0ustar deepayanuserslibrary("testthat") test_check("worrms") worrms/NAMESPACE0000644000177500001440000000063213027323224013341 0ustar deepayanusers# Generated by roxygen2: do not edit by hand export(wm_children) export(wm_classification) export(wm_common_id) export(wm_distribution) export(wm_external) export(wm_id2name) export(wm_name2id) export(wm_record) export(wm_record_by_external) export(wm_records_common) export(wm_records_date) export(wm_records_name) export(wm_records_names) export(wm_records_taxamatch) export(wm_sources) export(wm_synonyms) worrms/NEWS.md0000644000177500001440000000010113033053453013210 0ustar deepayanusersworrms 0.1.0 ============ ### NEW FEATURES * Released to CRAN. worrms/R/0000755000177500001440000000000013036237401012323 5ustar deepayanusersworrms/R/wm_records_date.R0000644000177500001440000000157013033052222015603 0ustar deepayanusers#' Get records by date #' #' @export #' @param start_date (character) start date. required. #' @param end_date (character) end date. optional #' @param marine_only (logical) marine only or not. default: \code{TRUE} #' @param offset (integer) record to start at. default: 1 #' @template curl #' @examples #' a_date <- format(Sys.Date() - 1, "%Y-%m-%dT%H:%M:%S+00:00") #' wm_records_date(a_date) wm_records_date <- function(start_date, end_date = NULL, marine_only = TRUE, offset = 1, ...) { assert(start_date, c("character", "Date")) assert(end_date, c("character", "Date")) assert(marine_only, "logical") assert(offset, c('numeric', 'integer')) wm_GET(file.path(wm_base(), "AphiaRecordsByDate"), query = cc(list( startdate = start_date, enddate = end_date, marine_only = as_log(marine_only), offset = offset)), ...) } worrms/R/wm_record_by_external.R0000644000177500001440000000107313033062520017017 0ustar deepayanusers#' Get record by external ID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @param type (character) the type of external id. one of: tsn, bold, #' dyntaxa, eol, fishbase, iucn, lsid, ncbi, gisd. default: tsn #' @template curl #' @examples #' wm_record_by_external(id = 85257) #' wm_record_by_external(id = 159854) wm_record_by_external <- function(id, type = "tsn", ...) { assert(id, c("numeric", "integer")) assert(type, "character") wm_GET(file.path(wm_base(), "AphiaRecordByExternalID", id), query = cc(list(type = type)), ...) } worrms/R/wm_records_common.R0000644000177500001440000000164213036235250016165 0ustar deepayanusers#' Get records by vernacular name, optional fuzzy matching #' #' @export #' @param name (character) a species common name. required. #' @param fuzzy (logical) fuzzy search. default: \code{FALSE} #' @param offset (integer) record to start at. default: 1 #' @template curl #' @examples #' wm_records_common(name = 'dolphin') #' wm_records_common(name = 'clam') #' #' \dontrun{ #' wm_records_common(name = 'dolphin', fuzzy = TRUE) #' wm_records_common(name = 'clam', fuzzy = TRUE, offset = 5) #' } wm_records_common <- function(name, fuzzy = FALSE, offset = 1, ...) { assert(name, "character") assert(fuzzy, "logical") assert(offset, c('numeric', 'integer')) if (length(name) > 1) stop("'name' must be of length 1", call. = FALSE) args <- cc(list( like = as_log(fuzzy), offset = offset )) wm_GET(file.path(wm_base(), "AphiaRecordsByVernacular", name), query = args, ...) } worrms/R/wm_synonyms.R0000644000177500001440000000045213033062451015047 0ustar deepayanusers#' Get synonyms for an AphiaID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @template curl #' @examples #' wm_synonyms(id = 105706) wm_synonyms <- function(id, ...) { assert(id, c("numeric", "integer")) wm_GET(file.path(wm_base(), "AphiaSynonymsByAphiaID", id), ...) } worrms/R/wm_distribution.R0000644000177500001440000000045213033062402015663 0ustar deepayanusers#' Get distribution data by AphiaID #' #' @export #' @param id an AphiaID. required. #' @template curl #' @examples #' wm_distribution(id = 156806) wm_distribution <- function(id, ...) { assert(id, c("numeric", "integer")) wm_GET(file.path(wm_base(), "AphiaDistributionsByAphiaID", id), ...) } worrms/R/wm_id2name.R0000644000177500001440000000045213033062550014467 0ustar deepayanusers#' Get taxonomic name for an AphiaID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @template curl #' @examples #' wm_id2name(id = 105706) wm_id2name <- function(id, ...) { assert(id, c("numeric", "integer")) wm_GET(file.path(wm_base(), "AphiaNameByAphiaID", id), ...) } worrms/R/wm_sources.R0000644000177500001440000000044613033062460014636 0ustar deepayanusers#' Get sources for an AphiaID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @template curl #' @examples #' wm_sources(id = 105706) wm_sources <- function(id, ...) { assert(id, c("numeric", "integer")) wm_GET(file.path(wm_base(), "AphiaSourcesByAphiaID", id), ...) } worrms/R/wm_externalid.R0000644000177500001440000000147613034573777015341 0ustar deepayanusers#' Get an external ID via an AphiaID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @param type (character) the type of external id. one of: tsn, bold, #' dyntaxa, eol, fishbase, iucn, lsid, ncbi, gisd. default: tsn #' @template curl #' @examples #' # by default, get a TSN (an ITIS code) #' wm_external(id = 1080) #' #' # BOLD code #' wm_external(id = 278468, type = "bold") #' #' # NCBI code #' wm_external(id = 278468, type = "ncbi") #' #' # fishbase code #' wm_external(id = 278468, type = "fishbase") #' #' library(crul) #' wm_external(id = 105706, verbose = TRUE) wm_external <- function(id, type = "tsn", ...) { assert(id, c("numeric", "integer")) assert(type, "character") as.integer(wm_GET( file.path(wm_base(), "AphiaExternalIDByAphiaID", id), query = cc(list(type = type)), ...)) } worrms/R/wm_record.R0000644000177500001440000000046013033062532014425 0ustar deepayanusers#' Get complete AphiaRecord for an AphiaID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @template curl #' @examples #' wm_record(id = 105706) wm_record <- function(id, ...) { assert(id, c("numeric", "integer")) wm_GET(file.path(wm_base(), "AphiaRecordByAphiaID", id), ...) } worrms/R/wm_records_names.R0000644000177500001440000000166713027324164016012 0ustar deepayanusers#' Get records for onen or more taxonomic name(s) #' #' @export #' @param name (character) start date. required. #' @param fuzzy (logical) fuzzy search. default: \code{FALSE} #' @param marine_only (logical) marine only or not. default: \code{TRUE} #' @template curl #' @examples #' wm_records_names(name = 'Platanista gangetica') #' wm_records_names(name = 'Platanista gangetica', fuzzy = TRUE) #' wm_records_names(name = c('Platanista gangetica', 'Coryphaena')) wm_records_names <- function(name, fuzzy = FALSE, marine_only = TRUE, ...) { assert(name, "character") assert(fuzzy, "logical") assert(marine_only, "logical") args <- cc(list(like = as_log(fuzzy), marine_only = as_log(marine_only))) args <- c(args, stats::setNames(as.list(name), rep('scientificnames[]', length(name)))) wm_GET(file.path(wm_base(), "AphiaRecordsByNames"), query = args, ...) } worrms/R/worrms-package.R0000644000177500001440000000113213033053265015366 0ustar deepayanusers#' World Register of Marine Species Client #' #' @name worrms-package #' @aliases worrms #' @docType package #' @keywords package #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com} #' #' @section Fail behavior: #' The WoRMS REST API doesn't have sophisticated error messaging, so #' most errors will result in a \code{(204) - No Content} or #' in \code{(400) - Bad Request} #' #' Because WoRMS doesn't do comprehensive error reporting, we do a fair #' amount of checking user inputs to help prevent errors that will be #' meaningless to the user. Let us know if we can improve on this. NULL worrms/R/wm_records_taxamatch.R0000644000177500001440000000151013036235536016650 0ustar deepayanusers#' Get records for onen or more taxonomic name(s) using #' the TAXAMATCH fuzzy matching algorithm #' #' @export #' @param name (character) taxon name. required. #' @param marine_only (logical) marine only or not. default: \code{TRUE} #' @template curl #' @examples \dontrun{ #' wm_records_taxamatch(name = 'Platanista gangetica') #' wm_records_taxamatch(name = c('Platanista gangetica', 'Coryphaena')) #' } wm_records_taxamatch <- function(name, marine_only = TRUE, ...) { assert(name, "character") assert(marine_only, "logical") args <- cc(list(marine_only = as_log(marine_only))) args <- c(args, stats::setNames(as.list(name), rep('scientificnames[]', length(name)))) wm_GET(file.path(wm_base(), "AphiaRecordsByMatchNames"), query = args, ...) } worrms/R/wm_children.R0000644000177500001440000000131313033062472014740 0ustar deepayanusers#' Get children for an AphiaID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @param marine_only (logical) marine only or not. default: \code{TRUE} #' @param offset (integer) record to start at. default: 1 #' @template curl #' @examples #' wm_children(id = 105706) #' wm_children(id = 105706, FALSE) #' wm_children(id = 105706, offset = 5) wm_children <- function(id, marine_only = TRUE, offset = 1, ...) { assert(id, c("numeric", "integer")) assert(marine_only, "logical") assert(offset, c("numeric", "integer")) wm_GET(file.path(wm_base(), "AphiaChildrenByAphiaID", id), query = cc(list(marine_only = as_log(marine_only), offset = offset)), ...) } worrms/R/wm_classification.R0000644000177500001440000000154413035240245016147 0ustar deepayanusers#' Get classification for an AphiaID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @template curl #' @examples #' wm_classification(id = 105706) #' wm_classification(id = 126436) wm_classification <- function(id, ...) { assert(id, c("numeric", "integer")) res <- wm_GET(file.path(wm_base(), "AphiaClassificationByAphiaID", id), ...) done <- FALSE out <- list() it <- 0 while (!done) { it <- it + 1 ch <- res$child if (!is.null(ch)) { out[[it]] <- ch[!names(ch) %in% "child"] res <- list(child = ch$child) } else { done <- TRUE } } dat <- Filter(function(x) !is.null(x) && length(x) != 0, out) dat <- do.call("rbind.data.frame", dat) dat$rank <- as.character(dat$rank) dat$scientificname <- as.character(dat$scientificname) if (NROW(dat) == 0) dat <- NULL tibble::as_tibble(dat) } worrms/R/wm_common_id.R0000644000177500001440000000067013033062464015122 0ustar deepayanusers#' Get vernacular names from an AphiaID #' #' @export #' @param id (numeric/integer) an AphiaID. required. #' @template curl #' @examples #' wm_common_id(id = 105706) #' wm_common_id(id = 156806) #' wm_common_id(id = 397065) wm_common_id <- function(id, ...) { assert(id, c("numeric", "integer")) if (length(id) > 1) stop("'id' must be of length 1", call. = FALSE) wm_GET(file.path(wm_base(), "AphiaVernacularsByAphiaID", id), ...) } worrms/R/wm_records_name.R0000644000177500001440000000223313027324221015607 0ustar deepayanusers#' Get records by single name, optional fuzzy matching #' #' @export #' @param name (character) start date. required. #' @param fuzzy (logical) fuzzy search. default: \code{TRUE} #' @param marine_only (logical) marine only or not. default: \code{TRUE} #' @param offset (integer) record to start at. default: 1 #' @template curl #' @examples #' wm_records_name(name = 'Platanista gangetica') #' wm_records_name(name = 'Platanista gangetica', fuzzy = FALSE) #' wm_records_name(name = 'Platanista gangetica', marine_only = FALSE) #' wm_records_name(name = 'Platanista', marine_only = FALSE) #' wm_records_name(name = 'Platanista', marine_only = FALSE, offset = 5) wm_records_name <- function(name, fuzzy = TRUE, marine_only = TRUE, offset = 1, ...) { assert(name, "character") assert(fuzzy, "logical") assert(marine_only, "logical") assert(offset, c('numeric', 'integer')) if (length(name) > 1) stop("'name' must be of length 1", call. = FALSE) args <- cc(list( like = as_log(fuzzy), marine_only = as_log(marine_only), offset = offset )) wm_GET(file.path(wm_base(), "AphiaRecordsByName", name), query = args, ...) } worrms/R/wm_name2id.R0000644000177500001440000000043113027324314014466 0ustar deepayanusers#' Get AphiaID from a taxonomic name #' #' @export #' @param name (character) a taxon name #' @template curl #' @examples #' wm_name2id(name = "Rhincodon") wm_name2id <- function(name, ...) { assert(name, "character") wm_GET(file.path(wm_base(), "AphiaIDByName", name), ...) } worrms/R/zzz.R0000644000177500001440000000176513033061723013313 0ustar deepayanuserswm_GET <- function(url, query = list(), ...) { cli <- crul::HttpClient$new(url = url, opts = list(...)) temp <- cli$get(query = query) temp$raise_for_status() if (temp$status_code == 204) { stop(sprintf("(%s) %s", temp$status_code, temp$status_http()$message), call. = FALSE) } tmp <- jsonlite::fromJSON(temp$parse("UTF-8"), flatten = TRUE) if (inherits(tmp, "data.frame")) { tibble::as_data_frame(tmp) } else if (inherits(tmp, "list")) { if (all(sapply(tmp, class) == "data.frame")) { lapply(tmp, tibble::as_data_frame) } else { tmp } } else { tmp } } wm_base <- function() "http://www.marinespecies.org/rest" cc <- function(x) Filter(Negate(is.null), x) as_log <- function(x) { if (is.null(x)) { x } else { if (x) "true" else "false" } } assert <- function(x, y) { if (!is.null(x)) { if (!class(x) %in% y) { stop(deparse(substitute(x)), " must be of class ", paste0(y, collapse = ", "), call. = FALSE) } } } worrms/vignettes/0000755000177500001440000000000013036237401014132 5ustar deepayanusersworrms/vignettes/worrms_vignette.Rmd0000644000177500001440000000351013033122127020026 0ustar deepayanusers--- title: "Introduction to the worrms package" author: "Scott Chamberlain" date: "`r Sys.Date()`" output: html_document: toc: true toc_float: true theme: readable vignette: > %\VignetteIndexEntry{Introduction to the worrms package} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r echo=FALSE} knitr::opts_chunk$set( comment = "#>", collapse = TRUE, warning = FALSE, message = FALSE ) ``` worrms introduction =================== `worrms` is an R client for the [World Register of Marine Species](http://www.marinespecies.org/). ## Install Stable version from CRAN ```{r eval=FALSE} install.packages("worrms") ``` Development version from GitHub ```{r eval=FALSE} install.packages("devtools") devtools::install_github("ropensci/worrms") ``` ```{r} library("worrms") ``` ## Get records WoRMS 'records' are taxa, not specimen occurrences or something else. by date ```{r} wm_records_date('2016-12-23T05:59:45+00:00') ``` by a taxonomic name ```{r} wm_records_name(name = 'Platanista gangetica') ``` by many names ```{r} wm_records_names(name = c('Platanista gangetica', 'Coryphaena')) ``` by common name ```{r} wm_records_common(name = 'clam') ``` using the TAXMATCH algorithm ```{r} wm_records_taxamatch(name = 'Platanista gangetica') ``` ## APHIA ID <--> name ```{r} wm_name2id(name = "Rhincodon") ``` ```{r} wm_id2name(id = 105706) ``` ## Get AphiaID via an external ID ```{r} wm_external(id = 1080) wm_external(id = 105706) ``` ## Get vernacular names from an AphiaID ```{r} wm_common_id(id = 156806) ``` ## Children Get direct taxonomic children for an AphiaID ```{r} wm_classification(id = 105706) ``` ## Classification Get classification for an AphiaID ```{r} wm_classification(id = 105706) ``` ## Synonyms Get synonyms for an AphiaID ```{r} wm_synonyms(id = 105706) ``` worrms/README.md0000644000177500001440000001522713036232732013412 0ustar deepayanusersworrms ====== [![Build Status](https://travis-ci.org/ropensci/worrms.svg?branch=master)](https://travis-ci.org/ropensci/worrms) [![codecov](https://codecov.io/gh/ropensci/worrms/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/worrms) `worrms` is a R client for the World Register of Marine Species * [World Register of Marine Species (WoRMS)](http://www.marinespecies.org/) * [WoRMS REST API docs](http://www.marinespecies.org/rest/) ## Installation More stable CRAN version ```r install.packages("worrms") ``` Development version ```r devtools::install_github("ropensci/worrms") ``` ```r library("worrms") ``` ## get records by date ```r wm_records_date('2016-12-23T05:59:45+00:00') #> # A tibble: 50 × 25 #> AphiaID url #> * #> 1 894298 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894298 #> 2 894301 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894301 #> 3 894297 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894297 #> 4 894302 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894302 #> 5 894296 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894296 #> 6 894299 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894299 #> 7 894303 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894303 #> 8 906769 http://www.marinespecies.org/aphia.php?p=taxdetails&id=906769 #> 9 909454 http://www.marinespecies.org/aphia.php?p=taxdetails&id=909454 #> 10 915236 http://www.marinespecies.org/aphia.php?p=taxdetails&id=915236 #> # ... with 40 more rows, and 23 more variables: scientificname , #> # authority , status , unacceptreason , rank , #> # valid_AphiaID , valid_name , valid_authority , #> # kingdom , phylum , class , order , family , #> # genus , citation , lsid , isMarine , #> # isBrackish , isFreshwater , isTerrestrial , #> # isExtinct , match_type , modified ``` by a taxonomic name ```r wm_records_name(name = 'Platanista gangetica') #> # A tibble: 3 × 25 #> AphiaID url #> * #> 1 254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967 #> 2 383571 http://www.marinespecies.org/aphia.php?p=taxdetails&id=383571 #> 3 254969 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254969 #> # ... with 23 more variables: scientificname , authority , #> # status , unacceptreason , rank , valid_AphiaID , #> # valid_name , valid_authority , kingdom , phylum , #> # class , order , family , genus , citation , #> # lsid , isMarine , isBrackish , isFreshwater , #> # isTerrestrial , isExtinct , match_type , modified ``` by many names ```r wm_records_names(name = c('Platanista gangetica', 'Coryphaena')) #> [[1]] #> # A tibble: 1 × 25 #> AphiaID url #> * #> 1 254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967 #> # ... with 23 more variables: scientificname , authority , #> # status , unacceptreason , rank , valid_AphiaID , #> # valid_name , valid_authority , kingdom , phylum , #> # class , order , family , genus , citation , #> # lsid , isMarine , isBrackish , isFreshwater , #> # isTerrestrial , isExtinct , match_type , modified #> #> [[2]] #> # A tibble: 2 × 25 #> AphiaID url #> * #> 1 125960 http://www.marinespecies.org/aphia.php?p=taxdetails&id=125960 #> 2 843430 #> # ... with 23 more variables: scientificname , authority , #> # status , unacceptreason , rank , valid_AphiaID , #> # valid_name , valid_authority , kingdom , phylum , #> # class , order , family , genus , citation , #> # lsid , isMarine , isBrackish , isFreshwater , #> # isTerrestrial , isExtinct , match_type , modified ``` by common name ```r wm_records_common(name = 'clam') #> # A tibble: 2 × 25 #> AphiaID url #> * #> 1 141919 http://www.marinespecies.org/aphia.php?p=taxdetails&id=141919 #> 2 141936 http://www.marinespecies.org/aphia.php?p=taxdetails&id=141936 #> # ... with 23 more variables: scientificname , authority , #> # status , unacceptreason , rank , valid_AphiaID , #> # valid_name , valid_authority , kingdom , phylum , #> # class , order , family , genus , citation , #> # lsid , isMarine , isBrackish , isFreshwater , #> # isTerrestrial , isExtinct , match_type , modified ``` using the TAXMATCH algorithm ```r wm_records_taxamatch(name = 'Platanista gangetica') #> [[1]] #> # A tibble: 1 × 25 #> AphiaID url #> * #> 1 254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967 #> # ... with 23 more variables: scientificname , authority , #> # status , unacceptreason , rank , valid_AphiaID , #> # valid_name , valid_authority , kingdom , phylum , #> # class , order , family , genus , citation , #> # lsid , isMarine , isBrackish , isFreshwater , #> # isTerrestrial , isExtinct , match_type , modified ``` ## Meta * Please [report any issues or bugs](https://github.com/ropensci/worrms/issues). * License: MIT * Get citation information for `worrms` in R doing `citation(package = 'worrms')` * Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms. 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Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification. Version: 0.1.0 Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com")) License: MIT + file LICENSE URL: https://github.com/ropensci/worrms BugReports: https://github.com/ropensci/worrms/issues LazyData: true VignetteBuilder: knitr Imports: crul (>= 0.2.0), tibble (>= 1.2), jsonlite (>= 1.1) Suggests: roxygen2 (>= 5.0.1), knitr, rmarkdown, testthat, covr RoxygenNote: 5.0.1 NeedsCompilation: no Packaged: 2017-01-13 20:56:33 UTC; sacmac Author: Scott Chamberlain [aut, cre] Maintainer: Scott Chamberlain Repository: CRAN Date/Publication: 2017-01-14 12:46:41 worrms/man/0000755000177500001440000000000013036237401012675 5ustar deepayanusersworrms/man/wm_external.Rd0000644000177500001440000000150313035053131015503 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_externalid.R \name{wm_external} \alias{wm_external} \title{Get an external ID via an AphiaID} \usage{ wm_external(id, type = "tsn", ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{type}{(character) the type of external id. one of: tsn, bold, dyntaxa, eol, fishbase, iucn, lsid, ncbi, gisd. default: tsn} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get an external ID via an AphiaID } \examples{ # by default, get a TSN (an ITIS code) wm_external(id = 1080) # BOLD code wm_external(id = 278468, type = "bold") # NCBI code wm_external(id = 278468, type = "ncbi") # fishbase code wm_external(id = 278468, type = "fishbase") library(crul) wm_external(id = 105706, verbose = TRUE) } worrms/man/wm_id2name.Rd0000644000177500001440000000064713033062570015215 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_id2name.R \name{wm_id2name} \alias{wm_id2name} \title{Get taxonomic name for an AphiaID} \usage{ wm_id2name(id, ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get taxonomic name for an AphiaID } \examples{ wm_id2name(id = 105706) } worrms/man/wm_records_names.Rd0000644000177500001440000000142613027316664016527 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_records_names.R \name{wm_records_names} \alias{wm_records_names} \title{Get records for onen or more taxonomic name(s)} \usage{ wm_records_names(name, fuzzy = FALSE, marine_only = TRUE, ...) } \arguments{ \item{name}{(character) start date. required.} \item{fuzzy}{(logical) fuzzy search. default: \code{FALSE}} \item{marine_only}{(logical) marine only or not. default: \code{TRUE}} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get records for onen or more taxonomic name(s) } \examples{ wm_records_names(name = 'Platanista gangetica') wm_records_names(name = 'Platanista gangetica', fuzzy = TRUE) wm_records_names(name = c('Platanista gangetica', 'Coryphaena')) } worrms/man/worrms-package.Rd0000644000177500001440000000134413033053344016107 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/worrms-package.R \docType{package} \name{worrms-package} \alias{worrms} \alias{worrms-package} \title{World Register of Marine Species Client} \description{ World Register of Marine Species Client } \section{Fail behavior}{ The WoRMS REST API doesn't have sophisticated error messaging, so most errors will result in a \code{(204) - No Content} or in \code{(400) - Bad Request} Because WoRMS doesn't do comprehensive error reporting, we do a fair amount of checking user inputs to help prevent errors that will be meaningless to the user. Let us know if we can improve on this. } \author{ Scott Chamberlain \email{myrmecocystus@gmail.com} } \keyword{package} worrms/man/wm_children.Rd0000644000177500001440000000120613033062570015456 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_children.R \name{wm_children} \alias{wm_children} \title{Get children for an AphiaID} \usage{ wm_children(id, marine_only = TRUE, offset = 1, ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{marine_only}{(logical) marine only or not. default: \code{TRUE}} \item{offset}{(integer) record to start at. default: 1} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get children for an AphiaID } \examples{ wm_children(id = 105706) wm_children(id = 105706, FALSE) wm_children(id = 105706, offset = 5) } worrms/man/wm_sources.Rd0000644000177500001440000000063113033062570015352 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_sources.R \name{wm_sources} \alias{wm_sources} \title{Get sources for an AphiaID} \usage{ wm_sources(id, ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get sources for an AphiaID } \examples{ wm_sources(id = 105706) } worrms/man/wm_distribution.Rd0000644000177500001440000000065413033062570016413 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_distribution.R \name{wm_distribution} \alias{wm_distribution} \title{Get distribution data by AphiaID} \usage{ wm_distribution(id, ...) } \arguments{ \item{id}{an AphiaID. required.} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get distribution data by AphiaID } \examples{ wm_distribution(id = 156806) } worrms/man/wm_record.Rd0000644000177500001440000000065613033062570015154 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_record.R \name{wm_record} \alias{wm_record} \title{Get complete AphiaRecord for an AphiaID} \usage{ wm_record(id, ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get complete AphiaRecord for an AphiaID } \examples{ wm_record(id = 105706) } worrms/man/wm_records_name.Rd0000644000177500001440000000174113027316601016333 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_records_name.R \name{wm_records_name} \alias{wm_records_name} \title{Get records by single name, optional fuzzy matching} \usage{ wm_records_name(name, fuzzy = TRUE, marine_only = TRUE, offset = 1, ...) } \arguments{ \item{name}{(character) start date. required.} \item{fuzzy}{(logical) fuzzy search. default: \code{TRUE}} \item{marine_only}{(logical) marine only or not. default: \code{TRUE}} \item{offset}{(integer) record to start at. default: 1} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get records by single name, optional fuzzy matching } \examples{ wm_records_name(name = 'Platanista gangetica') wm_records_name(name = 'Platanista gangetica', fuzzy = FALSE) wm_records_name(name = 'Platanista gangetica', marine_only = FALSE) wm_records_name(name = 'Platanista', marine_only = FALSE) wm_records_name(name = 'Platanista', marine_only = FALSE, offset = 5) } worrms/man/wm_records_taxamatch.Rd0000644000177500001440000000141213036235542017364 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_records_taxamatch.R \name{wm_records_taxamatch} \alias{wm_records_taxamatch} \title{Get records for onen or more taxonomic name(s) using the TAXAMATCH fuzzy matching algorithm} \usage{ wm_records_taxamatch(name, marine_only = TRUE, ...) } \arguments{ \item{name}{(character) taxon name. required.} \item{marine_only}{(logical) marine only or not. default: \code{TRUE}} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get records for onen or more taxonomic name(s) using the TAXAMATCH fuzzy matching algorithm } \examples{ \dontrun{ wm_records_taxamatch(name = 'Platanista gangetica') wm_records_taxamatch(name = c('Platanista gangetica', 'Coryphaena')) } } worrms/man/wm_name2id.Rd0000644000177500001440000000064313027313464015215 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_name2id.R \name{wm_name2id} \alias{wm_name2id} \title{Get AphiaID from a taxonomic name} \usage{ wm_name2id(name, ...) } \arguments{ \item{name}{(character) a taxon name} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get AphiaID from a taxonomic name } \examples{ wm_name2id(name = "Rhincodon") } worrms/man/wm_common_id.Rd0000644000177500001440000000075313033062570015640 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_common_id.R \name{wm_common_id} \alias{wm_common_id} \title{Get vernacular names from an AphiaID} \usage{ wm_common_id(id, ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get vernacular names from an AphiaID } \examples{ wm_common_id(id = 105706) wm_common_id(id = 156806) wm_common_id(id = 397065) } worrms/man/wm_record_by_external.Rd0000644000177500001440000000120113033062570017533 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_record_by_external.R \name{wm_record_by_external} \alias{wm_record_by_external} \title{Get record by external ID} \usage{ wm_record_by_external(id, type = "tsn", ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{type}{(character) the type of external id. one of: tsn, bold, dyntaxa, eol, fishbase, iucn, lsid, ncbi, gisd. default: tsn} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get record by external ID } \examples{ wm_record_by_external(id = 85257) wm_record_by_external(id = 159854) } worrms/man/wm_records_date.Rd0000644000177500001440000000132013033052225016315 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_records_date.R \name{wm_records_date} \alias{wm_records_date} \title{Get records by date} \usage{ wm_records_date(start_date, end_date = NULL, marine_only = TRUE, offset = 1, ...) } \arguments{ \item{start_date}{(character) start date. required.} \item{end_date}{(character) end date. optional} \item{marine_only}{(logical) marine only or not. default: \code{TRUE}} \item{offset}{(integer) record to start at. default: 1} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get records by date } \examples{ a_date <- format(Sys.Date() - 1, "\%Y-\%m-\%dT\%H:\%M:\%S+00:00") wm_records_date(a_date) } worrms/man/wm_synonyms.Rd0000644000177500001440000000064013033062570015566 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_synonyms.R \name{wm_synonyms} \alias{wm_synonyms} \title{Get synonyms for an AphiaID} \usage{ wm_synonyms(id, ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get synonyms for an AphiaID } \examples{ wm_synonyms(id = 105706) } worrms/man/wm_classification.Rd0000644000177500001440000000075113035240322016660 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_classification.R \name{wm_classification} \alias{wm_classification} \title{Get classification for an AphiaID} \usage{ wm_classification(id, ...) } \arguments{ \item{id}{(numeric/integer) an AphiaID. required.} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get classification for an AphiaID } \examples{ wm_classification(id = 105706) wm_classification(id = 126436) } worrms/man/wm_records_common.Rd0000644000177500001440000000146013036235253016704 0ustar deepayanusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/wm_records_common.R \name{wm_records_common} \alias{wm_records_common} \title{Get records by vernacular name, optional fuzzy matching} \usage{ wm_records_common(name, fuzzy = FALSE, offset = 1, ...) } \arguments{ \item{name}{(character) a species common name. required.} \item{fuzzy}{(logical) fuzzy search. default: \code{FALSE}} \item{offset}{(integer) record to start at. default: 1} \item{...}{named curl options. see \code{\link[curl]{curl_options}}} } \description{ Get records by vernacular name, optional fuzzy matching } \examples{ wm_records_common(name = 'dolphin') wm_records_common(name = 'clam') \dontrun{ wm_records_common(name = 'dolphin', fuzzy = TRUE) wm_records_common(name = 'clam', fuzzy = TRUE, offset = 5) } } worrms/LICENSE0000644000177500001440000000005713033053405013126 0ustar deepayanusersYEAR: 2017 COPYRIGHT HOLDER: Scott Chamberlain