'spocc' - species name not matching when using "idigbio"

justropp · June 30, 2016, 2:19pm

I’m trying to retrieve species occurrence using the R package spocc. When I include from = 'idigbio' the species name that are returned do not match the species name that I submitted. Here is an example using only three species:

Retrieving data from gbif, bison, and ecoengine with the occ function

spnames<-c('Lindsaea lancea', 'Adiantum tomentosum', 'Trichomanes elegans')

df <- occ(query = spnames, from = c('gbif', 'bison', 'ecoengine'),
          gbifopts = list(limit = 100, hasCoordinate=TRUE, basisOfRecord = 'PRESERVED_SPECIMEN', hasGeospatialIssue = FALSE), 
          ecoengineopts = list(limit = 100, basisofRecord = 'specimen'),
          bisonopts = list(limit = 100, basisOfRecord = 'specimen'),
          geometry = c(-81,-22,-40,10)) 

out<-occ2df(df)
unique(out$name)
> unique(out$name)
[1] "Lindsaea lancea"     "Adiantum tomentosum" "Trichomanes elegans"

Retrieving data from idigbio with occ

df1 <- occ(query = spnames, from = 'idigbio',
           idigbioopts = list(limit = 100, basisOfRecord = 'specimen'),
          geometry = c(-81,-22,-40,10))  # This returns 100 different names (not synonyms)

Retrieving data from idigbio with idig_search_records (package ridigbio)

ff<-idig_search_records(rq=list(scientificname=spnames), limit=100)
unique(ff$scientificname)

[1] "lindsaea lancea"     "adiantum tomentosum" "trichomanes elegans"

Any idea why occ is not returning the correct species when searching idigbio?

Many thanks!

sckott · July 1, 2016, 4:18am

Thanks for your question!

Can you paste in the output of devtools::session_info() or sessionInfo() so I can see what package versions you have, thanks!

justropp · July 1, 2016, 7:58am

Hi Scott,

Thank you for looking at it. Here is the output of devtools::session_info()

Cheers,

devtools::session_info()
Session info --------------------------------------------------------------------------------------------------------------
setting value
version R version 3.2.3 (2015-12-10)
system x86_64, mingw32
ui RStudio (0.99.892)
language (EN)
collate English_United States.1252
tz Europe/Berlin
date 2016-07-01

Packages ------------------------------------------------------------------------------------------------------------------
package * version date source
assertthat 0.1 2013-12-06 CRAN (R 3.2.4)
brew 1.0-6 2011-04-13 CRAN (R 3.2.3)
chron 2.3-47 2015-06-24 CRAN (R 3.2.4)
colorspace 1.2-6 2015-03-11 CRAN (R 3.2.4)
curl 0.9.7 2016-04-10 CRAN (R 3.2.5)
data.table 1.9.6 2015-09-19 CRAN (R 3.2.5)
DBI 0.4-1 2016-05-08 CRAN (R 3.2.5)
devtools 1.10.0 2016-01-23 CRAN (R 3.2.4)
digest 0.6.9 2016-01-08 CRAN (R 3.2.4)
dplyr 0.5.0 2016-06-24 CRAN (R 3.2.5)
fields 8.4-1 2016-05-05 CRAN (R 3.2.5)
foreign 0.8-66 2015-08-19 CRAN (R 3.2.3)
geoaxe 0.1.0 2016-02-19 CRAN (R 3.2.5)
geosphere 1.5-1 2015-12-18 CRAN (R 3.2.4)
ggmap 2.6.1 2016-01-23 CRAN (R 3.2.5)
ggplot2 * 2.1.0 2016-03-01 CRAN (R 3.2.4)
gistr 0.3.6 2015-12-22 CRAN (R 3.2.5)
gtable 0.2.0 2016-02-26 CRAN (R 3.2.4)
htmltools 0.3.5 2016-03-21 CRAN (R 3.2.5)
httr 1.2.0 2016-06-15 CRAN (R 3.2.5)
jpeg 0.1-8 2014-01-23 CRAN (R 3.2.3)
jsonlite 0.9.22 2016-06-15 CRAN (R 3.2.5)
knitr 1.13 2016-05-09 CRAN (R 3.2.5)
labeling 0.3 2014-08-23 CRAN (R 3.2.3)
lattice 0.20-33 2015-07-14 CRAN (R 3.2.3)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.2.5)
leafletR 0.4-0 2016-04-01 CRAN (R 3.2.5)
lubridate 1.5.6 2016-04-06 CRAN (R 3.2.5)
magrittr 1.5 2014-11-22 CRAN (R 3.2.4)
mapproj 1.2-4 2015-08-03 CRAN (R 3.2.5)
maps * 3.1.0 2016-02-13 CRAN (R 3.2.4)
maptools 0.8-39 2016-01-30 CRAN (R 3.2.5)
memoise 1.0.0 2016-01-29 CRAN (R 3.2.4)
munsell 0.4.3 2016-02-13 CRAN (R 3.2.4)
oai 0.2.0 2016-02-06 CRAN (R 3.2.4)
plyr 1.8.3 2015-06-12 CRAN (R 3.2.5)
png 0.1-7 2013-12-03 CRAN (R 3.2.3)
proto 0.3-10 2012-12-22 CRAN (R 3.2.3)
R6 2.1.2 2016-01-26 CRAN (R 3.2.4)
rbison 0.4.8 2015-07-02 CRAN (R 3.2.5)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.2.3)
Rcpp 0.12.5 2016-05-14 CRAN (R 3.2.5)
rebird 0.3.0 2016-03-23 CRAN (R 3.2.5)
reshape2 1.4.1 2014-12-06 CRAN (R 3.2.4)
rgbif 0.9.3 2016-03-29 CRAN (R 3.2.5)
rgeos 0.3-19 2016-04-04 CRAN (R 3.2.5)
RgoogleMaps 1.2.0.7 2015-01-21 CRAN (R 3.2.5)
ridigbio * 0.3.3 2016-01-12 CRAN (R 3.2.5)
rjson 0.2.15 2014-11-03 CRAN (R 3.2.3)
RJSONIO 1.3-0 2014-07-28 CRAN (R 3.2.3)
rmarkdown 0.9.6 2016-05-01 CRAN (R 3.2.5)
rvertnet 0.4.4 2016-04-14 CRAN (R 3.2.5)
rworldmap 1.3-6 2016-02-03 CRAN (R 3.2.5)
scales 0.4.0 2016-02-26 CRAN (R 3.2.4)
sp 1.2-3 2016-04-14 CRAN (R 3.2.5)
spam 1.3-0 2015-10-29 CRAN (R 3.2.5)
spocc * 0.5.0 2016-04-23 CRAN (R 3.2.5)
spoccutils * 0.1.0 2015-07-07 CRAN (R 3.2.5)
stringi 1.1.1 2016-05-27 CRAN (R 3.2.5)
stringr 1.0.0 2015-04-30 CRAN (R 3.2.4)
tibble 1.0 2016-03-23 CRAN (R 3.2.5)
V8 1.0.3 2016-06-28 CRAN (R 3.2.5)
whisker 0.3-2 2013-04-28 CRAN (R 3.2.4)
xml2 1.0.0 2016-06-24 CRAN (R 3.2.5)

sckott · July 1, 2016, 4:34pm

@justropp

Reinstall from github devtools::install_github("ropensci/spocc") - it should work now - there was a wee bug in the idigbio internal function - but is fixed now, let me know if it works for you after reinstall

justropp · July 1, 2016, 10:04pm

Great! Yes, it is working after reinstalling.

sckott · July 1, 2016, 10:11pm

good, glad to hear it’s working