bioatlas / dyntaxa Goto Github PK

Provide record-level classification for taxon records, ie populate fields for "species", "genus" etc for other valid ranks.

I have not previously used or installed the dyntaxa package, but when I now try to install the package today following the instructions on the github pages, the installation fails. I'm running Windows 10 and R 4.0.2. Below is the messages I receive from R during installation. It seems to be some sort of parsing issue? Known issue and can it be solved?
Regards// Peter Hellström, Swedish Museum of Natural History

library(devtools)
Loading required package: usethis
install_github("bioatlas/dyntaxa", build_opts = c("--no-resave-data", "--no-manual"))
Downloading GitHub repo bioatlas/dyntaxa@HEAD

checking for file 'C:\Users\petehell\AppData\Local\Temp\RtmpcfqMJq\remotesab86c356661\bioatlas-dyntaxa-f486779/DESCRIPTION' ...

√ checking for file 'C:\Users\petehell\AppData\Local\Temp\RtmpcfqMJq\remotesab86c356661\bioatlas-dyntaxa-f486779/DESCRIPTION' (438ms)

• preparing 'dyntaxa':
  checking DESCRIPTION meta-information ...

  checking DESCRIPTION meta-information ...

√ checking DESCRIPTION meta-information

• checking for LF line-endings in source and make files and shell scripts

• checking for empty or unneeded directories

• building 'dyntaxa_0.1.tar.gz'

'\moria\users\petehell'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.

• installing source package 'dyntaxa' ...
  ** using staged installation
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  converting help for package 'dyntaxa'
  finding HTML links ... done
  dyntaxa-package html
  dyntaxa_children html
  dyntaxa_classification html
  dyntaxa_downstream html
  dyntaxa_dwca html
  dyntaxa_export html
  dyntaxa_id_from_name html
  dyntaxa_init html
  dyntaxa_links html
  dyntaxa_name_from_id html
  dyntaxa_rank_from_id html
  dyntaxa_redlist html
  dyntaxa_resolve html
  dyntaxa_search_all html
  dyntaxa_search_id html
  dyntaxa_search_name html
  dyntaxa_search_vernacular html
  dyntaxa_synonyms html
  pipe html
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  *** arch - i386
  Warning in dwca_parse_dyntaxa(file) :
  Found parsing issues in C:\Users\petehell\AppData\Local\dyntaxa\dyntaxa/dyntaxa.zip, details are in result$parsing_issues

Storing dyntaxa graph relations inC:\Users\petehell\AppData\Local\dyntaxa\dyntaxa/dyntaxa.rds
Error: package or namespace load failed for 'dyntaxa':
.onAttach failed in attachNamespace() for 'dyntaxa', details:
call: graph_from_data_frame(d = e, vertices = v, directed = TRUE)
error: Some vertex names in edge list are not listed in vertex data frame
Error: loading failed
Execution halted
*** arch - x64
Warning in dwca_parse_dyntaxa(file) :
Found parsing issues in C:\Users\petehell\AppData\Local\dyntaxa\dyntaxa/dyntaxa.zip, details are in result$parsing_issues

Storing dyntaxa graph relations inC:\Users\petehell\AppData\Local\dyntaxa\dyntaxa/dyntaxa.rds
Error: package or namespace load failed for 'dyntaxa':
.onAttach failed in attachNamespace() for 'dyntaxa', details:
call: graph_from_data_frame(d = e, vertices = v, directed = TRUE)
error: Some vertex names in edge list are not listed in vertex data frame
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'

• removing 'C:/Program Files/R/R-4.0.2/library/dyntaxa'
  Error: Failed to install 'dyntaxa' from GitHub:
  (converted from warning) installation of package ‘C:/Users/petehell/AppData/Local/Temp/RtmpcfqMJq/fileab8142734eb/dyntaxa_0.1.tar.gz’ had non-zero exit status

• set up data flow so that Dyntaxa is being published from our shared instance of IPT currently at http://www.gbif.se/ipt/ rather than directly from https://api.artdatabanken.se/taxonservice/v1/DarwinCore/DarwinCoreArchiveFile?Subscription-Key=4b068709e7f2427d9fc76bf42d8e2b57

• have metadata curation happen at the IPT instance

Background: Debora mentions biotopes and substrates - available for Alces alces from http://artfakta.artdatabanken.se/taxon/206046 in the Ecology box

Could or should this info be added to the checklist export of Dyntaxa?

If so, what terms should/would be used?

The species profile extension to the taxon core has "habitat" as a term.

But is there a good term to use for substrate? Or would it have to go into dynamicProperties? Is there a better way to include this info? Using the Description extension with fields "description" and "type" for a comma separated list of substrates and "substrate"? similar to the exemplar taxon checklist at Canadian Vascular Plants available to inspect at http://data.canadensys.net/ipt/archive.do?r=vascan.

Here is a naive first approach to try to map values into the nomenclaturalStatus term:

https://github.com/bioatlas/dyntaxa/blob/master/R/dyntaxa.R#L53-L68

Can such a mapping be used in the Dyntaxa dataset?

A taxon information page at for example https://www.dyntaxa.se/Taxon/Info/223657?changeRoot=True includes data for establishment means and reproductive conditions as well as the threat status for the taxon.

This data is part of Dyntaxa according to the About text at https://www.slu.se/dyntaxa/ which writes that the Dyntaxa data includes this information. This is not included in the darwin core archive export, though.

Perhaps some of this data could be mapped to the Distribution extension - https://tools.gbif.org/dwca-validator/extension.do?id=gbif:Distribution - for establishmentMeans and threatStatus?

Perhaps (parts of?) the data that is labelled "svensk förekomst" could be mapped to http://rs.tdwg.org/dwc/terms/#dwc:reproductiveCondition?

Review and resolve if there are comments in the author field. For example, for recordid 238715 scientificNameAuthorship should only contain “A. Braun, 1855”.

Review and resolve duplicates or errors such as

• Hirudinida rank should be changed to subclass, resolving most of the conflicting cases.
• Urodiaspididae should clearly be a family.
• Salpida should be a suborder.
• Myxozoa should be a subclass.

Validation of the latest Dyntaxa dataset raises some complaints and warnings. Here is the full report:

first please read the gbif validation report here: https://www.gbif.org/tools/data-validator/1556043575857
|==========================================================================================| 100%   35 MB
check if dyntaxa dwca file has parsing issues: FALSE
check that all files are present in dwca: TRUE
vocab for establishmentMeans is ok: TRUE
vocab for occurrenceStatus is ok: TRUE
vocab for threatStatus is ok: FALSE
correct these threatStatus values: EN°, LC°, NT°, VU°
vernacular ext, term source is valid:FALSE
please use valid http link to source web page in vernacular ext
check references ext for valid dates: FALSE
invalid date values in use are: 0
check for valid nomenclaturalStatus values: FALSE
invalid values used for nomenclaturalStatus are: Correct, Incorrect citation, Incorrect (other), Informal, Misspelled, Observation system name, Occupied/unneccessary, Preliminary suggestion, Provisional, Suppressed, Undescribed, Unpublished
please use either of these values for nomenclaturalStatus: abortivum, alternativum, ambigua, available, combinatio, confusum, conservandum, conservandumProp, correctum, dubium, illegitimum, invalidum, legitimate, negatum, novum, nudum, nullum, oblitum, oppressa, orthographia, protectum, provisorium, rejiciendum, rejiciendumProp, rejiciendumUtique, rejiciendumUtiqueProp, subnudum, superfluum, valid
forest or tree? should unrooted kingdom nodes have a Biota parent?

Have been looking for a functioning API for the dyntaxa database, and this package seems to fill this gap. Two questions though:

(1) A quick browse through the R-code indicates that the package uses a static local copy of the dyntaxa database. I was looking for an API call, but did only find request to files included in the package. Is that correct?

(2) If the package uses a local copy - how is the update cycle of the information in dyntaxa managed? Are you keeping versions in sync with Artportalen? Or is updates not addressed yet?