I'd like to integrate the name alignment tool into my R script

[jhpoelen]

I used R to do analysis and have to align names as part of it.

Currently, my workflow is semi-automated.

First, I get some names through R (e.g., download the entire GloBI dataset, do filtering on names (e.g., replacement etc) to compile a list of names to be aligned).

Then I load a csv file into the name alignment tool

then, I take the results and copy them into my R script.

Desired:

I'd like to figure out way to make it easier to "call" the name alignment tool automatically from R, without any manual steps.

[jhpoelen]

@seltmann suggests the install nomer tool locally and call it from R using some kind of helper script. I know I can call command-line from R. I don't know much about how to do that.

@jhpoelen (via Brave search engine with "command line from R" ), found a possible starting point at https://stat.ethz.ch/R-manual/R-devel/library/base/html/system.html .

[jhpoelen]

@seltmann suggests to come up with one example of how to call Nomer from R.

[jhpoelen]

@jhpoelen ask: Perhaps use https://github.com/cboettig/taxalight or https://github.com/cboettig/taxadb .

Also, a Nomer wrapper for python - https://github.com/nleguillarme/pynomer . might inspire ideas for for creating an R wrapper for Nomer.