Questions tagged [ropensci]
R packages created by the organization R Open Science (rOpenSci for short) that interact with scientific data repositories, journals, and providers of scientific metrics.
ropensci
64
questions
1
vote
1
answer
146
views
Targets does not recognize other targets inside `values` of `tar_map()`
I want to use another target to generate the values for tar_map(), this is to avoid end users to edit the code and just editing the config file. I tried this:
library(targets)
tar_script({
library(...
- 775
1
vote
2
answers
164
views
Targets dynamic branching to add columns to matrix
I have multiple rasters in a R targets pipeline that I load with tar_files() and then iterate over it in the next target to add one column per file to a matrix. However, only the first column is ...
- 775
0
votes
1
answer
93
views
Why rAltmetric package is removed from CRAN?
I want to fetch the altmetric score of articles using altmetrics() function from the R package rAltmetric. However, it seems that the package has been removed from CRAN. Does anyone knows the reason ...
- 623
1
vote
1
answer
153
views
Fetching altmetric data using R
Why the following code repeatedly gives me an error?
library(rcrossref)
library(rAltmetric)
alt <- altmetrics(doi = '10.1111/j.1475-2743.2006.00029.x')
Error: lexical error: invalid char in json ...
- 623
1
vote
1
answer
574
views
Is there a faster way to find synonyms for a large list of taxa in R?
I have a list of about ~96,000 species names I need to collect all synonyms for. I have tried the 'taxize' package with the synonyms() function, which outputs the information I need but my list is too ...
- 21
3
votes
1
answer
197
views
How can I add timestamp in osmdata_sf() results?
When I query osm data, I want to receive the timestamp, when some object was added or changed, is it possible to include this data?
There is my query:
q <- opq("London",timeout = 20000) %&...
- 31
1
vote
1
answer
100
views
Unable to install the package rmetadata in R
My primary goal is to extract metadata of an article using the title and journal name. To do so, rmetadata package is useful according to the blog https://ropensci.org/blog/2013/03/15/r-metadata/. ...
- 623
3
votes
3
answers
862
views
Convert scanned PDF to searcheable PDF (in R)
I'm trying to convert a series of scanned PDF into searchable PDF using the tesseract and pdftools packages. I've accomplished two steps. Now I need to write back to a searchable pdf.
Read scanned ...
- 1,421
2
votes
2
answers
750
views
How to use rgbif to download occurrence data from multiple polygons at once?
I am trying to download occurrence data of multiple taxonomic groups from multiple regions using the R package rgbif. I prefer to have one download by combining all the regions together (because I ...
- 697
0
votes
2
answers
605
views
Downloading NOAA data
I'm trying to download NOAA data using the rnoaa package and I'm running into a bit of trouble.
I took a vector from a dataframe and it looks like this:
df <- dataframe$ghcnd
Grabbing necessary ...
- 58
0
votes
1
answer
143
views
Is there some way to change the characters encoding to its English equivalent IN R?
In R
I am extracting data from Pdf tables using Tabulizer library and the Name are on Nepali language
and after extracting i Get this Table
[1]: https://i.sstatic.net/Ltpqv.png
But now i want that ...
- 19
4
votes
2
answers
2k
views
Is there any R function to extract all taxonomy name (phylum, class, order, family ...) from species taxonomic ID/ species name or genus name?
I have the taxonomic ID of species and I can get the species and genus name from NCBI (https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi). But I want phylum, class, order.. all ...
- 61
1
vote
1
answer
180
views
Return only non-missing values from osm search
I'm trying to just get non-na values returned from osmdata. For example, take email address. However, the below returns mostly missing emails. How can I set up the query so that it returns only non-...
- 642
1
vote
1
answer
180
views
Why does textreuse packge in R make LSH buckets way larger than the original minhashes?
As far as I understand one of the main functions of the LSH method is data reduction even beyond the underlying hashes (often minhashes). I have been using the textreuse package in R, and I am ...
- 6,632
1
vote
2
answers
2k
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Extract count of intersections for Open Street Map way IDs, by route type
Edited with additional details added
I have a shapefile of 2,061 Open Street Map (OSM) road segments. Each segment in my shapefile is is identified by its OSM Way ID.
Here is an example of five ...
- 67