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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.

We develop open source R packages that provide programmatic access to a variety of scientific data, full-text of journal articles, and repositories that provide real-time metrics of scholarly impact. Visit our packages section for a full list of production and development versions of packages.

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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 long for it to work properly. I have looked into…
mfertakos
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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/. However, I'm unable to install the package using the…
iGada
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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 column This gives me an output like: [1]…
Tobin Brooks
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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.stack.imgur.com/Ltpqv.png But now i want that column 2's name To change, in its English…
Rustam
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'qualtRics' R package API call returns "port 443: Connection refused". What am I missing?

Good afternoon! I'm a self-taught R developer so I might not be using the correct jargon, but please bear with me. I have written a script to clean and process data which has been manually exported from Qualtrics, however I would like to further…
TMac88
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Customizing {drake} plan with {data.table}

My goal is to customize {drake} plan to reduce duplication of codes for both simple and complex cases, for example, setting drake::trigger for multiple targets based on specific conditions of the plans (ie programmatically identify the targets to be…
kar9222
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How to create a plan target to cross over the results of previous map targets and a new variable?

From multiple target (a) created with map I have 2 other targets (b and d) that iterate over the first target. Now I would like to use the results of these targets in another target. In addition I would like to cross with another variable (model). I…
Jean
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Wait for rgbif download to complete before proceeding

I am developing a small application in R Shiny. Part of the application will need to query GBIF to download species occurrence data. This is possible using rgbif. The function rgbif::occ_download() will download the data and…
Simon
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Passing a variable in a solr auery

I'm working with solr using r library solrium After the connection to solr in the variable conn1, I make queries like this: solr_search(conn1,"collection_name", params = list(q = "price:1000",start = 0, rows = 20000,fl=c('column_name'))) But…
Khalid Askia
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linking functions with purrr and referencing nested variables

I'm scraping data from a large online database (GBIF), which requires three steps: (1) match a GBIF "key" identifier to a species name, (2) send a query to the database, getting a download key ("res") in return, and (3) download, import, and filter…
AFH
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Error using elastic on linux server but no error on windows

When I execute elastic::Search(index=index,body=body,size=1000,scroll="3m") on a linux server I receive the following error. invalid char in json text.
Jensxy
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Elastic with_position_offsets

I get an error when I execute the following body in elastic in R. {"stored_fields": ["CONTENT.LENGTH"], "_source":["DOC_ID", "DELIVERY_ID", "SRC_SYSTEM", "CONVERS_ID", "CONTRIB_ID", "CONTRIB_TYPE", "PRTCPNT_ID", "CONTRIB_TS",…
Jensxy
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Create, validate and compare data schema (for data harvest) in ckanr

This is a data harvest exercise. The code below ingests data as JSON. I would like to (a) print/extract the data schema from this data into Schema1. Then (b) compare it against some Schema2, because I need to change some metadata header names and…
Susie
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Memory Issues using rnoaa package

Working with rnoaa package to take add US station IDs to a df of weather events. Below is str() for the rain df. google drive link to csv file of subset 'data.frame': 4395 obs. of 63 variables: $ YEAR : int 2009 2009 2012 2013…
Francisco
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Mixing R and LaTeX code in an Rnw file

I'm trying to italicise a scientific name when converting a .Rnw file to a .tex file using knitr. I'm getting an error when running knit. This is my code contained within my .Rnw file (needs taxize and stringr libraries to run): Excepteur sint…
luciano
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