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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.

63 questions
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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-missing values... value = "!null" didn't work…
dca
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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 surprised by the size of the data it generates.…
retrography
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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 segments from my data: data = structure(list(osm_id…
Ashley Asmus
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Halting drake plan makes it rebuild targets it already had built previously

I'm currently using drake to run a set of >1k simulations. I've estimated that it would take about two days to run the complete set, but I also expect my computer to crash at any point during that period because, well, it has. Apparently stopping…
overdisperse
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how to index data using index_create() in elastic package in R

This is my code in R to index iris data. library(elastic) iris<-datasets::iris body <- list(data = list(iris)) index_create(index = 'iris',body = body) but it gives the following error. Error: 400 - Failed to parse content to map. Please explain…
Farid ullah
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automate input to user query in R

I apologize if this question has been asked with terminology I don't recognize but it doesn't appear to be. I am using the function comm2sci in the library taxize to search for the scientific names for a database of over 120,000 rows of common…
E Lundgren
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R can't connect to Spigot server using ropenscilabs miner package

I would like to try out the miner Minecraft API from ROpenSci and am having trouble connecting to the server from R. I am sure this is a networking issue rather than a R or Minecraft issue but I don't really have any experience in this area. I have…
G_T
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How to download NY state all County data in R for leaflet map

# From http://eric.clst.org/Stuff/USGeoJSON and # https://en.wikipedia.org/wiki/List_of_United_States_counties_and_county_equivalents nycounties <- geojsonio::geojson_read("json/nycounties.geojson", what = "sp") # Or use the rgdal equivalent: #…
Bin
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Parsing XML file in R using rentrez

I am not an XML expert. I am having an issue when parsing XML file using rentrez. I am trying to have author and affiliation by each pmid (article id in PubMed database) as an output. I have code that works well except when author has multiple…
Santosh M.
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PubMed XML parsing using entrez_fetch in rentrez

I am collecting author's information and article information for a search term in PubMed. I am getting author name, publication year and other information successfully using entrez_fetch in rentrez package. Following is my example…
Santosh M.
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How to obtain files included in initial commit using git2r (libgit2)?

I am using the R package git2r to interface with libgit2. I would like to obtain the list of files that were updated in each commit, similar to the output from git log --stat or git log --name-only. However, I am unable to obtain the files that were…
John Blischak
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Convert data to geojson error

I am trying to use the geojsonio package to write some geojson files from data.frames pulled from some other R packages. library(ggplot2) library(geojsonio) us_state <- map_data('state') geojson_write(us_state, geometry="polygon", …
moman822
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R: rgdal writing GeoJSON

I'm having a problem with rgdal which drops the projection information when writing geoJSON files. library(rgdal) inputJSON<- readOGR("test.geojson", "OGRGeoJSON") # works! If i type summary(inputJSON) i get the following output: Object of class…
Deset
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How do I load my api key into rnoaa using R?

I am new to r and trying to load my api token to get access to the rnoaa package. I have the API token I just don't know how to access it. Can anyone explain how to load my API key into rnoaa using R? Thanks!
kellis13
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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 and suggest other ways to get altmetric…
iGada
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