inst/notebook/codemeta-parsing.md
In codemeta/codemetar: Generate 'CodeMeta' Metadata for R Packages
Parsing codemeta data
NB: sources moved to vignettes
library(jsonld)
library(jsonlite)
library(magrittr)
library(codemetar)
library(tidyverse)
library(printr)
write_codemeta("codemetar", "codemeta.json")
Digest input with a frame:
frame <- system.file("schema/frame_schema.json", package="codemetar")
meta <-
jsonld_frame("codemeta.json", frame) %>%
fromJSON(FALSE) %>% getElement("@graph") %>% getElement(1)
Construct a citation
authors <-
lapply(meta$author,
function(author)
person(given = author$given,
family = author$family,
email = author$email,
role = "aut"))
year <- meta$datePublished
if(is.null(year))
year <- format(Sys.Date(), "%Y")
bibitem <-
bibentry(
bibtype = "Manual",
title = meta$name,
author = authors,
year = year,
note = paste0("R package version ", meta$version),
url = meta$URL,
key = meta$identifier
)
cat(format(bibitem, "bibtex"))
## @Manual{codemetar,
## title = {codemetar: Generate CodeMeta Metadata for R Packages},
## author = {Carl Boettiger},
## year = {2017},
## note = {R package version 0.1.0},
## }
bibitem
## Boettiger C (2017). _codemetar: Generate CodeMeta Metadata for R
## Packages_. R package version 0.1.0.
Parsing the ropensci corpus
Frame, expanding any referenced nodes
corpus <-
jsonld_frame("ropensci.json", frame) %>%
fromJSON(simplifyVector = FALSE) %>%
getElement("@graph")
Some basics:
## deal with nulls explicitly by starting with map
pkgs <- map(corpus, "name") %>% compact() %>% as.character()
# keep only those with package identifiers (names)
keep <- map_lgl(corpus, ~ length(.x$identifier) > 0)
corpus <- corpus[keep]
## now we can just do
all_pkgs <- map_chr(corpus, "name")
head(all_pkgs)
## [1] "AntWeb: programmatic interface to the AntWeb"
## [2] "aRxiv: Interface to the arXiv API"
## [3] "chromer: Interface to Chromosome Counts Database API"
## [4] "ckanr: Client for the Comprehensive Knowledge Archive Network ('CKAN') 'API'"
## [5] "dashboard: A package status dashboard"
## [6] "ggit: Git Graphics"
## 60 unique maintainers
map_chr(corpus, c("maintainer", "familyName")) %>% unique() %>% length()
## [1] 61
## Mostly Scott
map_chr(corpus, c("maintainer", "familyName")) %>%
as_tibble() %>%
group_by(value) %>%
tally(sort=TRUE)
| value | n|
|:-------------|----:|
| Chamberlain | 105|
| Ooms | 12|
| Mullen | 8|
| Ram | 8|
| Boettiger | 6|
| Salmon | 5|
| FitzJohn | 4|
| Hart | 2|
| Leeper | 2|
| Marwick | 2|
| Müller | 2|
| Padgham | 2|
| South | 2|
| Varela | 2|
| Vitolo | 2|
| Arnold | 1|
| Attali | 1|
| Banbury | 1|
| Becker | 1|
| Bengtsson | 1|
| Braginsky | 1|
| Broman | 1|
| Bryan | 1|
| Dallas | 1|
| de Queiroz | 1|
| Drost | 1|
| Fischetti | 1|
| Ghahraman | 1|
| Goring | 1|
| hackathoners | 1|
| Harrison | 1|
| Hughes | 1|
| Jahn | 1|
| Jones | 1|
| Keyes | 1|
| Krah | 1|
| Lehtomaki | 1|
| Lovelace | 1|
| Lundstrom | 1|
| McGlinn | 1|
| McVey | 1|
| Meissner | 1|
| Michonneau | 1|
| Moroz | 1|
| Otegui | 1|
| Pardo | 1|
| Pennell | 1|
| Poelen | 1|
| Robinson | 1|
| Ross | 1|
| Rowlingson | 1|
| Scott | 1|
| Seers | 1|
| Shotwell | 1|
| Sievert | 1|
| Sparks | 1|
| Stachelek | 1|
| Szöcs | 1|
| Widgren | 1|
| Wiggin | 1|
| Winter | 1|
## number of co-authors ...
map_int(corpus, function(r) length(r$author)) %>%
as_tibble() %>%
group_by(value) %>%
tally(sort=TRUE)
| value| n|
|------:|----:|
| 1| 146|
| 2| 30|
| 3| 17|
| 4| 8|
| 5| 5|
| 7| 3|
| 13| 1|
## Contributors isn't used as much...
map_int(corpus, function(r) length(r$contributor)) %>%
as_tibble() %>%
group_by(value) %>%
tally(sort=TRUE)
| value| n|
|------:|----:|
| 0| 178|
| 2| 13|
| 4| 9|
| 3| 7|
| 5| 1|
| 6| 1|
| 8| 1|
Numbers (n) of packages with a total of (value) dependencies:
map_int(corpus, function(r) length(r$softwareRequirements)) %>%
as_tibble() %>%
group_by(value) %>%
tally(sort=TRUE)
| value| n|
|------:|----:|
| 4| 39|
| 5| 35|
| 2| 25|
| 3| 25|
| 7| 19|
| 6| 16|
| 8| 13|
| 9| 8|
| 12| 7|
| 10| 6|
| 11| 6|
| 13| 3|
| 0| 2|
| 14| 1|
| 17| 1|
| 18| 1|
| 21| 1|
| 22| 1|
| 23| 1|
which dependencies are used most frequently?
corpus %>%
map_df(function(x){
## single, unboxed dep
if("name" %in% names(x$softwareRequirements))
dep <- x$name
else if("name" %in% names(x$softwareRequirements[[1]]))
dep <- map_chr(x$softwareRequirements, "name")
else { ## No requirementsß
dep <- NA
}
tibble(identifier = x$identifier, dep = dep)
}) -> dep_df
dep_df %>%
group_by(dep) %>%
tally(sort = TRUE)
| dep | n|
|:-----------------------------------------------------------------|----:|
| jsonlite | 99|
| httr | 92|
| R | 66|
| tibble | 46|
| dplyr | 43|
| methods | 37|
| xml2 | 37|
| data.table | 35|
| utils | 35|
| crul | 31|
| plyr | 29|
| XML | 25|
| magrittr | 24|
| sp | 22|
| stringr | 21|
| curl | 18|
| ggplot2 | 18|
| lazyeval | 17|
| stats | 17|
| lubridate | 14|
| R6 | 14|
| rappdirs | 13|
| assertthat | 12|
| digest | 12|
| RCurl | 12|
| readr | 11|
| rgdal | 10|
| whisker | 10|
| scales | 9|
| ape | 8|
| raster | 8|
| tidyr | 8|
| Rcpp | 7|
| reshape2 | 7|
| rvest | 7|
| rgeos | 6|
| V8 | 6|
| hoardr | 5|
| rjson | 5|
| taxize | 5|
| tools | 5|
| git2r | 4|
| maps | 4|
| oai | 4|
| openssl | 4|
| R(>=3.2.1) | 4|
| solrium | 4|
| urltools | 4|
| foreach | 3|
| knitr | 3|
| leaflet | 3|
| maptools | 3|
| memoise | 3|
| mime | 3|
| pdftools | 3|
| purrr | 3|
| RColorBrewer | 3|
| rgbif | 3|
| rmarkdown | 3|
| shiny | 3|
| spocc | 3|
| stringi | 3|
| uuid | 3|
| wicket | 3|
| yaml | 3|
| base64enc | 2|
| bibtex | 2|
| Biostrings | 2|
| crayon | 2|
| devtools | 2|
| downloader | 2|
| fauxpas | 2|
| gdata | 2|
| gistr | 2|
| graphics | 2|
| grid | 2|
| htmltools | 2|
| htmlwidgets | 2|
| httpcode | 2|
| igraph | 2|
| jqr | 2|
| MASS | 2|
| miniUI | 2|
| ncdf4 | 2|
| png | 2|
| R.cache | 2|
| R.utils | 2|
| rcrossref | 2|
| rentrez | 2|
| reshape | 2|
| rmapshaper | 2|
| rplos | 2|
| rvertnet | 2|
| shinyjs | 2|
| storr | 2|
| tm | 2|
| NA | 2|
| analogue | 1|
| antiword: Extract Text from Microsoft Word Documents | 1|
| apipkgen: Package Generator for HTTP API Wrapper Packages | 1|
| appl: Approximate POMDP Planning Software | 1|
| aRxiv | 1|
| binman | 1|
| Biobase | 1|
| BiocGenerics | 1|
| biomaRt | 1|
| bold | 1|
| caTools | 1|
| ckanr | 1|
| cld2: Google's Compact Language Detector 2 | 1|
| countrycode | 1|
| cranlogs | 1|
| crminer | 1|
| crosstalk | 1|
| DBI | 1|
| dirdf: Extracts Metadata from Directory and File Names | 1|
| doParallel | 1|
| DT(>=0.1) | 1|
| elastic | 1|
| EML | 1|
| fastmatch | 1|
| foreign | 1|
| functionMap | 1|
| genderdata: Historical Datasets for Predicting Gender from Names | 1|
| GenomeInfoDb | 1|
| GenomicFeatures | 1|
| GenomicRanges(>=1.23.24) | 1|
| geoaxe | 1|
| geojson | 1|
| geojsonrewind: Fix 'GeoJSON' Winding Direction | 1|
| geonames | 1|
| geoops: 'GeoJSON' Manipulation Operations | 1|
| geosphere | 1|
| getPass | 1|
| ggm | 1|
| ggmap | 1|
| ggthemes | 1|
| graphql | 1|
| grDevices | 1|
| gridExtra | 1|
| gtools | 1|
| hash | 1|
| hexbin | 1|
| historydata: Data Sets for Historians | 1|
| Hmisc | 1|
| httpuv | 1|
| IRanges | 1|
| isdparser | 1|
| jsonvalidate | 1|
| jsonvalidate: Validate 'JSON' | 1|
| leafletR | 1|
| loggr | 1|
| mapproj | 1|
| markdown | 1|
| Matrix | 1|
| memisc | 1|
| miniUI(>=0.1.1) | 1|
| nabor | 1|
| natserv | 1|
| openxlsx | 1|
| osmar | 1|
| outliers | 1|
| pdftools: Text Extraction and Rendering of PDF Documents | 1|
| phytools | 1|
| plotly | 1|
| plumber | 1|
| progress | 1|
| protolite | 1|
| qlcMatrix | 1|
| RApiSerialize | 1|
| rapport | 1|
| rbhl | 1|
| rbison | 1|
| rebird | 1|
| redland | 1|
| redux | 1|
| remotes | 1|
| ridigbio | 1|
| ritis | 1|
| rJava | 1|
| RJSONIO | 1|
| rlist | 1|
| Rmpfr | 1|
| RMySQL | 1|
| rncl | 1|
| rnoaa | 1|
| rnrfa | 1|
| rotl | 1|
| rowr | 1|
| RPostgreSQL | 1|
| rredis | 1|
| rredlist | 1|
| RSQLite | 1|
| rstudioapi(>=0.5) | 1|
| rtracklayer | 1|
| rworldmap | 1|
| rzmq: R Bindings for ZeroMQ | 1|
| S4Vectors | 1|
| scrapeR | 1|
| selectr | 1|
| sf | 1|
| shiny(>=0.13.2) | 1|
| snow | 1|
| SnowballC | 1|
| spatstat | 1|
| SSOAP | 1|
| stringdist | 1|
| sys | 1|
| tabulizerjars | 1|
| testthat | 1|
| tif: Text Interchange Format | 1|
| USAboundariesData: Datasets for the 'USAboundaries' package | 1|
| VariantAnnotation | 1|
| viridisLite | 1|
| wdman(>=0.2.2) | 1|
| wellknown | 1|
| wicket: Utilities to Handle WKT Spatial Data | 1|
| WikidataR | 1|
| wikitaxa | 1|
| withr | 1|
| worrms | 1|
| xslt: XSLT 1.0 Transformations | 1|
| zoo | 1|
Alternate approach using a frame, gets all Depends and suggests (really all SoftwareApplication types mentioned)
dep_frame <- '{
"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
"@explicit": "true",
"name": {}
}'
jsonld_frame("ropensci.json", dep_frame) %>%
fromJSON() %>%
getElement("@graph") %>%
filter(type == "SoftwareApplication") %>%
group_by(name) %>%
tally(sort = TRUE)
| name | n|
|:----------------------------|----:|
| testthat | 168|
| knitr | 122|
| jsonlite | 105|
| httr | 96|
| roxygen2 | 92|
| R | 72|
| rmarkdown | 68|
| covr | 52|
| dplyr | 49|
| tibble | 48|
| xml2 | 41|
| methods | 38|
| utils | 37|
| data.table | 36|
| ggplot2 | 36|
| crul | 33|
| plyr | 32|
| magrittr | 28|
| sp | 26|
| XML | 25|
| curl | 21|
| stringr | 21|
| lazyeval | 18|
| stats | 18|
| lubridate | 16|
| R6 | 14|
| readr | 14|
| rgdal | 14|
| rappdirs | 13|
| assertthat | 12|
| devtools | 12|
| digest | 12|
| raster | 12|
| RCurl | 12|
| scales | 12|
| Rcpp | 11|
| whisker | 11|
| leaflet | 10|
| rgeos | 10|
| taxize | 10|
| tidyr | 10|
| reshape2 | 9|
| ape | 8|
| maps | 8|
| V8 | 8|
| maptools | 7|
| purrr | 7|
| rvest | 7|
| pdftools | 6|
| rgbif | 6|
| shiny | 6|
| ggmap | 5|
| git2r | 5|
| hoardr | 5|
| ncdf4 | 5|
| png | 5|
| rjson | 5|
| tools | 5|
| oai | 4|
| openssl | 4|
| R(>=3.2.1) | 4|
| rcrossref | 4|
| RSQLite | 4|
| sf | 4|
| solrium | 4|
| urltools | 4|
| uuid | 4|
| yaml | 4|
| DBI | 3|
| fauxpas | 3|
| foreach | 3|
| gdata | 3|
| gistr | 3|
| graphics | 3|
| lintr | 3|
| MASS | 3|
| memoise | 3|
| mime | 3|
| miniUI | 3|
| R.utils | 3|
| RColorBrewer | 3|
| rentrez | 3|
| rmapshaper | 3|
| rvertnet | 3|
| rworldmap | 3|
| spocc | 3|
| stringi | 3|
| wicket | 3|
| base64enc | 2|
| bibtex | 2|
| Biostrings | 2|
| broom | 2|
| crayon | 2|
| downloader | 2|
| elastic | 2|
| geiger | 2|
| getPass | 2|
| GGally | 2|
| ggthemes | 2|
| grDevices | 2|
| grid | 2|
| gridExtra | 2|
| htmltools | 2|
| htmlwidgets | 2|
| httpcode | 2|
| igraph | 2|
| jqr | 2|
| jsonvalidate | 2|
| listviewer | 2|
| mapproj | 2|
| Matrix | 2|
| phylobase | 2|
| phytools | 2|
| R.cache | 2|
| RcppRedis | 2|
| readxl | 2|
| remotes | 2|
| reshape | 2|
| rplos | 2|
| shinyjs | 2|
| storr | 2|
| sys | 2|
| tm | 2|
| viridis | 2|
| webp | 2|
| zoo | 2|
| akima | 1|
| analogue | 1|
| aRxiv | 1|
| binman | 1|
| Biobase | 1|
| BiocGenerics | 1|
| biomaRt | 1|
| bold | 1|
| Cairo | 1|
| caTools | 1|
| ckanr | 1|
| corrplot | 1|
| countrycode | 1|
| cranlogs | 1|
| crminer | 1|
| crosstalk | 1|
| dendextend | 1|
| doParallel | 1|
| dplyr(>=0.3.0.2) | 1|
| DT(>=0.1) | 1|
| EML | 1|
| etseed | 1|
| fastmatch | 1|
| fields | 1|
| forecast | 1|
| foreign | 1|
| fulltext | 1|
| functionMap | 1|
| genderdata | 1|
| GenomeInfoDb | 1|
| GenomicFeatures | 1|
| GenomicRanges(>=1.23.24) | 1|
| geoaxe | 1|
| geojson | 1|
| geojsonio | 1|
| geojsonlint | 1|
| geonames | 1|
| geosphere | 1|
| ggalt | 1|
| ggm | 1|
| graphql | 1|
| GSODR | 1|
| gtools | 1|
| hash | 1|
| hexbin | 1|
| historydata | 1|
| Hmisc | 1|
| httpuv | 1|
| IRanges | 1|
| IRdisplay | 1|
| isdparser | 1|
| janeaustenr | 1|
| jpeg | 1|
| knitcitations | 1|
| leafletR | 1|
| loggr | 1|
| magick | 1|
| mapdata | 1|
| markdown | 1|
| MCMCglmm | 1|
| memisc | 1|
| miniUI(>=0.1.1) | 1|
| mongolite | 1|
| nabor | 1|
| natserv | 1|
| openair | 1|
| openxlsx | 1|
| osmar | 1|
| outliers | 1|
| pander | 1|
| parallel | 1|
| plot3D | 1|
| plotKML | 1|
| plotly | 1|
| plumber | 1|
| progress | 1|
| protolite | 1|
| purrrlyr | 1|
| qlcMatrix | 1|
| RApiSerialize | 1|
| rapport | 1|
| rbhl | 1|
| rbison | 1|
| rcdk | 1|
| Rcompression | 1|
| readtext | 1|
| rebird | 1|
| RedisAPI | 1|
| redland | 1|
| redux | 1|
| reeack | 1|
| rfigshare | 1|
| ridigbio | 1|
| rinat | 1|
| ritis | 1|
| rJava | 1|
| RJSONIO | 1|
| rlist | 1|
| Rmpfr | 1|
| RMySQL | 1|
| rnaturalearthdata | 1|
| rnaturalearthhires | 1|
| rncl | 1|
| RNeXML | 1|
| rnoaa | 1|
| rnrfa | 1|
| ropenaq | 1|
| rotl | 1|
| rowr | 1|
| RPostgreSQL | 1|
| rrdf | 1|
| rredis | 1|
| rredlist | 1|
| rrlite | 1|
| RSclient | 1|
| RSelenium | 1|
| Rserve | 1|
| rstudioapi(>=0.5) | 1|
| rsvg | 1|
| rtracklayer | 1|
| RUnit | 1|
| S4Vectors | 1|
| sangerseqR | 1|
| scrapeR | 1|
| selectr | 1|
| seqinr | 1|
| shiny(>=0.13.2) | 1|
| snow | 1|
| SnowballC | 1|
| sofa | 1|
| spacetime | 1|
| spatstat | 1|
| SSOAP | 1|
| stringdist | 1|
| Suggests:testthat | 1|
| Sxslt | 1|
| tabulizerjars | 1|
| testthat(>=0.7) | 1|
| tidytext | 1|
| tidyverse | 1|
| tiff | 1|
| tmap | 1|
| USAboundaries | 1|
| USAboundariesData | 1|
| VariantAnnotation | 1|
| vegan | 1|
| viridisLite | 1|
| wdman(>=0.2.2) | 1|
| weathermetrics | 1|
| webmockr | 1|
| webshot | 1|
| wellknown | 1|
| WikidataR | 1|
| wikitaxa | 1|
| withr | 1|
| wordcloud2 | 1|
| worrms | 1|
| XMLSchema | 1|
| xtable | 1|
| xts | 1|
# summarise(count(name))
codemeta/codemetar documentation built on Feb. 21, 2024, 3:27 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Parsing codemeta data
NB: sources moved to vignettes
library(jsonld)
library(jsonlite)
library(magrittr)
library(codemetar)
library(tidyverse)
library(printr)
write_codemeta("codemetar", "codemeta.json")
Digest input with a frame:
frame <- system.file("schema/frame_schema.json", package="codemetar")
meta <-
jsonld_frame("codemeta.json", frame) %>%
fromJSON(FALSE) %>% getElement("@graph") %>% getElement(1)
Construct a citation
authors <-
lapply(meta$author,
function(author)
person(given = author$given,
family = author$family,
email = author$email,
role = "aut"))
year <- meta$datePublished
if(is.null(year))
year <- format(Sys.Date(), "%Y")
bibitem <-
bibentry(
bibtype = "Manual",
title = meta$name,
author = authors,
year = year,
note = paste0("R package version ", meta$version),
url = meta$URL,
key = meta$identifier
)
cat(format(bibitem, "bibtex"))
## @Manual{codemetar,
## title = {codemetar: Generate CodeMeta Metadata for R Packages},
## author = {Carl Boettiger},
## year = {2017},
## note = {R package version 0.1.0},
## }
bibitem
## Boettiger C (2017). _codemetar: Generate CodeMeta Metadata for R
## Packages_. R package version 0.1.0.
Parsing the ropensci corpus
Frame, expanding any referenced nodes
corpus <-
jsonld_frame("ropensci.json", frame) %>%
fromJSON(simplifyVector = FALSE) %>%
getElement("@graph")
Some basics:
## deal with nulls explicitly by starting with map
pkgs <- map(corpus, "name") %>% compact() %>% as.character()
# keep only those with package identifiers (names)
keep <- map_lgl(corpus, ~ length(.x$identifier) > 0)
corpus <- corpus[keep]
## now we can just do
all_pkgs <- map_chr(corpus, "name")
head(all_pkgs)
## [1] "AntWeb: programmatic interface to the AntWeb"
## [2] "aRxiv: Interface to the arXiv API"
## [3] "chromer: Interface to Chromosome Counts Database API"
## [4] "ckanr: Client for the Comprehensive Knowledge Archive Network ('CKAN') 'API'"
## [5] "dashboard: A package status dashboard"
## [6] "ggit: Git Graphics"
## 60 unique maintainers
map_chr(corpus, c("maintainer", "familyName")) %>% unique() %>% length()
## [1] 61
## Mostly Scott
map_chr(corpus, c("maintainer", "familyName")) %>%
as_tibble() %>%
group_by(value) %>%
tally(sort=TRUE)
| value | n| |:-------------|----:| | Chamberlain | 105| | Ooms | 12| | Mullen | 8| | Ram | 8| | Boettiger | 6| | Salmon | 5| | FitzJohn | 4| | Hart | 2| | Leeper | 2| | Marwick | 2| | Müller | 2| | Padgham | 2| | South | 2| | Varela | 2| | Vitolo | 2| | Arnold | 1| | Attali | 1| | Banbury | 1| | Becker | 1| | Bengtsson | 1| | Braginsky | 1| | Broman | 1| | Bryan | 1| | Dallas | 1| | de Queiroz | 1| | Drost | 1| | Fischetti | 1| | Ghahraman | 1| | Goring | 1| | hackathoners | 1| | Harrison | 1| | Hughes | 1| | Jahn | 1| | Jones | 1| | Keyes | 1| | Krah | 1| | Lehtomaki | 1| | Lovelace | 1| | Lundstrom | 1| | McGlinn | 1| | McVey | 1| | Meissner | 1| | Michonneau | 1| | Moroz | 1| | Otegui | 1| | Pardo | 1| | Pennell | 1| | Poelen | 1| | Robinson | 1| | Ross | 1| | Rowlingson | 1| | Scott | 1| | Seers | 1| | Shotwell | 1| | Sievert | 1| | Sparks | 1| | Stachelek | 1| | Szöcs | 1| | Widgren | 1| | Wiggin | 1| | Winter | 1|
## number of co-authors ...
map_int(corpus, function(r) length(r$author)) %>%
as_tibble() %>%
group_by(value) %>%
tally(sort=TRUE)
| value| n| |------:|----:| | 1| 146| | 2| 30| | 3| 17| | 4| 8| | 5| 5| | 7| 3| | 13| 1|
## Contributors isn't used as much...
map_int(corpus, function(r) length(r$contributor)) %>%
as_tibble() %>%
group_by(value) %>%
tally(sort=TRUE)
| value| n| |------:|----:| | 0| 178| | 2| 13| | 4| 9| | 3| 7| | 5| 1| | 6| 1| | 8| 1|
Numbers (n) of packages with a total of (value) dependencies:
map_int(corpus, function(r) length(r$softwareRequirements)) %>%
as_tibble() %>%
group_by(value) %>%
tally(sort=TRUE)
| value| n| |------:|----:| | 4| 39| | 5| 35| | 2| 25| | 3| 25| | 7| 19| | 6| 16| | 8| 13| | 9| 8| | 12| 7| | 10| 6| | 11| 6| | 13| 3| | 0| 2| | 14| 1| | 17| 1| | 18| 1| | 21| 1| | 22| 1| | 23| 1|
which dependencies are used most frequently?
corpus %>%
map_df(function(x){
## single, unboxed dep
if("name" %in% names(x$softwareRequirements))
dep <- x$name
else if("name" %in% names(x$softwareRequirements[[1]]))
dep <- map_chr(x$softwareRequirements, "name")
else { ## No requirementsß
dep <- NA
}
tibble(identifier = x$identifier, dep = dep)
}) -> dep_df
dep_df %>%
group_by(dep) %>%
tally(sort = TRUE)
| dep | n| |:-----------------------------------------------------------------|----:| | jsonlite | 99| | httr | 92| | R | 66| | tibble | 46| | dplyr | 43| | methods | 37| | xml2 | 37| | data.table | 35| | utils | 35| | crul | 31| | plyr | 29| | XML | 25| | magrittr | 24| | sp | 22| | stringr | 21| | curl | 18| | ggplot2 | 18| | lazyeval | 17| | stats | 17| | lubridate | 14| | R6 | 14| | rappdirs | 13| | assertthat | 12| | digest | 12| | RCurl | 12| | readr | 11| | rgdal | 10| | whisker | 10| | scales | 9| | ape | 8| | raster | 8| | tidyr | 8| | Rcpp | 7| | reshape2 | 7| | rvest | 7| | rgeos | 6| | V8 | 6| | hoardr | 5| | rjson | 5| | taxize | 5| | tools | 5| | git2r | 4| | maps | 4| | oai | 4| | openssl | 4| | R(>=3.2.1) | 4| | solrium | 4| | urltools | 4| | foreach | 3| | knitr | 3| | leaflet | 3| | maptools | 3| | memoise | 3| | mime | 3| | pdftools | 3| | purrr | 3| | RColorBrewer | 3| | rgbif | 3| | rmarkdown | 3| | shiny | 3| | spocc | 3| | stringi | 3| | uuid | 3| | wicket | 3| | yaml | 3| | base64enc | 2| | bibtex | 2| | Biostrings | 2| | crayon | 2| | devtools | 2| | downloader | 2| | fauxpas | 2| | gdata | 2| | gistr | 2| | graphics | 2| | grid | 2| | htmltools | 2| | htmlwidgets | 2| | httpcode | 2| | igraph | 2| | jqr | 2| | MASS | 2| | miniUI | 2| | ncdf4 | 2| | png | 2| | R.cache | 2| | R.utils | 2| | rcrossref | 2| | rentrez | 2| | reshape | 2| | rmapshaper | 2| | rplos | 2| | rvertnet | 2| | shinyjs | 2| | storr | 2| | tm | 2| | NA | 2| | analogue | 1| | antiword: Extract Text from Microsoft Word Documents | 1| | apipkgen: Package Generator for HTTP API Wrapper Packages | 1| | appl: Approximate POMDP Planning Software | 1| | aRxiv | 1| | binman | 1| | Biobase | 1| | BiocGenerics | 1| | biomaRt | 1| | bold | 1| | caTools | 1| | ckanr | 1| | cld2: Google's Compact Language Detector 2 | 1| | countrycode | 1| | cranlogs | 1| | crminer | 1| | crosstalk | 1| | DBI | 1| | dirdf: Extracts Metadata from Directory and File Names | 1| | doParallel | 1| | DT(>=0.1) | 1| | elastic | 1| | EML | 1| | fastmatch | 1| | foreign | 1| | functionMap | 1| | genderdata: Historical Datasets for Predicting Gender from Names | 1| | GenomeInfoDb | 1| | GenomicFeatures | 1| | GenomicRanges(>=1.23.24) | 1| | geoaxe | 1| | geojson | 1| | geojsonrewind: Fix 'GeoJSON' Winding Direction | 1| | geonames | 1| | geoops: 'GeoJSON' Manipulation Operations | 1| | geosphere | 1| | getPass | 1| | ggm | 1| | ggmap | 1| | ggthemes | 1| | graphql | 1| | grDevices | 1| | gridExtra | 1| | gtools | 1| | hash | 1| | hexbin | 1| | historydata: Data Sets for Historians | 1| | Hmisc | 1| | httpuv | 1| | IRanges | 1| | isdparser | 1| | jsonvalidate | 1| | jsonvalidate: Validate 'JSON' | 1| | leafletR | 1| | loggr | 1| | mapproj | 1| | markdown | 1| | Matrix | 1| | memisc | 1| | miniUI(>=0.1.1) | 1| | nabor | 1| | natserv | 1| | openxlsx | 1| | osmar | 1| | outliers | 1| | pdftools: Text Extraction and Rendering of PDF Documents | 1| | phytools | 1| | plotly | 1| | plumber | 1| | progress | 1| | protolite | 1| | qlcMatrix | 1| | RApiSerialize | 1| | rapport | 1| | rbhl | 1| | rbison | 1| | rebird | 1| | redland | 1| | redux | 1| | remotes | 1| | ridigbio | 1| | ritis | 1| | rJava | 1| | RJSONIO | 1| | rlist | 1| | Rmpfr | 1| | RMySQL | 1| | rncl | 1| | rnoaa | 1| | rnrfa | 1| | rotl | 1| | rowr | 1| | RPostgreSQL | 1| | rredis | 1| | rredlist | 1| | RSQLite | 1| | rstudioapi(>=0.5) | 1| | rtracklayer | 1| | rworldmap | 1| | rzmq: R Bindings for ZeroMQ | 1| | S4Vectors | 1| | scrapeR | 1| | selectr | 1| | sf | 1| | shiny(>=0.13.2) | 1| | snow | 1| | SnowballC | 1| | spatstat | 1| | SSOAP | 1| | stringdist | 1| | sys | 1| | tabulizerjars | 1| | testthat | 1| | tif: Text Interchange Format | 1| | USAboundariesData: Datasets for the 'USAboundaries' package | 1| | VariantAnnotation | 1| | viridisLite | 1| | wdman(>=0.2.2) | 1| | wellknown | 1| | wicket: Utilities to Handle WKT Spatial Data | 1| | WikidataR | 1| | wikitaxa | 1| | withr | 1| | worrms | 1| | xslt: XSLT 1.0 Transformations | 1| | zoo | 1|
Alternate approach using a frame, gets all Depends and suggests (really all SoftwareApplication types mentioned)
dep_frame <- '{
"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
"@explicit": "true",
"name": {}
}'
jsonld_frame("ropensci.json", dep_frame) %>%
fromJSON() %>%
getElement("@graph") %>%
filter(type == "SoftwareApplication") %>%
group_by(name) %>%
tally(sort = TRUE)
| name | n| |:----------------------------|----:| | testthat | 168| | knitr | 122| | jsonlite | 105| | httr | 96| | roxygen2 | 92| | R | 72| | rmarkdown | 68| | covr | 52| | dplyr | 49| | tibble | 48| | xml2 | 41| | methods | 38| | utils | 37| | data.table | 36| | ggplot2 | 36| | crul | 33| | plyr | 32| | magrittr | 28| | sp | 26| | XML | 25| | curl | 21| | stringr | 21| | lazyeval | 18| | stats | 18| | lubridate | 16| | R6 | 14| | readr | 14| | rgdal | 14| | rappdirs | 13| | assertthat | 12| | devtools | 12| | digest | 12| | raster | 12| | RCurl | 12| | scales | 12| | Rcpp | 11| | whisker | 11| | leaflet | 10| | rgeos | 10| | taxize | 10| | tidyr | 10| | reshape2 | 9| | ape | 8| | maps | 8| | V8 | 8| | maptools | 7| | purrr | 7| | rvest | 7| | pdftools | 6| | rgbif | 6| | shiny | 6| | ggmap | 5| | git2r | 5| | hoardr | 5| | ncdf4 | 5| | png | 5| | rjson | 5| | tools | 5| | oai | 4| | openssl | 4| | R(>=3.2.1) | 4| | rcrossref | 4| | RSQLite | 4| | sf | 4| | solrium | 4| | urltools | 4| | uuid | 4| | yaml | 4| | DBI | 3| | fauxpas | 3| | foreach | 3| | gdata | 3| | gistr | 3| | graphics | 3| | lintr | 3| | MASS | 3| | memoise | 3| | mime | 3| | miniUI | 3| | R.utils | 3| | RColorBrewer | 3| | rentrez | 3| | rmapshaper | 3| | rvertnet | 3| | rworldmap | 3| | spocc | 3| | stringi | 3| | wicket | 3| | base64enc | 2| | bibtex | 2| | Biostrings | 2| | broom | 2| | crayon | 2| | downloader | 2| | elastic | 2| | geiger | 2| | getPass | 2| | GGally | 2| | ggthemes | 2| | grDevices | 2| | grid | 2| | gridExtra | 2| | htmltools | 2| | htmlwidgets | 2| | httpcode | 2| | igraph | 2| | jqr | 2| | jsonvalidate | 2| | listviewer | 2| | mapproj | 2| | Matrix | 2| | phylobase | 2| | phytools | 2| | R.cache | 2| | RcppRedis | 2| | readxl | 2| | remotes | 2| | reshape | 2| | rplos | 2| | shinyjs | 2| | storr | 2| | sys | 2| | tm | 2| | viridis | 2| | webp | 2| | zoo | 2| | akima | 1| | analogue | 1| | aRxiv | 1| | binman | 1| | Biobase | 1| | BiocGenerics | 1| | biomaRt | 1| | bold | 1| | Cairo | 1| | caTools | 1| | ckanr | 1| | corrplot | 1| | countrycode | 1| | cranlogs | 1| | crminer | 1| | crosstalk | 1| | dendextend | 1| | doParallel | 1| | dplyr(>=0.3.0.2) | 1| | DT(>=0.1) | 1| | EML | 1| | etseed | 1| | fastmatch | 1| | fields | 1| | forecast | 1| | foreign | 1| | fulltext | 1| | functionMap | 1| | genderdata | 1| | GenomeInfoDb | 1| | GenomicFeatures | 1| | GenomicRanges(>=1.23.24) | 1| | geoaxe | 1| | geojson | 1| | geojsonio | 1| | geojsonlint | 1| | geonames | 1| | geosphere | 1| | ggalt | 1| | ggm | 1| | graphql | 1| | GSODR | 1| | gtools | 1| | hash | 1| | hexbin | 1| | historydata | 1| | Hmisc | 1| | httpuv | 1| | IRanges | 1| | IRdisplay | 1| | isdparser | 1| | janeaustenr | 1| | jpeg | 1| | knitcitations | 1| | leafletR | 1| | loggr | 1| | magick | 1| | mapdata | 1| | markdown | 1| | MCMCglmm | 1| | memisc | 1| | miniUI(>=0.1.1) | 1| | mongolite | 1| | nabor | 1| | natserv | 1| | openair | 1| | openxlsx | 1| | osmar | 1| | outliers | 1| | pander | 1| | parallel | 1| | plot3D | 1| | plotKML | 1| | plotly | 1| | plumber | 1| | progress | 1| | protolite | 1| | purrrlyr | 1| | qlcMatrix | 1| | RApiSerialize | 1| | rapport | 1| | rbhl | 1| | rbison | 1| | rcdk | 1| | Rcompression | 1| | readtext | 1| | rebird | 1| | RedisAPI | 1| | redland | 1| | redux | 1| | reeack | 1| | rfigshare | 1| | ridigbio | 1| | rinat | 1| | ritis | 1| | rJava | 1| | RJSONIO | 1| | rlist | 1| | Rmpfr | 1| | RMySQL | 1| | rnaturalearthdata | 1| | rnaturalearthhires | 1| | rncl | 1| | RNeXML | 1| | rnoaa | 1| | rnrfa | 1| | ropenaq | 1| | rotl | 1| | rowr | 1| | RPostgreSQL | 1| | rrdf | 1| | rredis | 1| | rredlist | 1| | rrlite | 1| | RSclient | 1| | RSelenium | 1| | Rserve | 1| | rstudioapi(>=0.5) | 1| | rsvg | 1| | rtracklayer | 1| | RUnit | 1| | S4Vectors | 1| | sangerseqR | 1| | scrapeR | 1| | selectr | 1| | seqinr | 1| | shiny(>=0.13.2) | 1| | snow | 1| | SnowballC | 1| | sofa | 1| | spacetime | 1| | spatstat | 1| | SSOAP | 1| | stringdist | 1| | Suggests:testthat | 1| | Sxslt | 1| | tabulizerjars | 1| | testthat(>=0.7) | 1| | tidytext | 1| | tidyverse | 1| | tiff | 1| | tmap | 1| | USAboundaries | 1| | USAboundariesData | 1| | VariantAnnotation | 1| | vegan | 1| | viridisLite | 1| | wdman(>=0.2.2) | 1| | weathermetrics | 1| | webmockr | 1| | webshot | 1| | wellknown | 1| | WikidataR | 1| | wikitaxa | 1| | withr | 1| | wordcloud2 | 1| | worrms | 1| | XMLSchema | 1| | xtable | 1| | xts | 1|
# summarise(count(name))
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