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Extracting information from cranly package networks: extractors and word clouds

Ioannis Kosmidis

2022-08-26

cranly extractor functions

Since version 0.3, cranly includes functions for extracting information from cranly_network objects (see ?extractor-functions). All extractor functions in cranly try to figure out what y is in the statements

y is [the] extractor-function a package/author

CRAN package directives and author collaboration networks

Let’s attach cranly

library("cranly")

and use instances of the package directives and author collaboration networks

package_network <- readRDS(url("https://raw.githubusercontent.com/ikosmidis/cranly/develop/inst/extdata/package_network.rds"))
author_network <- readRDS(url("https://raw.githubusercontent.com/ikosmidis/cranly/develop/inst/extdata/author_network.rds"))

from CRAN’s state on 2022-08-26 14:43:43 BST

Alternatively, today’s package directives and author collaboration networks can be constructed by doing

cran_db <- clean_CRAN_db()
package_network <- build_network(cran_db)
author_network <- build_network(cran_db, perspective = "author")

Example queries

Packages by Kurt Hornik

package_network |> package_by("Kurt Hornik", exact = TRUE)
#>  [1] "arules"             "bibtex"             "bindata"           
#>  [4] "cclust"             "chron"              "clue"              
#>  [7] "cluster"            "coin"               "colorspace"        
#> [10] "cordillera"         "ctv"                "date"              
#> [13] "dendextend"         "digest"             "e1071"             
#> [16] "exactRankTests"     "fortunes"           "gap"               
#> [19] "gsignal"            "ISOcodes"           "isotone"           
#> [22] "kernlab"            "lpSolveAPI"         "MASS"              
#> [25] "mda"                "mistr"              "movMF"             
#> [28] "mvord"              "nloptr"             "NLP"               
#> [31] "NLPclient"          "NLPutils"           "OAIHarvester"      
#> [34] "openNLP"            "openNLPdata"        "opGMMassessment"   
#> [37] "oz"                 "pandocfilters"      "party"             
#> [40] "polyclip"           "polynom"            "PolynomF"          
#> [43] "princurve"          "qrmdata"            "qrmtools"          
#> [46] "Rcplex"             "relations"          "Rglpk"             
#> [49] "RKEA"               "RKEAjars"           "ROI"               
#> [52] "ROI.plugin.msbinlp" "Rpoppler"           "Rsymphony"         
#> [55] "RWeka"              "RWekajars"          "seriation"         
#> [58] "sets"               "signal"             "skmeans"           
#> [61] "slam"               "stablelearner"      "strucchange"       
#> [64] "strucchangeRcpp"    "tau"                "textcat"           
#> [67] "textplot"           "tm"                 "tm.plugin.mail"    
#> [70] "topicmodels"        "tseries"            "TSP"               
#> [73] "Unicode"            "vcd"                "W3CMarkupValidator"
#> [76] "WeightSVM"          "wordnet"

Packages by people named “Ioannis”

package_network |> package_by("Ioannis")
#>  [1] "BCT"              "betareg"          "brglm"            "brglm2"          
#>  [5] "camtrapR"         "detectseparation" "enrichwith"       "FLR"             
#>  [9] "IPMbook"          "MXM"              "PlackettLuce"     "profileModel"    
#> [13] "Rfast"            "trackeR"          "trackeRapp"       "USP"

Packages with “glm” in their name

author_network |> package_with("glm")
#>  [1] "glmlep"          "glmnet"          "biglm"           "biglmm"         
#>  [5] "dbglm"           "glm2"            "glmertree"       "glmx"           
#>  [9] "cglm"            "glmmTMB"         "aglm"            "StroupGLMM"     
#> [13] "fastglm"         "r2glmm"          "bestglm"         "eventglm"       
#> [17] "GLMaSPU"         "glmbb"           "glmm"            "AutoStepwiseGLM"
#> [21] "glmnetUtils"     "glmvsd"          "GLMpack"         "poisson.glm.mix"
#> [25] "glmmfields"      "HBglm"           "brglm"           "brglm2"         
#> [29] "GLMMRR"          "plsRglm"         "GLMMadaptive"    "BranchGLM"      
#> [33] "glm.predict"     "mbrglm"          "CPMCGLM"         "hdpGLM"         
#> [37] "glmdisc"         "CIS.DGLM"        "SplitGLM"        "icdGLM"         
#> [41] "misclassGLM"     "pglm"            "hglm"            "hglm.data"      
#> [45] "RPEGLMEN"        "glmpath"         "GlmSimulatoR"    "glmc"           
#> [49] "randomGLM"       "glmmEP"          "dglm"            "GLMsData"       
#> [53] "DGLMExtPois"     "dhglm"           "mdhglm"          "ezglm"          
#> [57] "parglm"          "glmmSeq"         "holiglm"         "glmmML"         
#> [61] "MGLM"            "FGLMtrunc"       "gglm"            "speedglm"       
#> [65] "glmm.hp"         "glm.deploy"      "glmtlp"          "GLMcat"         
#> [69] "glmtree"         "glme"            "glmglrt"         "glmmLasso"      
#> [73] "glmmPen"         "glmnetcr"        "glmpathcr"       "glmnetSE"       
#> [77] "glmpca"          "glmtoolbox"      "glmtrans"        "glmulti"        
#> [81] "glmxdiag"        "HDGLM"           "simglm"          "htmcglm"        
#> [85] "mcglm"           "ICglm"           "mglmn"           "lsplsGlm"       
#> [89] "MCMCglmm"        "mcemGLM"         "robmixglm"       "mvglmmRank"     
#> [93] "oglmx"           "prettyglm"       "QGglmm"          "stepjglm"

Authors of the lubridate package

package_network |> author_of("lubridate", exact = TRUE)
#>  [1] "Vitalie Spinu"     "Garrett Grolemund" "Hadley Wickham"   
#>  [4] "Davis Vaughan"     "Ian Lyttle"        "Imanuel Costigan" 
#>  [7] "Jason Law"         "Doug Mitarotonda"  "Joseph Larmarange"
#> [10] "Jonathan Boiser"   "Chel Hee Lee"      "Google Inc"

Authors with “Ioan” in their name

package_network |> author_with("Ioan")
#>  [1] "Ioan Gabriel Bucur"     "Ioannis Papageorgiou"   "Ioannis Kontoyiannis"  
#>  [4] "Ioannis Kosmidis"       "Ioanna Manolopoulou"    "Ioannis Alexiou"       
#>  [7] "Ioannis N Athanasiadis" "Ioannis Ntzoufras"      "Ioannis Tsamardinos"   
#> [10] "Alex Ioannides"         "Eleni Ioanna Delatola"  "Ioana-Elena Oana"      
#> [13] "Lazaros Ioannidis"

Packages suggested by, imported by and enhanced by the sf package

package_network |> suggested_by("sf", exact = TRUE)
#>  [1] "blob"            "covr"            "dplyr"           "ggplot2"        
#>  [5] "knitr"           "lwgeom"          "maps"            "mapview"        
#>  [9] "Matrix"          "microbenchmark"  "odbc"            "pbapply"        
#> [13] "pillar"          "pool"            "raster"          "rlang"          
#> [17] "rmarkdown"       "RPostgres"       "RPostgreSQL"     "RSQLite"        
#> [21] "sp"              "spatstat"        "spatstat.geom"   "spatstat.random"
#> [25] "spatstat.linnet" "spatstat.utils"  "stars"           "terra"          
#> [29] "testthat"        "tibble"          "tidyr"           "tidyselect"     
#> [33] "tmap"            "vctrs"           "wk"
package_network |> imported_by("sf", exact = TRUE)
#>  [1] "classInt"  "DBI"       "graphics"  "grDevices" "grid"      "magrittr" 
#>  [7] "Rcpp"      "s2"        "stats"     "tools"     "units"     "utils"
package_network |> enhanced_by("sf", exact = TRUE)
#> character(0)

Packages that are suggesting, importing, enhancing the sf package

package_network |> suggesting("sf", exact = TRUE)
#>   [1] "accessibility"    "adklakedata"      "AMAPVox"         
#>   [4] "apsimx"           "argoFloats"       "auk"             
#>   [7] "BiodiversityR"    "BIOMASS"          "biscale"         
#>  [10] "bmstdr"           "BSBT"             "cancensus"       
#>  [13] "CAST"             "censusxy"         "ckanr"           
#>  [16] "climaemet"        "climatrends"      "cmhc"            
#>  [19] "colorist"         "ctmm"             "dataRetrieval"   
#>  [22] "deckgl"           "DeclareDesign"    "disdat"          
#>  [25] "dodgr"            "echelon"          "echor"           
#>  [28] "EcoIndR"          "efdm"             "ENMeval"         
#>  [31] "eRTG3D"           "eurostat"         "fasterize"       
#>  [34] "febr"             "FlickrAPI"        "gdalcubes"       
#>  [37] "gear"             "geocmeans"        "geodaData"       
#>  [40] "geohashTools"     "geojson"          "geometa"         
#>  [43] "geomtextpath"     "geos"             "gfcanalysis"     
#>  [46] "ggblanket"        "ggformula"        "gghighlight"     
#>  [49] "gginnards"        "ggiraph"          "ggpattern"       
#>  [52] "ggplot2"          "ggrastr"          "googlePolylines" 
#>  [55] "graphhopper"      "graticule"        "grwat"           
#>  [58] "gstat"            "gtfsrouter"       "ipumsr"          
#>  [61] "isoband"          "janitor"          "jsonlite"        
#>  [64] "kdtools"          "leaflet"          "leaflet.extras2" 
#>  [67] "leri"             "lutz"             "mapsFinland"     
#>  [70] "mdsr"             "metamer"          "mlr"             
#>  [73] "mlr3spatiotempcv" "mudata2"          "nlaR"            
#>  [76] "o2geosocial"      "oce"              "od"              
#>  [79] "onemapsgapi"      "opencage"         "osmdata"         
#>  [82] "palmid"           "pinochet"         "plainview"       
#>  [85] "plotly"           "plumber"          "PointedSDMs"     
#>  [88] "polyCub"          "polylabelr"       "protolite"       
#>  [91] "raster"           "rasterVis"        "rayrender"       
#>  [94] "rayshader"        "rcartocolor"      "rdhs"            
#>  [97] "readwritesqlite"  "recogito"         "regional"        
#> [100] "regweight"        "reproducible"     "rgbif"           
#> [103] "rgee"             "RGENERATEPREC"    "rGhanaCensus"    
#> [106] "rgrass"           "rgrass7"          "rinat"           
#> [109] "rmangal"          "RtD3"             "sbtools"         
#> [112] "sdcSpatial"       "sdmApp"           "sociome"         
#> [115] "soilDB"           "sp"               "spacetime"       
#> [118] "SpaceTimeBSS"     "SpaDES.tools"     "SpatialBSS"      
#> [121] "spbabel"          "spData"           "spflow"          
#> [124] "spotoroo"         "spsur"            "swmmr"           
#> [127] "terra"            "tgver"            "tricolore"       
#> [130] "ukpolice"         "unifir"           "ursa"            
#> [133] "USAboundaries"    "waterquality"     "wk"
package_network |> importing("sf", exact = TRUE)
#>   [1] "abmR"                 "abstr"                "adw"                 
#>   [4] "amt"                  "aopdata"              "areal"               
#>   [7] "ARPALData"            "ascotraceR"           "aurin"               
#>  [10] "BARIS"                "basemaps"             "bayesmove"           
#>  [13] "bbsBayes"             "bcdata"               "bcputility"          
#>  [16] "bdc"                  "bdl"                  "BIEN"                
#>  [19] "bigDM"                "blockCV"              "bluebike"            
#>  [22] "bnspatial"            "briskaR"              "btb"                 
#>  [25] "buffeRs"              "camtrapR"             "capm"                
#>  [28] "CARBayes"             "CARBayesdata"         "CARBayesST"          
#>  [31] "card"                 "cartograflow"         "cartogram"           
#>  [34] "cartogramR"           "cartography"          "CatastRo"            
#>  [37] "cdcfluview"           "cdrcR"                "censable"            
#>  [40] "chirps"               "clhs"                 "ClimMobTools"        
#>  [43] "comorosmaps"          "concaveman"           "conleyreg"           
#>  [46] "ConR"                 "CopernicusDEM"        "covid19br"           
#>  [49] "covid19sf"            "covidcast"            "crawl"               
#>  [52] "crimedata"            "CropScapeR"           "crsuggest"           
#>  [55] "cshapes"              "cubble"               "cyclestreets"        
#>  [58] "datazoom.amazonia"    "daymetr"              "Directional"         
#>  [61] "distanceto"           "divseg"               "dots"                
#>  [64] "dsims"                "dssd"                 "dwp"                 
#>  [67] "ebirdst"              "edbuildmapr"          "eks"                 
#>  [70] "elevatr"              "EmissV"               "envirem"             
#>  [73] "epiR"                 "epm"                  "eSDM"                
#>  [76] "exactextractr"        "extRatum"             "FedData"             
#>  [79] "fgdr"                 "FIESTA"               "FIESTAutils"         
#>  [82] "fisheye"              "fitbitViz"            "flexpolyline"        
#>  [85] "flightplot"           "foieGras"             "forestecology"       
#>  [88] "FORTLS"               "fsr"                  "galah"               
#>  [91] "GapAnalysis"          "gbm.auto"             "gdalUtilities"       
#>  [94] "GeNetIt"              "geobr"                "geodimension"        
#>  [97] "geodiv"               "geodrawr"             "geofacet"            
#> [100] "geofi"                "geogrid"              "geojsonio"           
#> [103] "geoknife"             "geomander"            "geomaroc"            
#> [106] "geometr"              "geonetwork"           "geostan"             
#> [109] "geouy"                "geoviz"               "ggOceanMaps"         
#> [112] "ggseg"                "ggsn"                 "ggspatial"           
#> [115] "ggVennDiagram"        "giscoR"               "glottospace"         
#> [118] "grainchanger"         "graph4lg"             "GREENeR"             
#> [121] "gridpattern"          "gtfs2gps"             "gtfstools"           
#> [124] "gwavr"                "GWnnegPCA"            "GWpcor"              
#> [127] "gwpcormapper"         "GWSDAT"               "h3jsr"               
#> [130] "happign"              "HDSpatialScan"        "helsinki"            
#> [133] "hereR"                "himach"               "hwsdr"               
#> [136] "hypsoLoop"            "IceSat2R"             "idbr"                
#> [139] "imcRtools"            "IRexamples"           "itsdm"               
#> [142] "japanmesh"            "jpgrid"               "jpmesh"              
#> [145] "klexdatr"             "kokudosuuchi"         "LAGOSNE"             
#> [148] "landsepi"             "latticeDensity"       "layer"               
#> [151] "lazysf"               "lconnect"             "leafem"              
#> [154] "leafgl"               "leafpm"               "leafpop"             
#> [157] "lidaRtRee"            "lidR"                 "linemap"             
#> [160] "link2GI"              "LMoFit"               "lwgeom"              
#> [163] "macleish"             "MainExistingDatasets" "mapboxapi"           
#> [166] "mapchina"             "mapedit"              "mapi"                
#> [169] "mapiso"               "mapme.biodiversity"   "mapping"             
#> [172] "mapsapi"              "mapscanner"           "mapsf"               
#> [175] "mapSpain"             "maptiles"             "mapview"             
#> [178] "MazamaSpatialPlots"   "meteoland"            "meteospain"          
#> [181] "mgwrsar"              "micromapST"           "mlr3spatial"         
#> [184] "MODISTools"           "MODIStsp"             "motif"               
#> [187] "moveVis"              "mregions"             "MTA"                 
#> [190] "naturaList"           "ncdfgeom"             "ndi"                 
#> [193] "NetLogoR"             "netmap"               "nhdplusTools"        
#> [196] "nhdR"                 "NipponMap"            "njgeo"               
#> [199] "nlrx"                 "nominatimlite"        "oceanic"             
#> [202] "oceanis"              "opendatatoronto"      "openeo"              
#> [205] "opentripplanner"      "Orcs"                 "osmextract"          
#> [208] "osrm"                 "otpr"                 "owidR"               
#> [211] "ows4R"                "ozmaps"               "paleopop"            
#> [214] "parlitools"           "pct"                  "pgirmess"            
#> [217] "PL94171"              "PlanetNICFI"          "plotdap"             
#> [220] "plotKML"              "populR"               "potential"           
#> [223] "pRecipe"              "prisonbrief"          "pspatreg"            
#> [226] "PWFSLSmoke"           "qualmap"              "quickmapr"           
#> [229] "r5r"                  "raceland"             "rangemap"            
#> [232] "rangeMapper"          "rasterbc"             "rasterDT"            
#> [235] "rasterpic"            "raytracing"           "rbenvo"              
#> [238] "rcage"                "redist"               "redistmetrics"       
#> [241] "Relectoral"           "remap"                "rerddapXtracto"      
#> [244] "rFIA"                 "rfishnet2"            "RFmerge"             
#> [247] "rgeoda"               "rgeopat2"             "rgugik"              
#> [250] "rmapshaper"           "rmapzen"              "rnaturalearth"       
#> [253] "rnrfa"                "roads"                "robis"               
#> [256] "RPyGeo"               "Rsagacmd"             "RStoolbox"           
#> [259] "rts2"                 "rtsVis"               "RWmisc"              
#> [262] "sabre"                "safedata"             "sandwichr"           
#> [265] "SDLfilter"            "secr"                 "seedreg"             
#> [268] "segmetric"            "sen2r"                "sfarrow"             
#> [271] "sfdct"                "sfdep"                "sfhotspot"           
#> [274] "sfnetworks"           "sftrack"              "sgsR"                
#> [277] "simodels"             "simplevis"            "sits"                
#> [280] "slendr"               "smartmap"             "smile"               
#> [283] "SMITIDstruct"         "smoothr"              "spacejamr"           
#> [286] "spatgeom"             "spatialEco"           "SpatialKDE"          
#> [289] "SpatialPosition"      "spatialrisk"          "spatialsample"       
#> [292] "spectator"            "spectralR"            "sphet"               
#> [295] "spmodel"              "spnaf"                "spNetwork"           
#> [298] "spqdep"               "SRTsim"               "starsTileServer"     
#> [301] "stats19"              "stplanr"              "stppSim"             
#> [304] "sugarbag"             "SUNGEO"               "supercells"          
#> [307] "swfscDAS"             "swfscMisc"            "SWMPrExtension"      
#> [310] "SWTools"              "synoptReg"            "tanaka"              
#> [313] "telemac"              "terrainr"             "tidycensus"          
#> [316] "tidygeoRSS"           "tidyterra"            "tidytransit"         
#> [319] "tidyUSDA"             "tigris"               "tilemaps"            
#> [322] "tinytiger"            "tmap"                 "tmaptools"           
#> [325] "tongfen"              "track2KBA"            "trackeRapp"          
#> [328] "transformr"           "treePlotArea"         "treetop"             
#> [331] "trigpoints"           "uavRmp"               "upstartr"            
#> [334] "valhallr"             "valuemap"             "VancouvR"            
#> [337] "VARMER"               "vein"                 "velociraptr"         
#> [340] "VicmapR"              "vietnameseConverter"  "waywiser"            
#> [343] "weed"                 "WEGE"                 "wildlifeDI"          
#> [346] "zonebuilder"
package_network |> enhancing("sf", exact = TRUE)
#> [1] "landscapemetrics"

Packages that depend on the sf package

package_network |> depending_on("sf", exact = TRUE)
#>  [1] "APAtree"    "arcpullr"   "basf"       "bcmaps"     "canadamaps"
#>  [6] "CCAMLRGIS"  "chilemapas" "ecochange"  "GADMTools"  "habCluster"
#> [11] "micromap"   "nngeo"      "prioritizr" "RCzechia"   "RGISTools" 
#> [16] "rLFT"       "sftime"     "siland"     "spatialreg" "spdep"     
#> [21] "spsurvey"   "sspm"       "stars"      "starsExtra" "stcos"     
#> [26] "tilegramsR" "transfR"    "wdnr.gis"   "wdpar"      "windAC"

Packages that are dependencies of the sf package

package_network |> dependency_of("sf", exact = TRUE)
#> [1] "methods"

Packages maintained by everyone with “Helen” in their name

package_network |> maintained_by("Helen")
#> [1] "bild"     "cold"     "GENLIB"   "microPop" "villager"

All available info, on packages maintained by everyone with “Helen” in their name

package_network |> maintained_by("Helen", flat = FALSE) |> dim()
#> [1]  5 67

The maintainer of data.table

package_network |> maintainer_of("data.table", exact = TRUE)
#> [1] "Matt Dowle"

The email of the maintainer of trackeRapp

trackeRapp_maintainer <- package_network |> maintainer_of("trackeRapp", exact = TRUE)
package_network |> email_of(trackeRapp_maintainer, exact = TRUE)
#> [1] "ioannis.kosmidis@warwick.ac.uk"

All emails of maintainers using an email address from University of Warwick

package_network |> email_with("warwick.ac.uk")
#>  [1] "nick.parsons@warwick.ac.uk"       "ioannis.kosmidis@warwick.ac.uk"  
#>  [3] "haotian.xu@warwick.ac.uk"         "s.tavakoli@warwick.ac.uk"        
#>  [5] "d.selby@warwick.ac.uk"            "s.stein@warwick.ac.uk"           
#>  [7] "Nicole.Schwitter.1@warwick.ac.uk" "tom.berrett@warwick.ac.uk"       
#>  [9] "a.dickerson@warwick.ac.uk"        "d.firth@warwick.ac.uk"           
#> [11] "michelle.kendall@warwick.ac.uk"

The title, the description, the version and the license of the semnar package

package_network |> title_of("semnar", exact = TRUE)
#> character(0)
package_network |> description_of("semnar", exact = TRUE)
#> character(0)
package_network |> version_of("semnar", exact = TRUE)
#> character(0)

Distribution of the release dates of all packages in CRAN

package_network |> release_date_of(Inf) |>
    hist(breaks = 50, main = "", xlab = "date", freq = TRUE)

plot of chunk unnamed-chunk-19

Word clouds

Since version 0.5 cranly provides methods to construct word clouds of either author names, package descriptions or package titles. For example, the word cloud of the descriptions of the packages maintained by me and Edzer Pebesma are

word_cloud(package_network, maintainer = "Ioannis Kosmidis", exact = TRUE, min.freq = 1)

plot of chunk unnamed-chunk-20

word_cloud(package_network, maintainer = "Edzer Pebesma", exact = TRUE, min.freq = 1)

plot of chunk unnamed-chunk-20

or the word cloud of the titles of those packages are

word_cloud(package_network, maintainer = "Ioannis Kosmidis", perspective = "title", exact = TRUE,
           scale = c(2, 0.1), min.freq = 1)

plot of chunk unnamed-chunk-21

word_cloud(package_network, maintainer = "Edzer Pebesma", perspective = "title", exact = TRUE,
           scale = c(2, 0.1), min.freq = 1)

plot of chunk unnamed-chunk-21

More complex queries can be achieved by using the extractor functions and computing the term frequencies manually. For example, the word cloud of all packages maintained by people with “warwick.ac.uk” in their email is

warwick_emails <- package_network |> email_with("warwick.ac.uk", flat = FALSE)
warwick_pkgs  <- warwick_emails$package
descriptions <- package_network |> description_of(warwick_pkgs, exact = FALSE)
term_frequency <- compute_term_frequency(descriptions)
word_cloud(term_frequency, min.freq = 5)

plot of chunk unnamed-chunk-22

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.