Author: Ioannis Kosmidis
Date: 2022-08-26

# 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)

# 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)

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

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)

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

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)