explore-libraries
01_explore-libraries_jenny.R
elliotthazen Wed Jan 31 15:09:04 2018
library(fs)
library(tidyverse)
## ── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
## ✔ ggplot2 2.2.1.9000 ✔ purrr 0.2.4
## ✔ tibble 1.4.2 ✔ dplyr 0.7.4
## ✔ tidyr 0.7.2 ✔ stringr 1.2.0
## ✔ readr 1.1.1 ✔ forcats 0.2.0
## ── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
library(stringr)
library(igraph)
##
## Attaching package: 'igraph'
## The following objects are masked from 'package:dplyr':
##
## as_data_frame, groups, union
## The following objects are masked from 'package:purrr':
##
## compose, simplify
## The following object is masked from 'package:tidyr':
##
## crossing
## The following object is masked from 'package:tibble':
##
## as_data_frame
## The following object is masked from 'package:fs':
##
## path
## The following objects are masked from 'package:stats':
##
## decompose, spectrum
## The following object is masked from 'package:base':
##
## union
library(ggraph)
library(here)
## here() starts at /Users/elliotthazen/Documents/R/github/explore-libraries
## how jenny might do this in a first exploration
## purposely leaving a few things to change later!
Which libraries does R search for packages?
.libPaths()
## [1] "/Library/Frameworks/R.framework/Versions/3.3/Resources/library"
## let's confirm the second element is, in fact, the default library
.Library
## [1] "/Library/Frameworks/R.framework/Resources/library"
path_real(.Library)
## /Library/Frameworks/R.framework/Versions/3.3/Resources/library
Installed packages
ipt <- installed.packages() %>%
as_tibble()
## how many packages?
nrow(ipt)
## [1] 272
Exploring the packages
## count some things! inspiration
## * tabulate by LibPath, Priority, or both
ipt %>%
count(LibPath, Priority)
## # A tibble: 3 x 3
## LibPath Priority n
## <chr> <chr> <int>
## 1 /Library/Frameworks/R.framework/Versions/3.3/Resources… base 14
## 2 /Library/Frameworks/R.framework/Versions/3.3/Resources… recommend… 15
## 3 /Library/Frameworks/R.framework/Versions/3.3/Resources… <NA> 243
## * what proportion need compilation?
ipt %>%
count(NeedsCompilation) %>%
mutate(prop = n / sum(n))
## # A tibble: 3 x 3
## NeedsCompilation n prop
## <chr> <int> <dbl>
## 1 no 106 0.390
## 2 yes 142 0.522
## 3 <NA> 24 0.0882
## * how break down re: version of R they were built on
ipt %>%
count(Built) %>%
mutate(prop = n / sum(n))
## # A tibble: 2 x 3
## Built n prop
## <chr> <int> <dbl>
## 1 3.3.0 63 0.232
## 2 3.3.2 209 0.768
Reflections
## reflect on ^^ and make a few notes to yourself; inspiration
## * does the number of base + recommended packages make sense to you?
## * how does the result of .libPaths() relate to the result of .Library?
Going further
## if you have time to do more ...
## is every package in .Library either base or recommended?
all_default_pkgs <- list.files(.Library)
all_br_pkgs <- ipt %>%
filter(Priority %in% c("base", "recommended")) %>%
pull(Package)
setdiff(all_default_pkgs, all_br_pkgs)
## [1] "acepack" "ade4" "adehabitat"
## [4] "adehabitatHR" "adehabitatHS" "adehabitatLT"
## [7] "adehabitatMA" "akima" "animation"
## [10] "assertthat" "backports" "base64enc"
## [13] "BH" "bindr" "bindrcpp"
## [16] "bitops" "broom" "callr"
## [19] "caTools" "CCA" "cellranger"
## [22] "checkmate" "CircStats" "classInt"
## [25] "cli" "clipr" "clisymbols"
## [28] "coda" "colorRamps" "colorspace"
## [31] "corpcor" "covr" "crayon"
## [34] "crosstalk" "curl" "data.table"
## [37] "DBI" "dbplyr" "deldir"
## [40] "Deriv" "desc" "devtools"
## [43] "dichromat" "digest" "doParallel"
## [46] "dotCall64" "dplyr" "e1071"
## [49] "enc" "evaluate" "fda"
## [52] "FGN" "fields" "filehash"
## [55] "FNN" "forcats" "foreach"
## [58] "Formula" "fs" "gamm4"
## [61] "gbm" "gdtools" "geosphere"
## [64] "GGally" "gganimate" "ggforce"
## [67] "ggmap" "ggplot2" "ggplot2movies"
## [70] "ggraph" "ggrepel" "ggsn"
## [73] "gh" "GISTools" "git2r"
## [76] "glue" "gmt" "gridBase"
## [79] "gridExtra" "gstat" "gtable"
## [82] "gtools" "haven" "here"
## [85] "hexbin" "highr" "HKprocess"
## [88] "Hmisc" "hms" "hoardr"
## [91] "htmlTable" "htmltools" "htmlwidgets"
## [94] "httpuv" "httr" "igraph"
## [97] "ini" "INLA" "intervals"
## [100] "irlba" "iterators" "jpeg"
## [103] "jsonlite" "knitr" "labeling"
## [106] "latticeExtra" "lazyeval" "leaflet"
## [109] "lme4" "ltsa" "lubridate"
## [112] "lunar" "magrittr" "mapdata"
## [115] "mapproj" "maps" "maptools"
## [118] "markdown" "MatrixModels" "mcmc"
## [121] "MCMCpack" "memoise" "mime"
## [124] "minqa" "misc3d" "mixtools"
## [127] "mnormt" "modelr" "multcomp"
## [130] "munsell" "mvtnorm" "ncdf4"
## [133] "nloptr" "NMF" "numDeriv"
## [136] "openssl" "orthopolynom" "PBSmapping"
## [139] "pillar" "pixmap" "pkgconfig"
## [142] "pkgmaker" "plogr" "plot3D"
## [145] "plotdap" "plyr" "png"
## [148] "polynom" "praise" "prettymapr"
## [151] "prettyunits" "progress" "proj4"
## [154] "proto" "psych" "purrr"
## [157] "quantreg" "R.methodsS3" "R.oo"
## [160] "R.utils" "R6" "RandomFields"
## [163] "RandomFieldsUtils" "RANN" "rappdirs"
## [166] "raster" "rasterVis" "RColorBrewer"
## [169] "Rcpp" "RcppEigen" "RCurl"
## [172] "readr" "readxl" "registry"
## [175] "rematch" "rematch2" "reprex"
## [178] "rerddap" "reshape" "reshape2"
## [181] "rex" "rgdal" "rgeos"
## [184] "rgl" "RgoogleMaps" "rjson"
## [187] "rlang" "rmarkdown" "rngtools"
## [190] "rprojroot" "rstudioapi" "RUnit"
## [193] "rvest" "sandwich" "scales"
## [196] "SDMTools" "segmented" "selectr"
## [199] "sf" "shape" "shapefiles"
## [202] "shiny" "sourcetools" "sp"
## [205] "spacetime" "spam" "SparseM"
## [208] "SpatialDeltaGLMM" "SpatialDFA" "splancs"
## [211] "stabledist" "statmod" "stringi"
## [214] "stringr" "styler" "svglite"
## [217] "testthat" "TH.data" "ThorsonUtilities"
## [220] "tibble" "tidyr" "tidyselect"
## [223] "tidyverse" "tkrplot" "TMB"
## [226] "TMBhelper" "translations" "tweedie"
## [229] "tweenr" "udunits2" "units"
## [232] "usethis" "utf8" "VAST"
## [235] "viridis" "viridisLite" "whisker"
## [238] "withr" "XML" "xml2"
## [241] "xtable" "xts" "yaml"
## [244] "zoo"
## study package naming style (all lower case, contains '.', etc
## use `fields` argument to installed.packages() to get more info and use it!
ipt2 <- installed.packages(fields = "URL") %>%
as_tibble()
ipt2 %>%
mutate(github = grepl("github", URL)) %>%
count(github) %>%
mutate(prop = n / sum(n))
## # A tibble: 2 x 3
## github n prop
## <lgl> <int> <dbl>
## 1 F 157 0.577
## 2 T 115 0.423
Try out some plotting created here: https://github.com/aedobbyn/what-they-forgot/blob/5aced5a4061848bfb58ece7e3d8a742550145ab3/day1_s1_explore-libraries/package_links.R
# Tibble of installed packages
inst_packages <- installed.packages() %>% as_tibble()
# Take a look at what we've got in LinkingTo; seems like a comma separated string
inst_packages$LinkingTo[1:50]
## [1] NA NA NA NA NA
## [6] NA NA NA NA NA
## [11] NA NA NA NA NA
## [16] "Rcpp, plogr" NA NA NA NA
## [21] NA NA NA NA NA
## [26] NA NA NA NA NA
## [31] NA NA NA NA NA
## [36] NA NA NA NA NA
## [41] NA NA NA NA NA
## [46] NA NA NA NA NA
# For now, take just the first link and remove trailing commas
inst_packages <- inst_packages %>%
mutate(
linking_to = str_split(LinkingTo, " ") %>% map_chr(first) %>% gsub(",", "", .)
)
# Create the links between packages and their first LinkingTo package
package_links <- inst_packages %>%
drop_na(linking_to) %>%
select(Package, linking_to) %>%
as_tibble() %>%
igraph::graph_from_data_frame()
# Make the graph!
link_graph <- ggraph::ggraph(package_links, layout = "fr") +
geom_edge_link(alpha = 0.5) +
geom_node_point(color = "blue", size = 5, alpha = 0.5) +
geom_node_text(aes(label = name), repel = TRUE) +
theme_void() +
ggtitle("Packages LinkingTo other packages")
link_graph
devtools::session_info()
## Warning in as.POSIXlt.POSIXct(Sys.time()): unknown timezone 'zone/tz/2017c.
## 1.0/zoneinfo/America/Los_Angeles'
## Session info -------------------------------------------------------------
## setting value
## version R version 3.3.2 (2016-10-31)
## system x86_64, darwin13.4.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz <NA>
## date 2018-01-31
## Packages -----------------------------------------------------------------
## package * version date source
## assertthat 0.2.0 2017-04-11 CRAN (R 3.3.2)
## backports 1.1.2 2017-12-13 CRAN (R 3.3.2)
## base * 3.3.2 2016-10-31 local
## bindr 0.1 2016-11-13 CRAN (R 3.3.2)
## bindrcpp * 0.2 2017-06-17 CRAN (R 3.3.2)
## broom 0.4.3 2017-11-20 CRAN (R 3.3.2)
## cellranger 1.1.0 2016-07-27 CRAN (R 3.3.0)
## cli 1.0.0 2017-11-05 CRAN (R 3.3.2)
## colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
## crayon 1.3.4 2017-09-16 CRAN (R 3.3.2)
## datasets * 3.3.2 2016-10-31 local
## devtools 1.13.4 2017-11-09 CRAN (R 3.3.2)
## digest 0.6.14 2018-01-14 CRAN (R 3.3.2)
## dplyr * 0.7.4 2017-09-28 CRAN (R 3.3.2)
## evaluate 0.10.1 2017-06-24 CRAN (R 3.3.2)
## forcats * 0.2.0 2017-01-23 CRAN (R 3.3.2)
## foreign 0.8-69 2017-06-21 CRAN (R 3.3.2)
## fs * 1.1.0 2018-01-26 CRAN (R 3.3.2)
## ggforce 0.1.1 2016-11-28 CRAN (R 3.3.2)
## ggplot2 * 2.2.1.9000 2017-08-22 Github (hadley/ggplot2@41f154f)
## ggraph * 1.0.1 2018-01-29 CRAN (R 3.3.2)
## ggrepel 0.7.0 2017-09-29 CRAN (R 3.3.2)
## glue 1.2.0 2017-10-29 CRAN (R 3.3.2)
## graphics * 3.3.2 2016-10-31 local
## grDevices * 3.3.2 2016-10-31 local
## grid 3.3.2 2016-10-31 local
## gridExtra 2.3 2017-09-09 CRAN (R 3.3.2)
## gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
## haven 1.1.1 2018-01-18 CRAN (R 3.3.2)
## here * 0.1 2017-05-28 CRAN (R 3.3.2)
## hms 0.4.1 2018-01-24 CRAN (R 3.3.2)
## htmltools 0.3.6 2017-04-28 cran (@0.3.6)
## httr 1.3.1 2017-08-20 cran (@1.3.1)
## igraph * 1.1.2 2017-07-21 CRAN (R 3.3.2)
## jsonlite 1.5 2017-06-01 cran (@1.5)
## knitr 1.18 2017-12-27 CRAN (R 3.3.2)
## labeling 0.3 2014-08-23 CRAN (R 3.3.0)
## lattice 0.20-35 2017-03-25 CRAN (R 3.3.2)
## lazyeval 0.2.1 2017-10-29 CRAN (R 3.3.2)
## lubridate 1.7.1 2017-11-03 CRAN (R 3.3.2)
## magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
## MASS 7.3-48 2017-12-25 CRAN (R 3.3.2)
## memoise 1.1.0 2017-04-21 CRAN (R 3.3.2)
## methods * 3.3.2 2016-10-31 local
## mnormt 1.5-5 2016-10-15 CRAN (R 3.3.0)
## modelr 0.1.1 2017-07-24 CRAN (R 3.3.2)
## munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
## nlme 3.1-131 2017-02-06 CRAN (R 3.3.2)
## parallel 3.3.2 2016-10-31 local
## pillar 1.1.0 2018-01-14 CRAN (R 3.3.2)
## pkgconfig 2.0.1 2017-03-21 CRAN (R 3.3.2)
## plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
## psych 1.7.8 2017-09-09 CRAN (R 3.3.2)
## purrr * 0.2.4 2017-10-18 CRAN (R 3.3.2)
## R6 2.2.2 2017-06-17 cran (@2.2.2)
## Rcpp 0.12.15 2018-01-20 CRAN (R 3.3.2)
## readr * 1.1.1 2017-05-16 CRAN (R 3.3.2)
## readxl 1.0.0 2017-04-18 CRAN (R 3.3.2)
## reshape2 1.4.3 2017-12-11 CRAN (R 3.3.2)
## rlang 0.1.6 2017-12-21 CRAN (R 3.3.2)
## rmarkdown 1.8 2017-11-17 CRAN (R 3.3.2)
## rprojroot 1.3-2 2018-01-03 CRAN (R 3.3.2)
## rstudioapi 0.7 2017-09-07 CRAN (R 3.3.2)
## rvest 0.3.2 2016-06-17 CRAN (R 3.3.0)
## scales 0.5.0 2017-08-24 CRAN (R 3.3.2)
## stats * 3.3.2 2016-10-31 local
## stringi 1.1.6 2017-11-17 CRAN (R 3.3.2)
## stringr * 1.2.0 2017-02-18 CRAN (R 3.3.2)
## tibble * 1.4.2 2018-01-22 CRAN (R 3.3.2)
## tidyr * 0.7.2 2017-10-16 CRAN (R 3.3.2)
## tidyselect 0.2.3 2017-11-06 CRAN (R 3.3.2)
## tidyverse * 1.2.1 2017-11-14 CRAN (R 3.3.2)
## tools 3.3.2 2016-10-31 local
## tweenr 0.1.5 2016-10-10 CRAN (R 3.3.0)
## udunits2 0.13 2016-11-17 cran (@0.13)
## units 0.5-1 2018-01-08 CRAN (R 3.3.2)
## utf8 1.1.3 2018-01-03 CRAN (R 3.3.2)
## utils * 3.3.2 2016-10-31 local
## viridis 0.4.1 2018-01-08 CRAN (R 3.3.2)
## viridisLite 0.2.0 2017-03-24 CRAN (R 3.3.2)
## withr 2.1.1 2017-12-19 CRAN (R 3.3.2)
## xml2 1.1.1 2017-01-24 CRAN (R 3.3.2)
## yaml 2.1.16 2017-12-12 CRAN (R 3.3.2) >>>>>>> d1ab9f0e3877f93bc3b63c27eb2e1be965d000a7