first_steps.md
In ventri2020/rraysplot: Make 2D Arrays Plots Less Aggravating
First Steps
More info…
- Package structure and state. 4.7 Package
libraries.
- Comparison of
fs functions, base R, and shell
commands
Managing package libraries
Here are the main two levers that control which libraries are active, in
order of scope and persistence:
- Environment variables, like
R_LIBS and R_LIBS_USER, which are
consulted at startup.
- Calling
.libPaths() with one or more filepaths.
mkdir -p ~/Library/R/4.0/library
cat ~/.Rprofile.site
#> # ?.libPaths
#> .Library.site = "~/Library/%v/library"
#> .libPaths(.libPaths())
echo $R_LIBS_USER
#> ~/Library/R/4.0/library
.Library
#> [1] "/Library/Frameworks/R.framework/Resources/library"
.Library.site
#> character(0)
In both cases we see two active libraries, consulted in this order:
- A user library.
- A system-level or global library.
.libPaths()
#> [1] "/Users/wbzyl/Library/R/4.0/library"
#> [2] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library"
lapply(
.libPaths(),
list.dirs,
recursive = FALSE,
full.names = FALSE)
#> [[1]]
#> [1] "available" "clisymbols" "hunspell" "janeaustenr" "ragg"
#> [6] "rraysplot" "SnowballC" "stringdist" "systemfonts" "textshaping"
#> [11] "tidytext" "tokenizers" "udapi" "yesno"
#>
#> [[2]]
#> [1] "abind" "ANTsR" "ANTsRCore" "ANTsRNet" "askpass"
#> [6] "assertthat" "backports" "base" "base64enc" "BBmisc"
#> [11] "BH" "bitops" "blob" "bmp" "boot"
#> [16] "brew" "brio" "broom" "callr" "cellranger"
#> [21] "checkmate" "class" "cli" "clipr" "cluster"
#> [26] "codetools" "colorspace" "commonmark" "compiler" "config"
#> [31] "covr" "cowplot" "cpp11" "crayon" "credentials"
#> [36] "crosstalk" "curl" "datasets" "DBI" "dbplyr"
#> [41] "desc" "devtools" "diffobj" "digest" "downloader"
#> [46] "dplyr" "DT" "ellipsis" "evaluate" "fansi"
#> [51] "farver" "fastmap" "fftwtools" "forcats" "foreign"
#> [56] "fs" "generics" "gert" "ggplot2" "gh"
#> [61] "git2r" "gitcreds" "glue" "graphics" "grDevices"
#> [66] "grid" "gridExtra" "gtable" "haven" "highr"
#> [71] "hms" "htmltools" "htmlwidgets" "httpuv" "httr"
#> [76] "igraph" "imager" "imagerExtra" "ini" "isoband"
#> [81] "ITKR" "jpeg" "jsonlite" "keras" "KernSmooth"
#> [86] "knitr" "labeling" "later" "lattice" "lazyeval"
#> [91] "learnr" "lifecycle" "lobstr" "lubridate" "magrittr"
#> [96] "markdown" "MASS" "Matrix" "memoise" "methods"
#> [101] "mgcv" "mime" "miniUI" "misc3d" "modelr"
#> [106] "munsell" "mvtnorm" "nlme" "nnet" "openssl"
#> [111] "oro.nifti" "parallel" "pillar" "pixmap" "pkgbuild"
#> [116] "pkgconfig" "pkgload" "plogr" "plyr" "png"
#> [121] "praise" "prettyunits" "processx" "progress" "promises"
#> [126] "ps" "purrr" "R6" "rappdirs" "raster"
#> [131] "rcmdcheck" "RColorBrewer" "Rcpp" "RcppEigen" "readbitmap"
#> [136] "readr" "readxl" "regexplain" "rematch" "rematch2"
#> [141] "remotes" "renv" "reprex" "reshape2" "reticulate"
#> [146] "rex" "rlang" "rmarkdown" "RNifti" "roxygen2"
#> [151] "rpart" "rprojroot" "rstudioapi" "rticles" "rversions"
#> [156] "rvest" "scales" "selectr" "sessioninfo" "shiny"
#> [161] "sloop" "sourcetools" "sp" "spatial" "splines"
#> [166] "spng" "stats" "stats4" "stringi" "stringr"
#> [171] "survival" "sys" "tcltk" "tensorflow" "testthat"
#> [176] "tfruns" "tibble" "tidyr" "tidyselect" "tidyverse"
#> [181] "tiff" "tinytex" "tools" "translations" "usethis"
#> [186] "utf8" "utils" "vctrs" "viridisLite" "waldo"
#> [191] "whisker" "withr" "xfun" "xml2" "xopen"
#> [196] "xtable" "yaml" "zeallot" "zip"
Check what is installed
packageVersion("devtools")
#> [1] '2.3.2'
options(buildtools.check = NULL)
# devtools::install_github("r-lib/devtools")
# packageVersion("devtools")
Optionally run:
# tidyverse::tidyverse_update()
# tidyverse::tidyverse_conflicts()
tidyverse::tidyverse_packages()
#> [1] "broom" "cli" "crayon" "dbplyr" "dplyr"
#> [6] "forcats" "ggplot2" "haven" "hms" "httr"
#> [11] "jsonlite" "lubridate" "magrittr" "modelr" "pillar"
#> [16] "purrr" "readr" "readxl" "reprex" "rlang"
#> [21] "rstudioapi" "rvest" "stringr" "tibble" "tidyr"
#> [26] "xml2" "tidyverse"
Name your package
There are three formal requirements:
- The name can only consist of letters, numbers, and periods.
- It must start with a letter.
- It cannot end with a period.
Unfortunately, this means you can’t use either hyphens (-) or
underscores (_) in your package name. We recommend against using
periods in package names, due to confusing associations with file
extensions and S3 methods.
The
available
package has a function called available() that helps you evaluate a
potential package name from many angles:
devtools::install_github("ropenscilabs/available")
available::suggest(text = "Plotting helpers for arrays.")
#> rraysplot
Create package
library(devtools)
#> Loading required package: usethis
library(tidyverse)
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
#> ✓ ggplot2 3.3.2 ✓ purrr 0.3.4
#> ✓ tibble 3.0.4 ✓ dplyr 1.0.2
#> ✓ tidyr 1.1.2 ✓ stringr 1.4.0
#> ✓ readr 1.4.0 ✓ forcats 0.5.0
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> x dplyr::filter() masks stats::filter()
#> x dplyr::lag() masks stats::lag()
source_directory <- "~/RPKGS/GUMED"
package_name <- "rraysplot"
# fs::dir_create(source_directory)
pkg_path <- fs::path(.libPaths()[[1]], package_name)
pkg_path
#> /Users/wbzyl/Library/R/4.0/library/rraysplot
src_path <- fs::path(source_directory, package_name)
src_path
#> ~/RPKGS/GUMED/rraysplot
usethis::create_package(src_path)
✓ Creating '/Users/wbzyl/RPKGS/GUMED/rraysplot/'
✓ Setting active project to '/Users/wbzyl/RPKGS/GUMED/rraysplot'
✓ Creating 'R/'
✓ Writing 'DESCRIPTION'
Package: rraysplot
Title: What the Package Does (One Line, Title Case)
Version: 0.0.0.9000
Authors@R (parsed):
* Wlodek <wlodek@rpkgs.com> [aut, cre]
Description: What the package does (one paragraph).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
✓ Writing 'NAMESPACE'
✓ Writing 'rraysplot.Rproj'
✓ Adding '.Rproj.user' to '.gitignore'
✓ Adding '^rraysplot\\.Rproj$', '^\\.Rproj\\.user$' to '.Rbuildignore'
✓ Opening '/Users/wbzyl/RPKGS/GUMED/rraysplot/' in new RStudio session
✓ Setting active project to '<no active project>'
fs::dir_info(
all = TRUE,
recurse = TRUE,
regexp = "^(.git|.Rproj.user)/.+",
invert = TRUE) %>%
dplyr::select(path, type)
#> # A tibble: 25 x 2
#> path type
#> <fs::path> <fct>
#> 1 .Rbuildignore file
#> 2 .Rproj.user directory
#> 3 .git directory
#> 4 .gitignore file
#> 5 DESCRIPTION file
#> 6 LICENSE file
#> 7 LICENSE.md file
#> 8 NAMESPACE file
#> 9 R directory
#> 10 R/make_arrays.R file
#> # … with 15 more rows
use_r("make_arrays")
#> ✓ Setting active project to '/Users/wbzyl/RPKGS/GUMED/rraysplot'
#> ● Edit 'R/make_arrays.R'
#> ● Call `use_test()` to create a matching test file
ventri2020/rraysplot documentation built on Jan. 1, 2021, 12:38 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.
First Steps
More info…
- Package structure and state. 4.7 Package libraries.
- Comparison of
fsfunctions, base R, and shell commands
Managing package libraries
Here are the main two levers that control which libraries are active, in order of scope and persistence:
- Environment variables, like
R_LIBSandR_LIBS_USER, which are consulted at startup. - Calling
.libPaths()with one or more filepaths.
mkdir -p ~/Library/R/4.0/library
cat ~/.Rprofile.site
#> # ?.libPaths
#> .Library.site = "~/Library/%v/library"
#> .libPaths(.libPaths())
echo $R_LIBS_USER
#> ~/Library/R/4.0/library
.Library
#> [1] "/Library/Frameworks/R.framework/Resources/library"
.Library.site
#> character(0)
In both cases we see two active libraries, consulted in this order:
- A user library.
- A system-level or global library.
.libPaths()
#> [1] "/Users/wbzyl/Library/R/4.0/library"
#> [2] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library"
lapply(
.libPaths(),
list.dirs,
recursive = FALSE,
full.names = FALSE)
#> [[1]]
#> [1] "available" "clisymbols" "hunspell" "janeaustenr" "ragg"
#> [6] "rraysplot" "SnowballC" "stringdist" "systemfonts" "textshaping"
#> [11] "tidytext" "tokenizers" "udapi" "yesno"
#>
#> [[2]]
#> [1] "abind" "ANTsR" "ANTsRCore" "ANTsRNet" "askpass"
#> [6] "assertthat" "backports" "base" "base64enc" "BBmisc"
#> [11] "BH" "bitops" "blob" "bmp" "boot"
#> [16] "brew" "brio" "broom" "callr" "cellranger"
#> [21] "checkmate" "class" "cli" "clipr" "cluster"
#> [26] "codetools" "colorspace" "commonmark" "compiler" "config"
#> [31] "covr" "cowplot" "cpp11" "crayon" "credentials"
#> [36] "crosstalk" "curl" "datasets" "DBI" "dbplyr"
#> [41] "desc" "devtools" "diffobj" "digest" "downloader"
#> [46] "dplyr" "DT" "ellipsis" "evaluate" "fansi"
#> [51] "farver" "fastmap" "fftwtools" "forcats" "foreign"
#> [56] "fs" "generics" "gert" "ggplot2" "gh"
#> [61] "git2r" "gitcreds" "glue" "graphics" "grDevices"
#> [66] "grid" "gridExtra" "gtable" "haven" "highr"
#> [71] "hms" "htmltools" "htmlwidgets" "httpuv" "httr"
#> [76] "igraph" "imager" "imagerExtra" "ini" "isoband"
#> [81] "ITKR" "jpeg" "jsonlite" "keras" "KernSmooth"
#> [86] "knitr" "labeling" "later" "lattice" "lazyeval"
#> [91] "learnr" "lifecycle" "lobstr" "lubridate" "magrittr"
#> [96] "markdown" "MASS" "Matrix" "memoise" "methods"
#> [101] "mgcv" "mime" "miniUI" "misc3d" "modelr"
#> [106] "munsell" "mvtnorm" "nlme" "nnet" "openssl"
#> [111] "oro.nifti" "parallel" "pillar" "pixmap" "pkgbuild"
#> [116] "pkgconfig" "pkgload" "plogr" "plyr" "png"
#> [121] "praise" "prettyunits" "processx" "progress" "promises"
#> [126] "ps" "purrr" "R6" "rappdirs" "raster"
#> [131] "rcmdcheck" "RColorBrewer" "Rcpp" "RcppEigen" "readbitmap"
#> [136] "readr" "readxl" "regexplain" "rematch" "rematch2"
#> [141] "remotes" "renv" "reprex" "reshape2" "reticulate"
#> [146] "rex" "rlang" "rmarkdown" "RNifti" "roxygen2"
#> [151] "rpart" "rprojroot" "rstudioapi" "rticles" "rversions"
#> [156] "rvest" "scales" "selectr" "sessioninfo" "shiny"
#> [161] "sloop" "sourcetools" "sp" "spatial" "splines"
#> [166] "spng" "stats" "stats4" "stringi" "stringr"
#> [171] "survival" "sys" "tcltk" "tensorflow" "testthat"
#> [176] "tfruns" "tibble" "tidyr" "tidyselect" "tidyverse"
#> [181] "tiff" "tinytex" "tools" "translations" "usethis"
#> [186] "utf8" "utils" "vctrs" "viridisLite" "waldo"
#> [191] "whisker" "withr" "xfun" "xml2" "xopen"
#> [196] "xtable" "yaml" "zeallot" "zip"
Check what is installed
packageVersion("devtools")
#> [1] '2.3.2'
options(buildtools.check = NULL)
# devtools::install_github("r-lib/devtools")
# packageVersion("devtools")
Optionally run:
# tidyverse::tidyverse_update()
# tidyverse::tidyverse_conflicts()
tidyverse::tidyverse_packages()
#> [1] "broom" "cli" "crayon" "dbplyr" "dplyr"
#> [6] "forcats" "ggplot2" "haven" "hms" "httr"
#> [11] "jsonlite" "lubridate" "magrittr" "modelr" "pillar"
#> [16] "purrr" "readr" "readxl" "reprex" "rlang"
#> [21] "rstudioapi" "rvest" "stringr" "tibble" "tidyr"
#> [26] "xml2" "tidyverse"
Name your package
There are three formal requirements:
- The name can only consist of letters, numbers, and periods.
- It must start with a letter.
- It cannot end with a period.
Unfortunately, this means you can’t use either hyphens (-) or
underscores (_) in your package name. We recommend against using
periods in package names, due to confusing associations with file
extensions and S3 methods.
The
available
package has a function called available() that helps you evaluate a
potential package name from many angles:
devtools::install_github("ropenscilabs/available")
available::suggest(text = "Plotting helpers for arrays.")
#> rraysplot
Create package
library(devtools)
#> Loading required package: usethis
library(tidyverse)
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
#> ✓ ggplot2 3.3.2 ✓ purrr 0.3.4
#> ✓ tibble 3.0.4 ✓ dplyr 1.0.2
#> ✓ tidyr 1.1.2 ✓ stringr 1.4.0
#> ✓ readr 1.4.0 ✓ forcats 0.5.0
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> x dplyr::filter() masks stats::filter()
#> x dplyr::lag() masks stats::lag()
source_directory <- "~/RPKGS/GUMED"
package_name <- "rraysplot"
# fs::dir_create(source_directory)
pkg_path <- fs::path(.libPaths()[[1]], package_name)
pkg_path
#> /Users/wbzyl/Library/R/4.0/library/rraysplot
src_path <- fs::path(source_directory, package_name)
src_path
#> ~/RPKGS/GUMED/rraysplot
usethis::create_package(src_path)
✓ Creating '/Users/wbzyl/RPKGS/GUMED/rraysplot/'
✓ Setting active project to '/Users/wbzyl/RPKGS/GUMED/rraysplot'
✓ Creating 'R/'
✓ Writing 'DESCRIPTION'
Package: rraysplot
Title: What the Package Does (One Line, Title Case)
Version: 0.0.0.9000
Authors@R (parsed):
* Wlodek <wlodek@rpkgs.com> [aut, cre]
Description: What the package does (one paragraph).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
✓ Writing 'NAMESPACE'
✓ Writing 'rraysplot.Rproj'
✓ Adding '.Rproj.user' to '.gitignore'
✓ Adding '^rraysplot\\.Rproj$', '^\\.Rproj\\.user$' to '.Rbuildignore'
✓ Opening '/Users/wbzyl/RPKGS/GUMED/rraysplot/' in new RStudio session
✓ Setting active project to '<no active project>'
fs::dir_info(
all = TRUE,
recurse = TRUE,
regexp = "^(.git|.Rproj.user)/.+",
invert = TRUE) %>%
dplyr::select(path, type)
#> # A tibble: 25 x 2
#> path type
#> <fs::path> <fct>
#> 1 .Rbuildignore file
#> 2 .Rproj.user directory
#> 3 .git directory
#> 4 .gitignore file
#> 5 DESCRIPTION file
#> 6 LICENSE file
#> 7 LICENSE.md file
#> 8 NAMESPACE file
#> 9 R directory
#> 10 R/make_arrays.R file
#> # … with 15 more rows
use_r("make_arrays")
#> ✓ Setting active project to '/Users/wbzyl/RPKGS/GUMED/rraysplot'
#> ● Edit 'R/make_arrays.R'
#> ● Call `use_test()` to create a matching test file
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.
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