See https://github.com/maurolepore/dverse
Dataframe the documentation of available packages, and reference objects
across multiple packages by package or concept. Combined with
krittr::kable() or DT::datatable(), pkgdoc allows you to
reference functions by package or concept across multiple packages and
to provide links to each topic’s help file (similar to the Reference
section of a pkgdown website but not
limited to a single package).
# install.packages("devtools")
devtools::install_github("maurolepore/pkgdoc")library(pkgdoc)search_docs() creates a dataframe of documentation available to you.
# Documentation of all installed packages
search_docs()
#> Warning: `as.tibble()` was deprecated in tibble 2.0.0.
#> ℹ Please use `as_tibble()` instead.
#> ℹ The signature and semantics have changed, see `?as_tibble`.
#> ℹ The deprecated feature was likely used in the pkgdoc package.
#> Please report the issue at <https://github.com/maurolepore/pkgdoc/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> # A tibble: 54,800 × 11
#> package libpath id name title topic encoding type alias keyword concept
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 askpass /home/… 1/1 askp… Pass… askp… "UTF-8" help askp… <NA> <NA>
#> 2 askpass /home/… 1/2 ssh_… ASKP… ssh_… "UTF-8" help ssh_… <NA> <NA>
#> 3 base64e… /home/… 2/1 base… Enco… base… "" help base… manip Data M…
#> 4 base64e… /home/… 2/1 base… Enco… base… "" help base… manip Data M…
#> 5 base64e… /home/… 2/1 base… Enco… base… "" help base… manip Data M…
#> 6 base64e… /home/… 2/2 chec… Chec… chec… "" help chec… manip Data M…
#> 7 base64e… /home/… 2/3 data… Crea… data… "" help data… manip Data M…
#> 8 bit /home/… 3/1 Coer… Coer… Coer… "UTF-8" help Coer… classes Data T…
#> 9 bit /home/… 3/1 Coer… Coer… Coer… "UTF-8" help Coer… classes Logica…
#> 10 bit /home/… 3/1 Coer… Coer… Coer… "UTF-8" help Coer… logic Data T…
#> # ℹ 54,790 more rows
some_packages <- c("utils", "base")
search_docs(some_packages)
#> # A tibble: 6,445 × 11
#> package libpath id name title topic encoding type alias keyword concept
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 base /opt/R/… 171/1 Arit… Arit… Arit… "" help arith remain…
#> 2 base /opt/R/… 171/1 Arit… Arit… Arit… "" help arith modulo
#> 3 base /opt/R/… 171/1 Arit… Arit… Arit… "" help arith modulus
#> 4 base /opt/R/… 171/1 Arit… Arit… Arit… "" help arith quotie…
#> 5 base /opt/R/… 171/1 Arit… Arit… Arit… "" help arith divisi…
#> 6 base /opt/R/… 171/1 Arit… Arit… Arit… "" help arith Basic …
#> 7 base /opt/R/… 171/1 Arit… Arit… Arit… "" help - arith remain…
#> 8 base /opt/R/… 171/1 Arit… Arit… Arit… "" help - arith modulo
#> 9 base /opt/R/… 171/1 Arit… Arit… Arit… "" help - arith modulus
#> 10 base /opt/R/… 171/1 Arit… Arit… Arit… "" help - arith quotie…
#> # ℹ 6,435 more rowsreference_package() and reference_concept() allow you to pick
specific documentation.
reference_package(c("stats", "MASS"))
#> Warning: All packages should be attached `strip_s3class` to work properly.
#> Not attached: MASS
#> # A tibble: 977 × 5
#> topic alias title concept package
#> <chr> <chr> <chr> <chr> <chr>
#> 1 .checkMFClasses .checkMFClasses, .MFclass, .getXlevels Func… Utilit… stats
#> 2 print.ts .preformat.ts, print Prin… Time S… stats
#> 3 AIC AIC, BIC Akai… Statis… stats
#> 4 ARMAacf ARMAacf Comp… Time S… stats
#> 5 ARMAtoMA ARMAtoMA Conv… Time S… stats
#> 6 Aids2 Aids2 Aust… Datase… MASS
#> 7 Animals Animals Brai… Datase… MASS
#> 8 Beta Beta, dbeta, pbeta, qbeta, rbeta The … incomp… stats
#> 9 Beta Beta, dbeta, pbeta, qbeta, rbeta The … Probab… stats
#> 10 Binomial Binomial, dbinom, pbinom, qbinom, rbin… The … Probab… stats
#> # ℹ 967 more rows
reference_concept(c("combine strings", "files", "PCA"))
#> # A tibble: 7 × 5
#> topic alias title concept package
#> <chr> <chr> <chr> <chr> <chr>
#> 1 find.package find.package, path.package, packageNot… Find… files base
#> 2 paste paste, paste0 Conc… combin… base
#> 3 prcomp prcomp, plot, predict, print, summary Prin… PCA stats
#> 4 princomp princomp, plot, print, predict Prin… PCA stats
#> 5 stri_read_lines stri_read_lines Read… files stringi
#> 6 stri_read_raw stri_read_raw Read… files stringi
#> 7 stri_write_lines stri_write_lines Writ… files stringiUse knittr::kable() or DT::datatable() for the links to become
clickable.
library(fgeo)
#> ── Attaching packages ──────────────────────────────────────────── fgeo 1.1.4 ──
#> ✔ fgeo.analyze 1.1.14 ✔ fgeo.tool 1.2.9
#> ✔ fgeo.plot 1.1.11 ✔ fgeo.x 1.1.4
#> ── Conflicts ─────────────────────────────────────────────── fgeo_conflicts() ──
#> ✖ fgeo.tool::filter() masks stats::filter()
reference_concept(
c("datasets", "plot functions"),
url = "https://forestgeo.github.io/",
) %>%
arrange(concept) %>%
head() %>%
knitr::kable()| topic | alias | title | concept | package |
|---|---|---|---|---|
| ? | datasets, elevation, habitat, stem5, stem6, tree5, tree6, vft_4quad, tree6_3species | Access data via ‘library(fgeo.x)’ or ‘fgeo.x::’. | datasets | fgeo.x |
| ? | download_data | Access data stored online. | datasets | fgeo.x |
| ? | example_path | Access data stored in system files. | datasets | fgeo.x |
| ? | autoplot | Plot habitats. | plot functions | fgeo.plot |
| ? | autoplot | Plot species distribution and/or topography. | plot functions | fgeo.plot |
| ? | autoplot_by_species | List plots of species distribution and topography (good for pdf output). | plot functions | fgeo.plot |