This document will capture the RAP (Reproducible Analytical Pipeline) learning from the CKP (Community Knowledge Profile) project.
The project has several factors that make it suitable for understanding RAP better:
The expectation is that the notes in this document will mature and reside outside a pipeline specific repo and in a Council-wide resource such as pinsheff, a Methods Manual, or something like Hackney’s Data Platform Playbook.
Load packages and declare functions.
library(renv)
library(tidyverse)
library(tools)
library(jsonlite)
library(janitor)
library(kableExtra)
library(here)
# Output & format a data frame as a table
table_style <- function(df, scroll_box = TRUE) {
df |>
kbl(format.args = list(big.mark = ",")) |>
kable_styling(
bootstrap_options = "striped",
full_width = F,
font_size = 12,
position = "left"
) |>
(\(.) if(scroll_box) scroll_box(., height = "400px") else .)()
}A requirement of the NHS Gold RAP - analysis as a product is:
Code is fully packaged.
The Government’s Analytical Services guidance includes the following RAP Principle:
Packaging.
We first looked at the repository template:
github.com/craig-shenton/rapR-package-template
However, this was too complex for a simple project that already involved learning for contributors around ggplot, version control etc.
Instead, we used create_package() function from the usethis R package and ran:
usethis::create_package(here::here(), check_name = FALSE)
Ch.11 Packaging your code, Building reproducible analytical pipelines with R by Bruno Rodrigues
R Packages (2e), by Hadley Wickham and Jennifer Bryan
Our motivation was to create a GitHub Codespace, or something like it, for the project. To allow the project to be used by anyone interested in starting to use R and contribute to the work. To pass them a URL that opened a development environment in their browser, with everything setup and ready for them to code. We haven’t succeeded in this yet, but the notes in this section include some useful reproducibility lessons.
The code in the CKP repo may not work in a year’s time if a new version of R introduces breaking changes. It might not work if some of the packages that the code in the repo depends on evolve and introduce some breaking changes. Similarly, if you’re collaborating on a project, a colleague may have different versions of the packages or R, and consequently you may get different results from the same code.
There are different ways of improving the reproducibility of code by specifying the dependencies (including versions) of what the code runs on. Containers is one option, an option that can also make other aspects easier, such as maintaining development environments, peer review, testing, deploying to the cloud for more computing power, and deploying to production.
One of the requirements of the NHS Silver RAP Maturity Level - implementing best practice is:
Repository includes dependency information (e.g. requirements.txt, PipFile, environment.yml).
Another option for R is renv.
The Government’s Analytical Services guidance includes the following RAP Principle:
Dependency management.
And, the following Reproducible Analysis Platform:
Reproducible infrastructure and containers, for example, docker.
Our CKP project is hosted in a public GitHub repo, so our preferred option would be GitHub Codespaces.
Codespaces does integrate with IDE’s other than VS Code. However, the example from David Smith at the 2022 RStudio Conference, only manages this via a VS Code port. We were able to replicate this for the community-knowledge-profiles repo by simply copying the .devcontainer directory from David’s example. This proved neither slick nor robust to changes, and as there’s a Posit Cloud option we didn’t spend long trying to improve this.
You can login to https://posit.cloud (formerly RStudio Cloud) using your GitHub account, which makes working with GitHub repos easier.
To setup Posit Cloud for CKP:
Create a New Project > New Project from Git Repository.
Add the HTTPS URL for our repo.
https://github.com/scc-pi/community-knowledge-profiles.git
From the RStudio terminal call renv::restore(). This will install the necessary packages into your Posit Cloud RStudio project. It can take twenty or thirty minutes, but only for the first time as part of setting up the project.
Setup your GitHub PAT for HTTPS as per Jenny Bryan’s instructions.
This process isn’t as slick as we’d like for people new to R. Ideally we’d authorise their use of a cloud based development environment for the project and pass them a URL. You can’t really do this with Posit Cloud without paying.
You can share and collaborate within a Posit Cloud Space. However, the time spent by others in a project you created is registered against your time. You only have 25 hours a month on the Posit Cloud free plan, so best to save this for code reviews etc.
This Posit Cloud setup makes use of the {renv} R package which handles project level package management, as opposed to the normal system or user level package management. We made use of the following renv guidance in particular:
If you add or remove packages from the CKP project (in a repo on your laptop or in Posit Cloud) you need to update the renv.lock file by calling renv::snapshot(). Then stage, commit, and push your renv.lock change to the CKP repo. If a change to renv.lock is pulled, you need to call renv::restore() to install or remove the packages.
{renv} also integrates with RStudio Packages pane:
See Section 7 for a deeper look at {renv} and our project dependencies.
TODO
?? Rocker
?? Development Environments preview
Microsoft Dev Box is an interesting option that could fit well with our projects that use PID and have repos on Azure DevOps.
Ch.10 Basic reproducibility: freezing packages, Building reproducible analytical pipelines with R by Bruno Rodrigues
Ch.14 Reproducible analytical pipelines with Docker, Building reproducible analytical pipelines with R by Bruno Rodrigues
A requirement of the NHS Gold RAP - analysis as a product is:
Repository automatically runs tests etc. via CI/CD or a different integration/deployment tool e.g. GitHub Actions.
The Government’s Analytical Services guidance includes the following RAP Principle:
Continuous integration.
And, the following Reproducible Analysis Platform:
Continuous integration tools, for example, GitHub Actions, GitLab CI, Travis CI, Jenkins, Concourse.
To render the RAP Learning Quarto (rap-docs\rap-learning.qmd) to GitHub Pages at scc-pi.github.io/community-knowledge-profiles we used the public GitHub repo quarto-dev/quarto-actions. In particular we followed the:
Basic example
Added quarto-publish.yml to .github\workflows.
We had to specify the .qmd file when doing the one time local quarto publish :
quarto publish gh-pages rap-docs\rap-learning.qmd.qmd
Otherwise we got an error like:
ERROR: The specified path (C:\repo\community-knowledge-profiles) is not a website or book project so cannot be published.
Added a .gitignore file in \rap-docs with *.html to exclude local renderings.
Non top level projects example
Added path: rap-docs to our quarto-publish.yml file.
TODO
Publish Quarto to GitHub Pages
Ch.15 Continuous integration and continuous deployment, Building reproducible analytical pipelines with R by Bruno Rodrigues
TODO
TODO
Our renv.lock file includes a lot of packages. We’ve not used {renv} before, so we need to check that the renv.lock file is right and that we’re using {renv} correctly.
# Convert the renv.lock json file to a data frame
renv_lock <- fromJSON(here("renv.lock"))$Packages |>
enframe() |>
as_tibble() |>
unnest_wider(value) |>
clean_names() |>
select(-name, -hash)
table_style(renv_lock)| package | version | source | repository | requirements |
|---|---|---|---|---|
| DBI | 1.1.3 | Repository | CRAN | R , methods |
| MASS | 7.3-60 | Repository | CRAN | R , grDevices, graphics , methods , stats , utils |
| Matrix | 1.5-4 | Repository | CRAN | R , graphics, grid , lattice , methods , stats , utils |
| R6 | 2.5.1 | Repository | CRAN | R |
| RColorBrewer | 1.1-3 | Repository | CRAN | R |
| Rcpp | 1.0.11 | Repository | CRAN | methods, utils |
| askpass | 1.1 | Repository | CRAN | sys |
| backports | 1.4.1 | Repository | CRAN | R |
| base64enc | 0.1-3 | Repository | CRAN | R |
| bit | 4.0.5 | Repository | CRAN | R |
| bit64 | 4.0.5 | Repository | CRAN | R , bit , methods, stats , utils |
| blob | 1.2.4 | Repository | CRAN | methods, rlang , vctrs |
| broom | 1.0.5 | Repository | CRAN | R , backports, dplyr , ellipsis , generics , glue , lifecycle, purrr , rlang , stringr , tibble , tidyr |
| bslib | 0.5.0 | Repository | CRAN | R , base64enc, cachem , grDevices, htmltools, jquerylib, jsonlite , memoise , mime , rlang , sass |
| cachem | 1.0.8 | Repository | CRAN | fastmap, rlang |
| callr | 3.7.3 | Repository | CRAN | R , R6 , processx, utils |
| cellranger | 1.1.0 | Repository | CRAN | R , rematch, tibble |
| cli | 3.6.1 | Repository | CRAN | R , utils |
| clipr | 0.8.0 | Repository | CRAN | utils |
| codetools | 0.2-19 | Repository | CRAN | R |
| colorspace | 2.1-0 | Repository | CRAN | R , grDevices, graphics , methods , stats |
| commonmark | 1.9.0 | Repository | CRAN | NULL |
| conflicted | 1.2.0 | Repository | CRAN | R , cli , memoise, rlang |
| cpp11 | 0.4.5 | Repository | CRAN | NULL |
| crayon | 1.5.2 | Repository | CRAN | grDevices, methods , utils |
| curl | 5.0.1 | Repository | CRAN | R |
| data.table | 1.14.8 | Repository | CRAN | R , methods |
| dbplyr | 2.3.3 | Repository | CRAN | DBI , R , R6 , blob , cli , dplyr , glue , lifecycle , magrittr , methods , pillar , purrr , rlang , tibble , tidyr , tidyselect, utils , vctrs , withr |
| digest | 0.6.33 | Repository | CRAN | R , utils |
| dplyr | 1.1.2 | Repository | CRAN | R , R6 , cli , generics , glue , lifecycle , magrittr , methods , pillar , rlang , tibble , tidyselect, utils , vctrs |
| dtplyr | 1.3.1 | Repository | CRAN | R , cli , data.table, dplyr , glue , lifecycle , rlang , tibble , tidyselect, vctrs |
| ellipsis | 0.3.2 | Repository | CRAN | R , rlang |
| evaluate | 0.21 | Repository | CRAN | R , methods |
| fansi | 1.0.4 | Repository | CRAN | R , grDevices, utils |
| farver | 2.1.1 | Repository | CRAN | NULL |
| fastmap | 1.1.1 | Repository | CRAN | NULL |
| fontawesome | 0.5.1 | Repository | CRAN | R , htmltools, rlang |
| forcats | 1.0.0 | Repository | CRAN | R , cli , glue , lifecycle, magrittr , rlang , tibble |
| fs | 1.6.2 | Repository | CRAN | R , methods |
| furrr | 0.3.1 | Repository | CRAN | R , future , globals , lifecycle, purrr , rlang , vctrs |
| future | 1.33.0 | Repository | CRAN | digest , globals , listenv , parallel , parallelly, utils |
| gargle | 1.5.2 | Repository | CRAN | R , cli , fs , glue , httr , jsonlite , lifecycle, openssl , rappdirs , rlang , stats , utils , withr |
| generics | 0.1.3 | Repository | CRAN | R , methods |
| ggplot2 | 3.4.2 | Repository | CRAN | MASS , R , cli , glue , grDevices, grid , gtable , isoband , lifecycle, mgcv , rlang , scales , stats , tibble , vctrs , withr |
| globals | 0.16.2 | Repository | CRAN | R , codetools |
| glue | 1.6.2 | Repository | CRAN | R , methods |
| googledrive | 2.1.1 | Repository | CRAN | R , cli , gargle , glue , httr , jsonlite , lifecycle, magrittr , pillar , purrr , rlang , tibble , utils , uuid , vctrs , withr |
| googlesheets4 | 1.1.1 | Repository | CRAN | R , cellranger , cli , curl , gargle , glue , googledrive, httr , ids , lifecycle , magrittr , methods , purrr , rematch2 , rlang , tibble , utils , vctrs , withr |
| gtable | 0.3.3 | Repository | CRAN | R , cli , glue , grid , lifecycle, rlang |
| haven | 2.5.3 | Repository | CRAN | R , cli , cpp11 , forcats , hms , lifecycle , methods , readr , rlang , tibble , tidyselect, vctrs |
| here | 1.0.1 | Repository | CRAN | rprojroot |
| highr | 0.10 | Repository | CRAN | R , xfun |
| hms | 1.1.3 | Repository | CRAN | lifecycle, methods , pkgconfig, rlang , vctrs |
| htmltools | 0.5.5 | Repository | CRAN | R , base64enc, digest , ellipsis , fastmap , grDevices, rlang , utils |
| httpuv | 1.6.11 | Repository | CRAN | R , R6 , Rcpp , later , promises, utils |
| httr | 1.4.6 | Repository | CRAN | R , R6 , curl , jsonlite, mime , openssl |
| httr2 | 0.2.3 | Repository | CRAN | R , R6 , cli , curl , glue , magrittr, openssl , rappdirs, rlang , withr |
| ids | 1.0.1 | Repository | CRAN | openssl, uuid |
| isoband | 0.2.7 | Repository | CRAN | grid , utils |
| janitor | 2.2.0 | Repository | CRAN | R , dplyr , hms , lifecycle , lubridate , magrittr , purrr , rlang , snakecase , stringi , stringr , tidyr , tidyselect |
| jquerylib | 0.1.4 | Repository | CRAN | htmltools |
| jsonlite | 1.8.7 | Repository | CRAN | methods |
| kableExtra | 1.3.4 | Repository | CRAN | R , digest , glue , grDevices , graphics , htmltools , knitr , magrittr , rmarkdown , rstudioapi , rvest , scales , stats , stringr , svglite , tools , viridisLite, webshot , xml2 |
| knitr | 1.43 | Repository | CRAN | R , evaluate, highr , methods , tools , xfun , yaml |
| labeling | 0.4.2 | Repository | CRAN | graphics, stats |
| later | 1.3.1 | Repository | CRAN | Rcpp , rlang |
| lattice | 0.21-8 | Repository | CRAN | R , grDevices, graphics , grid , stats , utils |
| lifecycle | 1.0.3 | Repository | CRAN | R , cli , glue , rlang |
| listenv | 0.9.0 | Repository | CRAN | R |
| lubridate | 1.9.2 | Repository | CRAN | R , generics , methods , timechange |
| magrittr | 2.0.3 | Repository | CRAN | R |
| memoise | 2.0.1 | Repository | CRAN | cachem, rlang |
| mgcv | 1.8-42 | Repository | CRAN | Matrix , R , graphics, methods , nlme , splines , stats , utils |
| mime | 0.12 | Repository | CRAN | tools |
| modelr | 0.1.11 | Repository | CRAN | R , broom , magrittr , purrr , rlang , tibble , tidyr , tidyselect, vctrs |
| munsell | 0.5.0 | Repository | CRAN | colorspace, methods |
| nlme | 3.1-162 | Repository | CRAN | R , graphics, lattice , stats , utils |
| onsr | 1.0.1 | Repository | CRAN | R , httr , jsonlite, readr , tibble |
| openssl | 2.1.0 | Repository | CRAN | askpass |
| packrat | 0.9.1 | Repository | CRAN | R , tools, utils |
| parallelly | 1.36.0 | Repository | CRAN | parallel, tools , utils |
| pillar | 1.9.0 | Repository | CRAN | cli , fansi , glue , lifecycle, rlang , utf8 , utils , vctrs |
| pkgconfig | 2.0.3 | Repository | CRAN | utils |
| prettyunits | 1.1.1 | Repository | CRAN | NULL |
| processx | 3.8.2 | Repository | CRAN | R , R6 , ps , utils |
| progress | 1.2.2 | Repository | CRAN | R6 , crayon , hms , prettyunits |
| promises | 1.2.0.1 | Repository | CRAN | R6 , Rcpp , later , magrittr, rlang , stats |
| ps | 1.7.5 | Repository | CRAN | R , utils |
| purrr | 1.0.1 | Repository | CRAN | R , cli , lifecycle, magrittr , rlang , vctrs |
| quarto | 1.2 | Repository | CRAN | jsonlite , later , processx , rmarkdown , rsconnect , rstudioapi, utils , yaml |
| ragg | 1.2.5 | Repository | CRAN | systemfonts, textshaping |
| rappdirs | 0.3.3 | Repository | CRAN | R |
| readr | 2.1.4 | Repository | CRAN | R , R6 , cli , clipr , cpp11 , crayon , hms , lifecycle, methods , rlang , tibble , tzdb , utils , vroom |
| readxl | 1.4.3 | Repository | CRAN | R , cellranger, cpp11 , progress , tibble , utils |
| rematch | 1.0.1 | Repository | CRAN | NULL |
| rematch2 | 2.1.2 | Repository | CRAN | tibble |
| renv | 1.0.0 | Repository | CRAN | utils |
| reprex | 2.0.2 | Repository | CRAN | R , callr , cli , clipr , fs , glue , knitr , lifecycle , rlang , rmarkdown , rstudioapi, utils , withr |
| rlang | 1.1.1 | Repository | CRAN | R , utils |
| rmarkdown | 2.23 | Repository | CRAN | R , bslib , evaluate , fontawesome, htmltools , jquerylib , jsonlite , knitr , methods , stringr , tinytex , tools , utils , xfun , yaml |
| rprojroot | 2.0.3 | Repository | CRAN | R |
| rsconnect | 1.0.1 | Repository | CRAN | R , cli , curl , digest , jsonlite , lifecycle , openssl , packrat , renv , rlang , rstudioapi, tools , yaml |
| rstudioapi | 0.15.0 | Repository | CRAN | NULL |
| rvest | 1.0.3 | Repository | CRAN | R , cli , glue , httr , lifecycle, magrittr , rlang , selectr , tibble , withr , xml2 |
| sass | 0.4.7 | Repository | CRAN | R6 , fs , htmltools, rappdirs , rlang |
| scales | 1.2.1 | Repository | CRAN | R , R6 , RColorBrewer, farver , labeling , lifecycle , munsell , rlang , viridisLite |
| selectr | 0.4-2 | Repository | CRAN | R , R6 , methods, stringr |
| shiny | 1.7.4.1 | Repository | CRAN | R , R6 , bslib , cachem , commonmark , crayon , ellipsis , fastmap , fontawesome, glue , grDevices , htmltools , httpuv , jsonlite , later , lifecycle , methods , mime , promises , rlang , sourcetools, tools , utils , withr , xtable |
| snakecase | 0.11.0 | Repository | CRAN | R , stringi, stringr |
| sourcetools | 0.1.7-1 | Repository | CRAN | R |
| stringi | 1.7.12 | Repository | CRAN | R , stats, tools, utils |
| stringr | 1.5.0 | Repository | CRAN | R , cli , glue , lifecycle, magrittr , rlang , stringi , vctrs |
| svglite | 2.1.1 | Repository | CRAN | R , cpp11 , systemfonts |
| sys | 3.4.2 | Repository | CRAN | NULL |
| systemfonts | 1.0.4 | Repository | CRAN | R , cpp11 |
| textshaping | 0.3.6 | Repository | CRAN | R , cpp11 , systemfonts |
| tibble | 3.2.1 | Repository | CRAN | R , fansi , lifecycle, magrittr , methods , pillar , pkgconfig, rlang , utils , vctrs |
| tidyr | 1.3.0 | Repository | CRAN | R , cli , cpp11 , dplyr , glue , lifecycle , magrittr , purrr , rlang , stringr , tibble , tidyselect, utils , vctrs |
| tidyselect | 1.2.0 | Repository | CRAN | R , cli , glue , lifecycle, rlang , vctrs , withr |
| tidyverse | 2.0.0 | Repository | CRAN | R , broom , cli , conflicted , dbplyr , dplyr , dtplyr , forcats , ggplot2 , googledrive , googlesheets4, haven , hms , httr , jsonlite , lubridate , magrittr , modelr , pillar , purrr , ragg , readr , readxl , reprex , rlang , rstudioapi , rvest , stringr , tibble , tidyr , xml2 |
| timechange | 0.2.0 | Repository | CRAN | R , cpp11 |
| tinytex | 0.45 | Repository | CRAN | xfun |
| tzdb | 0.4.0 | Repository | CRAN | R , cpp11 |
| utf8 | 1.2.3 | Repository | CRAN | R |
| uuid | 1.1-0 | Repository | CRAN | R |
| vctrs | 0.6.3 | Repository | CRAN | R , cli , glue , lifecycle, rlang |
| viridisLite | 0.4.2 | Repository | CRAN | R |
| vroom | 1.6.3 | Repository | CRAN | R , bit64 , cli , cpp11 , crayon , glue , hms , lifecycle , methods , progress , rlang , stats , tibble , tidyselect, tzdb , vctrs , withr |
| webshot | 0.5.5 | Repository | CRAN | R , callr , jsonlite, magrittr |
| withr | 2.5.0 | Repository | CRAN | R , grDevices, graphics , stats |
| xfun | 0.39 | Repository | CRAN | stats, tools |
| xml2 | 1.3.5 | Repository | CRAN | R , methods |
| xtable | 1.8-4 | Repository | CRAN | R , stats, utils |
| yaml | 2.3.7 | Repository | CRAN | NULL |
There are 134 packages listed in our renv.lock file.
{renv} does not install or maintain your R version, it just makes a note of it in the renv.lock file.
What are the base packages for our R.Version()? Some base R packages are loaded on startup, other base packages need to be explicitly loaded.
base_all <- rownames(installed.packages(priority = "base")) |>
as_tibble() |>
rename(package = value) |>
distinct() #FUDGE: duplicates packages when rendered via Quarto,
# but not when run interactively in RStudio
table_style(base_all)| package |
|---|
| base |
| compiler |
| datasets |
| graphics |
| grDevices |
| grid |
| methods |
| parallel |
| splines |
| stats |
| stats4 |
| tcltk |
| tools |
| utils |
There are 14 base R packages.
What are the base R packages loaded on startup? i.e. packages you do not need to explicitly load.
base_loaded <- c(getOption("defaultPackages"), "base") |>
as_tibble() |>
rename(package = value)
table_style(base_loaded, scroll_box = FALSE)| package |
|---|
| datasets |
| utils |
| grDevices |
| graphics |
| stats |
| methods |
| base |
There are 7 base R packages loaded on startup.
What are the base R packages not loaded on startup? i.e. packages you may need to explicitly load.
base_not_loaded <- base_all |>
anti_join(base_loaded, by = "package")
table_style(base_not_loaded, scroll_box = FALSE)| package |
|---|
| compiler |
| grid |
| parallel |
| splines |
| stats4 |
| tcltk |
| tools |
There are 7 base R packages not loaded on startup.
Packages explicitly loaded from the library by scripts in this project.
explicit <- dependencies(here(), progress = FALSE) |>
clean_names() |>
select(package, source)
table_style(explicit)| package | source |
|---|---|
| here | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/etl-ckp.R |
| janitor | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/etl-ckp.R |
| tidyverse | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/etl-ckp.R |
| here | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/one-ckp.qmd |
| tidyverse | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/one-ckp.qmd |
| scales | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/one-ckp.qmd |
| rmarkdown | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/one-ckp.qmd |
| here | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/ons-api.R |
| janitor | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/ons-api.R |
| onsr | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/ons-api.R |
| tibble | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/ons-api.R |
| tidyverse | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/ons-api.R |
| glue | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/ons-custom-dataset.R |
| httr2 | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/ons-custom-dataset.R |
| tidyverse | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/ons-custom-dataset.R |
| furrr | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/render-reports.R |
| here | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/render-reports.R |
| quarto | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/render-reports.R |
| tidyverse | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/render-reports.R |
| shiny | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/report-layout.qmd |
| here | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/report-layout.qmd |
| tidyverse | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/report-layout.qmd |
| rmarkdown | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/R/report-layout.qmd |
| here | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.qmd |
| janitor | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.qmd |
| jsonlite | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.qmd |
| kableExtra | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.qmd |
| renv | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.qmd |
| tidyverse | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.qmd |
| tools | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.qmd |
| rmarkdown | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.qmd |
| rmarkdown | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.rmarkdown |
| here | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.rmarkdown |
| janitor | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.rmarkdown |
| jsonlite | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.rmarkdown |
| kableExtra | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.rmarkdown |
| renv | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.rmarkdown |
| tidyverse | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.rmarkdown |
| tools | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/rap-docs/rap-learning.rmarkdown |
| renv | /home/runner/work/community-knowledge-profiles/community-knowledge-profiles/renv.lock |
Unique list of packages, irrespective of whether the package has been called by multiple scripts.
unique_explicit <- explicit |>
select(package) |>
distinct()
table_style(unique_explicit)| package |
|---|
| here |
| janitor |
| tidyverse |
| scales |
| rmarkdown |
| onsr |
| tibble |
| glue |
| httr2 |
| furrr |
| quarto |
| shiny |
| jsonlite |
| kableExtra |
| renv |
| tools |
There are 16 packages explicitly loaded from the library by scripts in this project.
“Implicit” packages that the explicitly loaded packages depend upon.
options(repos = c(CRAN = "https://cloud.r-project.org"))
# I think this makes a call to CRAN
implicit <- package_dependencies(
packages = pull(unique_explicit, package),
recursive = TRUE
) |>
enframe() |>
as_tibble() |>
unnest_longer(value) |>
rename(explicit = name, implicit = value)
#options(repos = c(CRAN = "https://cloud.r-project.org"))
table_style(implicit)| explicit | implicit |
|---|---|
| here | rprojroot |
| janitor | dplyr |
| janitor | hms |
| janitor | lifecycle |
| janitor | lubridate |
| janitor | magrittr |
| janitor | purrr |
| janitor | rlang |
| janitor | stringi |
| janitor | stringr |
| janitor | snakecase |
| janitor | tidyselect |
| janitor | tidyr |
| janitor | cli |
| janitor | generics |
| janitor | glue |
| janitor | methods |
| janitor | pillar |
| janitor | R6 |
| janitor | tibble |
| janitor | utils |
| janitor | vctrs |
| janitor | pkgconfig |
| janitor | timechange |
| janitor | tools |
| janitor | stats |
| janitor | cpp11 |
| janitor | withr |
| janitor | fansi |
| janitor | utf8 |
| janitor | graphics |
| janitor | grDevices |
| tidyverse | broom |
| tidyverse | conflicted |
| tidyverse | cli |
| tidyverse | dbplyr |
| tidyverse | dplyr |
| tidyverse | dtplyr |
| tidyverse | forcats |
| tidyverse | ggplot2 |
| tidyverse | googledrive |
| tidyverse | googlesheets4 |
| tidyverse | haven |
| tidyverse | hms |
| tidyverse | httr |
| tidyverse | jsonlite |
| tidyverse | lubridate |
| tidyverse | magrittr |
| tidyverse | modelr |
| tidyverse | pillar |
| tidyverse | purrr |
| tidyverse | ragg |
| tidyverse | readr |
| tidyverse | readxl |
| tidyverse | reprex |
| tidyverse | rlang |
| tidyverse | rstudioapi |
| tidyverse | rvest |
| tidyverse | stringr |
| tidyverse | tibble |
| tidyverse | tidyr |
| tidyverse | xml2 |
| tidyverse | backports |
| tidyverse | ellipsis |
| tidyverse | generics |
| tidyverse | glue |
| tidyverse | lifecycle |
| tidyverse | utils |
| tidyverse | memoise |
| tidyverse | blob |
| tidyverse | DBI |
| tidyverse | methods |
| tidyverse | R6 |
| tidyverse | tidyselect |
| tidyverse | vctrs |
| tidyverse | withr |
| tidyverse | data.table |
| tidyverse | grDevices |
| tidyverse | grid |
| tidyverse | gtable |
| tidyverse | isoband |
| tidyverse | MASS |
| tidyverse | mgcv |
| tidyverse | scales |
| tidyverse | stats |
| tidyverse | gargle |
| tidyverse | uuid |
| tidyverse | cellranger |
| tidyverse | curl |
| tidyverse | ids |
| tidyverse | rematch2 |
| tidyverse | cpp11 |
| tidyverse | pkgconfig |
| tidyverse | mime |
| tidyverse | openssl |
| tidyverse | timechange |
| tidyverse | fansi |
| tidyverse | utf8 |
| tidyverse | systemfonts |
| tidyverse | textshaping |
| tidyverse | clipr |
| tidyverse | crayon |
| tidyverse | vroom |
| tidyverse | tzdb |
| tidyverse | progress |
| tidyverse | callr |
| tidyverse | fs |
| tidyverse | knitr |
| tidyverse | rmarkdown |
| tidyverse | selectr |
| tidyverse | stringi |
| tidyverse | processx |
| tidyverse | rematch |
| tidyverse | rappdirs |
| tidyverse | evaluate |
| tidyverse | highr |
| tidyverse | tools |
| tidyverse | xfun |
| tidyverse | yaml |
| tidyverse | graphics |
| tidyverse | cachem |
| tidyverse | nlme |
| tidyverse | Matrix |
| tidyverse | splines |
| tidyverse | askpass |
| tidyverse | prettyunits |
| tidyverse | bslib |
| tidyverse | fontawesome |
| tidyverse | htmltools |
| tidyverse | jquerylib |
| tidyverse | tinytex |
| tidyverse | farver |
| tidyverse | labeling |
| tidyverse | munsell |
| tidyverse | RColorBrewer |
| tidyverse | viridisLite |
| tidyverse | bit64 |
| tidyverse | sys |
| tidyverse | bit |
| tidyverse | base64enc |
| tidyverse | sass |
| tidyverse | fastmap |
| tidyverse | digest |
| tidyverse | lattice |
| tidyverse | colorspace |
| tidyverse | ps |
| scales | farver |
| scales | labeling |
| scales | lifecycle |
| scales | munsell |
| scales | R6 |
| scales | RColorBrewer |
| scales | rlang |
| scales | viridisLite |
| scales | stats |
| scales | graphics |
| scales | cli |
| scales | glue |
| scales | colorspace |
| scales | methods |
| scales | utils |
| scales | grDevices |
| rmarkdown | bslib |
| rmarkdown | evaluate |
| rmarkdown | fontawesome |
| rmarkdown | htmltools |
| rmarkdown | jquerylib |
| rmarkdown | jsonlite |
| rmarkdown | knitr |
| rmarkdown | methods |
| rmarkdown | stringr |
| rmarkdown | tinytex |
| rmarkdown | tools |
| rmarkdown | utils |
| rmarkdown | xfun |
| rmarkdown | yaml |
| rmarkdown | base64enc |
| rmarkdown | cachem |
| rmarkdown | grDevices |
| rmarkdown | memoise |
| rmarkdown | mime |
| rmarkdown | rlang |
| rmarkdown | sass |
| rmarkdown | digest |
| rmarkdown | fastmap |
| rmarkdown | ellipsis |
| rmarkdown | highr |
| rmarkdown | cli |
| rmarkdown | glue |
| rmarkdown | lifecycle |
| rmarkdown | magrittr |
| rmarkdown | stringi |
| rmarkdown | vctrs |
| rmarkdown | stats |
| rmarkdown | fs |
| rmarkdown | R6 |
| rmarkdown | rappdirs |
| onsr | httr |
| onsr | jsonlite |
| onsr | readr |
| onsr | tibble |
| onsr | curl |
| onsr | mime |
| onsr | openssl |
| onsr | R6 |
| onsr | methods |
| onsr | cli |
| onsr | clipr |
| onsr | crayon |
| onsr | hms |
| onsr | lifecycle |
| onsr | rlang |
| onsr | utils |
| onsr | vroom |
| onsr | cpp11 |
| onsr | tzdb |
| onsr | fansi |
| onsr | magrittr |
| onsr | pillar |
| onsr | pkgconfig |
| onsr | vctrs |
| onsr | grDevices |
| onsr | glue |
| onsr | tools |
| onsr | askpass |
| onsr | utf8 |
| onsr | bit64 |
| onsr | stats |
| onsr | tidyselect |
| onsr | withr |
| onsr | progress |
| onsr | sys |
| onsr | bit |
| onsr | prettyunits |
| onsr | graphics |
| tibble | fansi |
| tibble | lifecycle |
| tibble | magrittr |
| tibble | methods |
| tibble | pillar |
| tibble | pkgconfig |
| tibble | rlang |
| tibble | utils |
| tibble | vctrs |
| tibble | grDevices |
| tibble | cli |
| tibble | glue |
| tibble | utf8 |
| glue | methods |
| httr2 | cli |
| httr2 | curl |
| httr2 | glue |
| httr2 | magrittr |
| httr2 | openssl |
| httr2 | R6 |
| httr2 | rappdirs |
| httr2 | rlang |
| httr2 | withr |
| httr2 | utils |
| httr2 | methods |
| httr2 | askpass |
| httr2 | graphics |
| httr2 | grDevices |
| httr2 | stats |
| httr2 | sys |
| furrr | future |
| furrr | globals |
| furrr | lifecycle |
| furrr | purrr |
| furrr | rlang |
| furrr | vctrs |
| furrr | digest |
| furrr | listenv |
| furrr | parallel |
| furrr | parallelly |
| furrr | utils |
| furrr | codetools |
| furrr | cli |
| furrr | glue |
| furrr | magrittr |
| furrr | methods |
| furrr | tools |
| quarto | utils |
| quarto | rmarkdown |
| quarto | jsonlite |
| quarto | yaml |
| quarto | processx |
| quarto | rstudioapi |
| quarto | later |
| quarto | rsconnect |
| quarto | methods |
| quarto | Rcpp |
| quarto | rlang |
| quarto | ps |
| quarto | R6 |
| quarto | bslib |
| quarto | evaluate |
| quarto | fontawesome |
| quarto | htmltools |
| quarto | jquerylib |
| quarto | knitr |
| quarto | stringr |
| quarto | tinytex |
| quarto | tools |
| quarto | xfun |
| quarto | cli |
| quarto | curl |
| quarto | digest |
| quarto | lifecycle |
| quarto | openssl |
| quarto | packrat |
| quarto | renv |
| quarto | base64enc |
| quarto | cachem |
| quarto | grDevices |
| quarto | memoise |
| quarto | mime |
| quarto | sass |
| quarto | fastmap |
| quarto | ellipsis |
| quarto | highr |
| quarto | glue |
| quarto | askpass |
| quarto | magrittr |
| quarto | stringi |
| quarto | vctrs |
| quarto | stats |
| quarto | sys |
| quarto | fs |
| quarto | rappdirs |
| shiny | methods |
| shiny | utils |
| shiny | grDevices |
| shiny | httpuv |
| shiny | mime |
| shiny | jsonlite |
| shiny | xtable |
| shiny | fontawesome |
| shiny | htmltools |
| shiny | R6 |
| shiny | sourcetools |
| shiny | later |
| shiny | promises |
| shiny | tools |
| shiny | crayon |
| shiny | rlang |
| shiny | fastmap |
| shiny | withr |
| shiny | commonmark |
| shiny | glue |
| shiny | bslib |
| shiny | cachem |
| shiny | ellipsis |
| shiny | lifecycle |
| shiny | base64enc |
| shiny | jquerylib |
| shiny | memoise |
| shiny | sass |
| shiny | digest |
| shiny | Rcpp |
| shiny | cli |
| shiny | stats |
| shiny | magrittr |
| shiny | graphics |
| shiny | fs |
| shiny | rappdirs |
| jsonlite | methods |
| kableExtra | knitr |
| kableExtra | magrittr |
| kableExtra | stringr |
| kableExtra | xml2 |
| kableExtra | rvest |
| kableExtra | rmarkdown |
| kableExtra | scales |
| kableExtra | viridisLite |
| kableExtra | stats |
| kableExtra | grDevices |
| kableExtra | htmltools |
| kableExtra | rstudioapi |
| kableExtra | glue |
| kableExtra | tools |
| kableExtra | webshot |
| kableExtra | digest |
| kableExtra | graphics |
| kableExtra | svglite |
| kableExtra | utils |
| kableExtra | methods |
| kableExtra | base64enc |
| kableExtra | rlang |
| kableExtra | fastmap |
| kableExtra | ellipsis |
| kableExtra | evaluate |
| kableExtra | highr |
| kableExtra | xfun |
| kableExtra | yaml |
| kableExtra | bslib |
| kableExtra | fontawesome |
| kableExtra | jquerylib |
| kableExtra | jsonlite |
| kableExtra | tinytex |
| kableExtra | cli |
| kableExtra | httr |
| kableExtra | lifecycle |
| kableExtra | selectr |
| kableExtra | tibble |
| kableExtra | withr |
| kableExtra | farver |
| kableExtra | labeling |
| kableExtra | munsell |
| kableExtra | R6 |
| kableExtra | RColorBrewer |
| kableExtra | stringi |
| kableExtra | vctrs |
| kableExtra | systemfonts |
| kableExtra | cpp11 |
| kableExtra | callr |
| kableExtra | cachem |
| kableExtra | memoise |
| kableExtra | mime |
| kableExtra | sass |
| kableExtra | processx |
| kableExtra | curl |
| kableExtra | openssl |
| kableExtra | colorspace |
| kableExtra | fansi |
| kableExtra | pillar |
| kableExtra | pkgconfig |
| kableExtra | askpass |
| kableExtra | utf8 |
| kableExtra | ps |
| kableExtra | fs |
| kableExtra | rappdirs |
| kableExtra | sys |
| renv | utils |
Unique list of implicit packages.
# Exclude explicit and base R packages
unique_implicit <- implicit |>
select(implicit) |>
distinct() |>
anti_join(explicit, by = join_by(implicit == package)) |>
anti_join(base_all, by = join_by(implicit == package))
table_style(unique_implicit)| implicit |
|---|
| rprojroot |
| dplyr |
| hms |
| lifecycle |
| lubridate |
| magrittr |
| purrr |
| rlang |
| stringi |
| stringr |
| snakecase |
| tidyselect |
| tidyr |
| cli |
| generics |
| pillar |
| R6 |
| vctrs |
| pkgconfig |
| timechange |
| cpp11 |
| withr |
| fansi |
| utf8 |
| broom |
| conflicted |
| dbplyr |
| dtplyr |
| forcats |
| ggplot2 |
| googledrive |
| googlesheets4 |
| haven |
| httr |
| modelr |
| ragg |
| readr |
| readxl |
| reprex |
| rstudioapi |
| rvest |
| xml2 |
| backports |
| ellipsis |
| memoise |
| blob |
| DBI |
| data.table |
| gtable |
| isoband |
| MASS |
| mgcv |
| gargle |
| uuid |
| cellranger |
| curl |
| ids |
| rematch2 |
| mime |
| openssl |
| systemfonts |
| textshaping |
| clipr |
| crayon |
| vroom |
| tzdb |
| progress |
| callr |
| fs |
| knitr |
| selectr |
| processx |
| rematch |
| rappdirs |
| evaluate |
| highr |
| xfun |
| yaml |
| cachem |
| nlme |
| Matrix |
| askpass |
| prettyunits |
| bslib |
| fontawesome |
| htmltools |
| jquerylib |
| tinytex |
| farver |
| labeling |
| munsell |
| RColorBrewer |
| viridisLite |
| bit64 |
| sys |
| bit |
| base64enc |
| sass |
| fastmap |
| digest |
| lattice |
| colorspace |
| ps |
| future |
| globals |
| listenv |
| parallelly |
| codetools |
| later |
| rsconnect |
| Rcpp |
| packrat |
| httpuv |
| xtable |
| sourcetools |
| promises |
| commonmark |
| webshot |
| svglite |
Excluding base R packages, there are 119 packages required by library packages explicitly loaded by scripts in this project.
The sum of explicit and implicit packages is 135. This compares with 134 packages listed in the renv.lock file.
This is close enough.
{renv} diagnostics report.
diagnostics()Diagnostics Report [renv 1.0.0]
===============================
# Session Info ---------------------------------------------------------------
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices datasets utils methods
[8] base
other attached packages:
[1] here_1.0.1 kableExtra_1.3.4 janitor_2.2.0 jsonlite_1.8.7
[5] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2
[9] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[13] ggplot2_3.4.2 tidyverse_2.0.0 renv_1.0.0
loaded via a namespace (and not attached):
[1] utf8_1.2.3 generics_0.1.3 xml2_1.3.5 stringi_1.7.12
[5] hms_1.1.3 digest_0.6.33 magrittr_2.0.3 evaluate_0.21
[9] grid_4.3.1 timechange_0.2.0 fastmap_1.1.1 rprojroot_2.0.3
[13] httr_1.4.6 rvest_1.0.3 fansi_1.0.4 viridisLite_0.4.2
[17] scales_1.2.1 cli_3.6.1 rlang_1.1.1 munsell_0.5.0
[21] withr_2.5.0 yaml_2.3.7 tzdb_0.4.0 colorspace_2.1-0
[25] webshot_0.5.5 vctrs_0.6.3 R6_2.5.1 lifecycle_1.0.3
[29] snakecase_0.11.0 pkgconfig_2.0.3 pillar_1.9.0 gtable_0.3.3
[33] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39
[37] tidyselect_1.2.0 rstudioapi_0.15.0 knitr_1.43 htmltools_0.5.5
[41] rmarkdown_2.23 svglite_2.1.1 compiler_4.3.1
# Project --------------------------------------------------------------------
Project path: "~/work/community-knowledge-profiles/community-knowledge-profiles"
# Status ---------------------------------------------------------------------
No issues found -- the project is in a consistent state.
# Packages -------------------------------------------------------------------
Library Source Lockfile Source Path Dependency
DBI 1.1.3 CRAN 1.1.3 CRAN [1] indirect
KernSmooth 2.23-21 CRAN <NA> <NA> [2] <NA>
MASS 7.3-60 CRAN 7.3-60 CRAN [2] indirect
Matrix 1.5-4 CRAN 1.5-4 CRAN [1] indirect
R6 2.5.1 CRAN 2.5.1 CRAN [1] indirect
RColorBrewer 1.1-3 CRAN 1.1-3 CRAN [1] indirect
Rcpp 1.0.11 CRAN 1.0.11 CRAN [1] indirect
askpass 1.1 CRAN 1.1 CRAN [1] indirect
backports 1.4.1 CRAN 1.4.1 CRAN [1] indirect
base64enc 0.1-3 CRAN 0.1-3 CRAN [1] indirect
bit 4.0.5 CRAN 4.0.5 CRAN [1] indirect
bit64 4.0.5 CRAN 4.0.5 CRAN [1] indirect
blob 1.2.4 CRAN 1.2.4 CRAN [1] indirect
boot 1.3-28.1 CRAN <NA> <NA> [2] <NA>
broom 1.0.5 CRAN 1.0.5 CRAN [1] indirect
bslib 0.5.0 CRAN 0.5.0 CRAN [1] indirect
cachem 1.0.8 CRAN 1.0.8 CRAN [1] indirect
callr 3.7.3 CRAN 3.7.3 CRAN [1] indirect
cellranger 1.1.0 CRAN 1.1.0 CRAN [1] indirect
class 7.3-22 CRAN <NA> <NA> [2] <NA>
cli 3.6.1 CRAN 3.6.1 CRAN [1] indirect
clipr 0.8.0 CRAN 0.8.0 CRAN [1] indirect
cluster 2.1.4 CRAN <NA> <NA> [2] <NA>
codetools 0.2-19 CRAN 0.2-19 CRAN [2] indirect
colorspace 2.1-0 CRAN 2.1-0 CRAN [1] indirect
commonmark 1.9.0 CRAN 1.9.0 CRAN [1] indirect
compiler <NA> <NA> <NA> <NA> [2] indirect
conflicted 1.2.0 CRAN 1.2.0 CRAN [1] indirect
cpp11 0.4.5 CRAN 0.4.5 CRAN [1] indirect
crayon 1.5.2 CRAN 1.5.2 CRAN [1] indirect
curl 5.0.1 CRAN 5.0.1 CRAN [1] indirect
data.table 1.14.8 CRAN 1.14.8 CRAN [1] indirect
dbplyr 2.3.3 CRAN 2.3.3 CRAN [1] indirect
digest 0.6.33 CRAN 0.6.33 CRAN [1] indirect
dplyr 1.1.2 CRAN 1.1.2 CRAN [1] indirect
dtplyr 1.3.1 CRAN 1.3.1 CRAN [1] indirect
ellipsis 0.3.2 CRAN 0.3.2 CRAN [1] indirect
evaluate 0.21 CRAN 0.21 CRAN [1] indirect
fansi 1.0.4 CRAN 1.0.4 CRAN [1] indirect
farver 2.1.1 CRAN 2.1.1 CRAN [1] indirect
fastmap 1.1.1 CRAN 1.1.1 CRAN [1] indirect
fontawesome 0.5.1 CRAN 0.5.1 CRAN [1] indirect
forcats 1.0.0 CRAN 1.0.0 CRAN [1] indirect
foreign 0.8-84 CRAN <NA> <NA> [2] <NA>
fs 1.6.2 CRAN 1.6.2 CRAN [1] indirect
furrr 0.3.1 CRAN 0.3.1 CRAN [1] direct
future 1.33.0 CRAN 1.33.0 CRAN [1] indirect
gargle 1.5.2 CRAN 1.5.2 CRAN [1] indirect
generics 0.1.3 CRAN 0.1.3 CRAN [1] indirect
ggplot2 3.4.2 CRAN 3.4.2 CRAN [1] indirect
globals 0.16.2 CRAN 0.16.2 CRAN [1] indirect
glue 1.6.2 CRAN 1.6.2 CRAN [1] direct
googledrive 2.1.1 CRAN 2.1.1 CRAN [1] indirect
googlesheets4 1.1.1 CRAN 1.1.1 CRAN [1] indirect
grDevices <NA> <NA> <NA> <NA> [2] indirect
graphics <NA> <NA> <NA> <NA> [2] indirect
grid <NA> <NA> <NA> <NA> [2] indirect
gtable 0.3.3 CRAN 0.3.3 CRAN [1] indirect
haven 2.5.3 CRAN 2.5.3 CRAN [1] indirect
here 1.0.1 CRAN 1.0.1 CRAN [1] direct
highr 0.10 CRAN 0.10 CRAN [1] indirect
hms 1.1.3 CRAN 1.1.3 CRAN [1] indirect
htmltools 0.5.5 CRAN 0.5.5 CRAN [1] indirect
httpuv 1.6.11 CRAN 1.6.11 CRAN [1] indirect
httr 1.4.6 CRAN 1.4.6 CRAN [1] indirect
httr2 0.2.3 CRAN 0.2.3 CRAN [1] direct
ids 1.0.1 CRAN 1.0.1 CRAN [1] indirect
isoband 0.2.7 CRAN 0.2.7 CRAN [1] indirect
janitor 2.2.0 CRAN 2.2.0 CRAN [1] direct
jquerylib 0.1.4 CRAN 0.1.4 CRAN [1] indirect
jsonlite 1.8.7 CRAN 1.8.7 CRAN [1] direct
kableExtra 1.3.4 CRAN 1.3.4 CRAN [1] direct
knitr 1.43 CRAN 1.43 CRAN [1] indirect
labeling 0.4.2 CRAN 0.4.2 CRAN [1] indirect
later 1.3.1 CRAN 1.3.1 CRAN [1] indirect
lattice 0.21-8 CRAN 0.21-8 CRAN [2] indirect
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magrittr 2.0.3 CRAN 2.0.3 CRAN [1] indirect
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nlme 3.1-162 CRAN 3.1-162 CRAN [2] indirect
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onsr 1.0.1 CRAN 1.0.1 CRAN [1] direct
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parallel <NA> <NA> <NA> <NA> [2] indirect
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pkgconfig 2.0.3 CRAN 2.0.3 CRAN [1] indirect
prettyunits 1.1.1 CRAN 1.1.1 CRAN [1] indirect
processx 3.8.2 CRAN 3.8.2 CRAN [1] indirect
progress 1.2.2 CRAN 1.2.2 CRAN [1] indirect
promises 1.2.0.1 CRAN 1.2.0.1 CRAN [1] indirect
ps 1.7.5 CRAN 1.7.5 CRAN [1] indirect
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quarto 1.2 CRAN 1.2 CRAN [1] direct
ragg 1.2.5 CRAN 1.2.5 CRAN [1] indirect
rappdirs 0.3.3 CRAN 0.3.3 CRAN [1] indirect
readr 2.1.4 CRAN 2.1.4 CRAN [1] indirect
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rematch 1.0.1 CRAN 1.0.1 CRAN [1] indirect
rematch2 2.1.2 CRAN 2.1.2 CRAN [1] indirect
renv 1.0.0 CRAN 1.0.0 CRAN [1] direct
reprex 2.0.2 CRAN 2.0.2 CRAN [1] indirect
rlang 1.1.1 CRAN 1.1.1 CRAN [1] indirect
rmarkdown 2.23 CRAN 2.23 CRAN [1] direct
rpart 4.1.19 CRAN <NA> <NA> [2] <NA>
rprojroot 2.0.3 CRAN 2.0.3 CRAN [1] indirect
rsconnect 1.0.1 CRAN 1.0.1 CRAN [1] indirect
rstudioapi 0.15.0 CRAN 0.15.0 CRAN [1] indirect
rvest 1.0.3 CRAN 1.0.3 CRAN [1] indirect
sass 0.4.7 CRAN 0.4.7 CRAN [1] indirect
scales 1.2.1 CRAN 1.2.1 CRAN [1] direct
selectr 0.4-2 CRAN 0.4-2 CRAN [1] indirect
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stats <NA> <NA> <NA> <NA> [2] indirect
stringi 1.7.12 CRAN 1.7.12 CRAN [1] indirect
stringr 1.5.0 CRAN 1.5.0 CRAN [1] indirect
survival 3.5-5 CRAN <NA> <NA> [2] <NA>
svglite 2.1.1 CRAN 2.1.1 CRAN [1] indirect
sys 3.4.2 CRAN 3.4.2 CRAN [1] indirect
systemfonts 1.0.4 CRAN 1.0.4 CRAN [1] indirect
textshaping 0.3.6 CRAN 0.3.6 CRAN [1] indirect
tibble 3.2.1 CRAN 3.2.1 CRAN [1] direct
tidyr 1.3.0 CRAN 1.3.0 CRAN [1] indirect
tidyselect 1.2.0 CRAN 1.2.0 CRAN [1] indirect
tidyverse 2.0.0 CRAN 2.0.0 CRAN [1] direct
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tinytex 0.45 CRAN 0.45 CRAN [1] indirect
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utf8 1.2.3 CRAN 1.2.3 CRAN [1] indirect
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uuid 1.1-0 CRAN 1.1-0 CRAN [1] indirect
vctrs 0.6.3 CRAN 0.6.3 CRAN [1] indirect
viridisLite 0.4.2 CRAN 0.4.2 CRAN [1] indirect
vroom 1.6.3 CRAN 1.6.3 CRAN [1] indirect
webshot 0.5.5 CRAN 0.5.5 CRAN [1] indirect
withr 2.5.0 CRAN 2.5.0 CRAN [1] indirect
xfun 0.39 CRAN 0.39 CRAN [1] indirect
xml2 1.3.5 CRAN 1.3.5 CRAN [1] indirect
xtable 1.8-4 CRAN 1.8-4 CRAN [1] indirect
yaml 2.3.7 CRAN 2.3.7 CRAN [1] indirect
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