mirror of
https://github.com/agdamsbo/stRoke.git
synced 2024-11-24 13:41:55 +01:00
moved vignettes out
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@ -28,8 +28,9 @@ Suggests:
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usethis,
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testthat,
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git2r,
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pak
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Language: en-US
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pak,
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here,
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rhub
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Config/testthat/edition: 3
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Imports:
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calendar,
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@ -49,3 +50,4 @@ Imports:
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Depends:
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R (>= 2.10)
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VignetteBuilder: knitr
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Language: en-US
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@ -1,15 +1,14 @@
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Andreas
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CMD
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Changelog
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Codecov
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DDMMYY
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DOI
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DataDictionary
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Gammelgaard
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Github
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Kraglund
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Labelling
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METACRAN
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MFI
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NA's
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OLR
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ORCID
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@ -43,11 +42,13 @@ colouring
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cpr
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cprs
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daDoctoR
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datetime
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ddmmyy
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ddmmyyxxxx
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difftime
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dk
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doi
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dplyr
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ds
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eeptools
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eg
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@ -82,6 +83,7 @@ sapply
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stackoverflow
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strsplit
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teppo
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tibble
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vapply
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vec
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winP
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@ -1,87 +0,0 @@
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---
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title: "ds2dd"
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date: "`r Sys.Date()`"
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{ds2dd}
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteEncoding{UTF-8}
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---
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```{r, include = FALSE}
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knitr::opts_chunk$set(
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collapse = TRUE,
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comment = "#>"
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)
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```
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```{r setup}
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library(stRoke)
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```
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# Easy data set to data base workflow
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This function can be used as a simple tool for creating at data base metadata file for REDCap (called a DataDictionary) based on a given data set file.
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## Step 1 - Load your data set
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Here we'll use the sample TALOS dataset included with the package.
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```{r}
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data("talos")
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ds <- talos
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# As the data set lacks an ID column, one is added
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ds$id <- seq_len(nrow(ds))
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```
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## Step 2 - Create the DataDictionary
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```{r}
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datadictionary <- ds2dd(ds,record.id = "id",include.column.names = TRUE)
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```
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Now additional specifications to the DataDictionary can be made manually, or it can be uploaded and modified manually in the graphical user interface on the web page.
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The function will transform column names to lower case and substitute spaces for underscores. The output is a list with the DataDictionary and a vector of new column names for the dataset to fit the meta data.
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## Step 3 - Meta data upload
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Now the DataDictionary can be exported as a spreadsheet and uploaded or it can be uploaded using the `REDCapR` package (only projects with "Development" status).
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Use one of the two approaches below:
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### Manual upload
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```{r eval=FALSE}
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write.csv(datadictionary$DataDictionary,"datadictionary.csv")
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```
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### Upload with `REDCapR`
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```{r eval=FALSE}
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REDCapR::redcap_metadata_write(
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datadictionary$DataDictionary,
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redcap_uri = keyring::key_get("DB_URI"),
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token = keyring::key_get("DB_TOKEN")
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)
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```
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In the ["REDCap R Handbook"](https://agdamsbo.github.io/redcap-r-handbook/) more is written on interfacing with REDCap in R using the `library(keyring)`to store credentials in [chapter 1.1](https://agdamsbo.github.io/redcap-r-handbook/access.html#sec-getting-access).
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## Step 4 - Data upload
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The same two options are available for data upload as meta data upload: manual or through `REDCapR`.
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Only the latter is shown here.
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```{r eval=FALSE}
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# new column names are applied
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colnames(ds) <- datadictionary$`Column names`
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REDCapR::redcap_write(
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ds,
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redcap_uri = keyring::key_get("DB_URI"),
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token = keyring::key_get("DB_TOKEN")
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)
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```
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@ -1,145 +0,0 @@
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---
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title: "New project checklist"
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date: "`r Sys.Date()`"
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{New project checklist}
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteEncoding{UTF-8}
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---
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## Creating and starting a new project
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This is very much started as a personal reference checklist when starting new *R*-projects.
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Much of it is based on work from [ROSTOOLS](), but I have added a few personal preferences.
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### Init renv
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After initiating renv, do
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```{r eval=FALSE}
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usethis::edit_r_profile()
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```
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Copy the following to the profile-file:
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```
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options(
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renv.settings.snapshot.type = "explicit",
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renv.config.auto.snapshot = TRUE,
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renv.config.pak.enabled = TRUE
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)
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source("renv/activate.R")
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if (interactive()) {
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suppressMessages(require(usethis))
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}
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```
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### Publishing the project
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Run in terminal:
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```
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quarto publish gh-pages
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```
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This will create a new `gh-pages` branches in the repository.
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Then run
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```{r eval=FALSE}
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edit_file(".github/workflows/build-website.yaml")
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```
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And then copy/paste this content to that file:
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```
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on:
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push:
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branches:
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- main
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- master
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workflow_dispatch:
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name: Render and Publish
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permissions:
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contents: write
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pages: write
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jobs:
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build-deploy:
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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with:
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# To install LaTeX to build PDF book
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tinytex: true
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# uncomment below and fill to pin a version
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# version: 0.9.600
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# The next two steps are used to setup the project when renv is used. Just uncomment and away you go!
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# - uses: r-lib/actions/setup-r@v2
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# - uses: r-lib/actions/setup-renv@v2
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# From https://github.com/r-lib/actions/tree/v2-branch/setup-r
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- name: Publish to GitHub Pages (and render)
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uses: quarto-dev/quarto-actions/publish@v2
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with:
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target: gh-pages
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env:
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# this secret is always available for github actions
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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```
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# New CRAN release checklist
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- Commit all changes to GIT
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- Checks for publishing with RHUB
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```{r eval=FALSE}
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results <- rhub::check_for_cran()
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```
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Let it run. Takes some hours.
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Check results:
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```{r eval=FALSE}
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results$cran_summary()
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```
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Copy results to `cran-comments.md`
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```{r eval=FALSE}
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usethis::use_cran_comments()
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```
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- Release on CRAN
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```{r eval=FALSE}
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devtools::release()
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```
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Follow instruction on e-mail to confirm upload
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- When approved, release to GitHub (this also publishes newest version to Zenodo if setup)
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```{r eval=FALSE}
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usethis::use_github_release()
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```
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