mirror of
https://github.com/agdamsbo/stRoke.git
synced 2024-11-21 12:30:23 +01:00
moved vignettes out
This commit is contained in:
parent
fea603defc
commit
cb81f715d1
@ -28,8 +28,9 @@ Suggests:
|
||||
usethis,
|
||||
testthat,
|
||||
git2r,
|
||||
pak
|
||||
Language: en-US
|
||||
pak,
|
||||
here,
|
||||
rhub
|
||||
Config/testthat/edition: 3
|
||||
Imports:
|
||||
calendar,
|
||||
@ -49,3 +50,4 @@ Imports:
|
||||
Depends:
|
||||
R (>= 2.10)
|
||||
VignetteBuilder: knitr
|
||||
Language: en-US
|
||||
|
||||
@ -1,15 +1,14 @@
|
||||
Andreas
|
||||
CMD
|
||||
Changelog
|
||||
Codecov
|
||||
DDMMYY
|
||||
DOI
|
||||
DataDictionary
|
||||
Gammelgaard
|
||||
Github
|
||||
Kraglund
|
||||
Labelling
|
||||
METACRAN
|
||||
MFI
|
||||
NA's
|
||||
OLR
|
||||
ORCID
|
||||
@ -43,11 +42,13 @@ colouring
|
||||
cpr
|
||||
cprs
|
||||
daDoctoR
|
||||
datetime
|
||||
ddmmyy
|
||||
ddmmyyxxxx
|
||||
difftime
|
||||
dk
|
||||
doi
|
||||
dplyr
|
||||
ds
|
||||
eeptools
|
||||
eg
|
||||
@ -82,6 +83,7 @@ sapply
|
||||
stackoverflow
|
||||
strsplit
|
||||
teppo
|
||||
tibble
|
||||
vapply
|
||||
vec
|
||||
winP
|
||||
|
||||
@ -1,87 +0,0 @@
|
||||
---
|
||||
title: "ds2dd"
|
||||
date: "`r Sys.Date()`"
|
||||
output: rmarkdown::html_vignette
|
||||
vignette: >
|
||||
%\VignetteIndexEntry{ds2dd}
|
||||
%\VignetteEngine{knitr::rmarkdown}
|
||||
%\VignetteEncoding{UTF-8}
|
||||
---
|
||||
|
||||
```{r, include = FALSE}
|
||||
knitr::opts_chunk$set(
|
||||
collapse = TRUE,
|
||||
comment = "#>"
|
||||
)
|
||||
```
|
||||
|
||||
```{r setup}
|
||||
library(stRoke)
|
||||
```
|
||||
|
||||
# Easy data set to data base workflow
|
||||
|
||||
This function can be used as a simple tool for creating at data base metadata file for REDCap (called a DataDictionary) based on a given data set file.
|
||||
|
||||
## Step 1 - Load your data set
|
||||
|
||||
Here we'll use the sample TALOS dataset included with the package.
|
||||
|
||||
```{r}
|
||||
data("talos")
|
||||
ds <- talos
|
||||
# As the data set lacks an ID column, one is added
|
||||
ds$id <- seq_len(nrow(ds))
|
||||
```
|
||||
|
||||
## Step 2 - Create the DataDictionary
|
||||
|
||||
```{r}
|
||||
datadictionary <- ds2dd(ds,record.id = "id",include.column.names = TRUE)
|
||||
```
|
||||
|
||||
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.
|
||||
|
||||
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.
|
||||
|
||||
## Step 3 - Meta data upload
|
||||
|
||||
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).
|
||||
|
||||
Use one of the two approaches below:
|
||||
|
||||
### Manual upload
|
||||
|
||||
```{r eval=FALSE}
|
||||
write.csv(datadictionary$DataDictionary,"datadictionary.csv")
|
||||
```
|
||||
|
||||
### Upload with `REDCapR`
|
||||
|
||||
```{r eval=FALSE}
|
||||
REDCapR::redcap_metadata_write(
|
||||
datadictionary$DataDictionary,
|
||||
redcap_uri = keyring::key_get("DB_URI"),
|
||||
token = keyring::key_get("DB_TOKEN")
|
||||
)
|
||||
```
|
||||
|
||||
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).
|
||||
|
||||
## Step 4 - Data upload
|
||||
|
||||
The same two options are available for data upload as meta data upload: manual or through `REDCapR`.
|
||||
|
||||
Only the latter is shown here.
|
||||
|
||||
```{r eval=FALSE}
|
||||
# new column names are applied
|
||||
colnames(ds) <- datadictionary$`Column names`
|
||||
|
||||
REDCapR::redcap_write(
|
||||
ds,
|
||||
redcap_uri = keyring::key_get("DB_URI"),
|
||||
token = keyring::key_get("DB_TOKEN")
|
||||
)
|
||||
```
|
||||
|
||||
@ -1,145 +0,0 @@
|
||||
---
|
||||
title: "New project checklist"
|
||||
date: "`r Sys.Date()`"
|
||||
output: rmarkdown::html_vignette
|
||||
vignette: >
|
||||
%\VignetteIndexEntry{New project checklist}
|
||||
%\VignetteEngine{knitr::rmarkdown}
|
||||
%\VignetteEncoding{UTF-8}
|
||||
---
|
||||
|
||||
## Creating and starting a new project
|
||||
|
||||
This is very much started as a personal reference checklist when starting new *R*-projects.
|
||||
|
||||
Much of it is based on work from [ROSTOOLS](), but I have added a few personal preferences.
|
||||
|
||||
### Init renv
|
||||
|
||||
After initiating renv, do
|
||||
|
||||
```{r eval=FALSE}
|
||||
usethis::edit_r_profile()
|
||||
```
|
||||
|
||||
Copy the following to the profile-file:
|
||||
|
||||
```
|
||||
options(
|
||||
renv.settings.snapshot.type = "explicit",
|
||||
renv.config.auto.snapshot = TRUE,
|
||||
renv.config.pak.enabled = TRUE
|
||||
)
|
||||
source("renv/activate.R")
|
||||
|
||||
if (interactive()) {
|
||||
suppressMessages(require(usethis))
|
||||
}
|
||||
```
|
||||
|
||||
|
||||
|
||||
### Publishing the project
|
||||
|
||||
Run in terminal:
|
||||
|
||||
```
|
||||
quarto publish gh-pages
|
||||
```
|
||||
|
||||
This will create a new `gh-pages` branches in the repository.
|
||||
|
||||
Then run
|
||||
|
||||
```{r eval=FALSE}
|
||||
edit_file(".github/workflows/build-website.yaml")
|
||||
```
|
||||
|
||||
And then copy/paste this content to that file:
|
||||
|
||||
```
|
||||
on:
|
||||
push:
|
||||
branches:
|
||||
- main
|
||||
- master
|
||||
workflow_dispatch:
|
||||
|
||||
name: Render and Publish
|
||||
|
||||
permissions:
|
||||
contents: write
|
||||
pages: write
|
||||
|
||||
jobs:
|
||||
build-deploy:
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- name: Check out repository
|
||||
uses: actions/checkout@v4
|
||||
|
||||
- name: Set up Quarto
|
||||
uses: quarto-dev/quarto-actions/setup@v2
|
||||
with:
|
||||
# To install LaTeX to build PDF book
|
||||
tinytex: true
|
||||
# uncomment below and fill to pin a version
|
||||
# version: 0.9.600
|
||||
|
||||
# The next two steps are used to setup the project when renv is used. Just uncomment and away you go!
|
||||
# - uses: r-lib/actions/setup-r@v2
|
||||
|
||||
# - uses: r-lib/actions/setup-renv@v2
|
||||
|
||||
# From https://github.com/r-lib/actions/tree/v2-branch/setup-r
|
||||
- name: Publish to GitHub Pages (and render)
|
||||
uses: quarto-dev/quarto-actions/publish@v2
|
||||
with:
|
||||
target: gh-pages
|
||||
env:
|
||||
# this secret is always available for github actions
|
||||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
|
||||
```
|
||||
|
||||
# New CRAN release checklist
|
||||
|
||||
- Commit all changes to GIT
|
||||
|
||||
- Checks for publishing with RHUB
|
||||
|
||||
```{r eval=FALSE}
|
||||
results <- rhub::check_for_cran()
|
||||
```
|
||||
|
||||
|
||||
Let it run. Takes some hours.
|
||||
Check results:
|
||||
|
||||
|
||||
```{r eval=FALSE}
|
||||
results$cran_summary()
|
||||
```
|
||||
|
||||
|
||||
Copy results to `cran-comments.md`
|
||||
|
||||
|
||||
```{r eval=FALSE}
|
||||
usethis::use_cran_comments()
|
||||
```
|
||||
|
||||
- Release on CRAN
|
||||
|
||||
```{r eval=FALSE}
|
||||
devtools::release()
|
||||
```
|
||||
|
||||
|
||||
Follow instruction on e-mail to confirm upload
|
||||
|
||||
|
||||
- When approved, release to GitHub (this also publishes newest version to Zenodo if setup)
|
||||
|
||||
```{r eval=FALSE}
|
||||
usethis::use_github_release()
|
||||
```
|
||||
Loading…
Reference in New Issue
Block a user