Merge branch 'main' into 125_xportr_0_4_0

.lycheeignore

@@ -9,3 +9,8 @@ https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numb
 https://go.appsilon.com/demo-apps
 https://doi.org/10.1177/17407745221123244
 https://appsilon.com/static/35215a117d1bc17fac2179f059c3709f/rhino_fda_pilot_r_shiny_app_e-ctd.webm
+http://localhost:8787/
+https://github.com/pharmaverse/blog/pkgs/container/blog
+https://stackoverflow.com/*
+https://stackoverflow.com/questions/12688717/round-up-from-5#comment110611119_12688836
+https://appsilon.com/docker-vs-podman-vs-singularity/amp/

Dockerfile

@@ -0,0 +1,26 @@
+FROM rocker/rstudio:latest
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        ca-certificates \
+        curl \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && curl -o quarto.deb -L https://github.com/quarto-dev/quarto-cli/releases/download/v1.4.550/quarto-1.4.550-linux-amd64.deb \
+    && dpkg --install quarto.deb \
+    && rm -f quarto.deb \
+    && R -e 'install.packages(c( \
+        "jsonlite", \
+        "tidyverse", \
+        "spelling", \
+        "janitor", \
+        "diffdf", \
+        "admiral", \
+        "patchwork", \
+        "here", \
+        "reactable", \
+        "pharmaversesdtm", \
+        "metacore", \
+        "metatools", \
+        "xportr", \
+        "pharmaverseadam"))'

R/create_blogpost.R

@@ -15,10 +15,10 @@ c(
 
 # Fill in the info, e.g.:
 create_post(
-  post_name = "iscr_conference", # needs to be character vector (length 1)
-  post_date = "2024-02-17", # needs to be character vector (length 1)
+  post_name = "My Blog", # needs to be character vector (length 1)
+  post_date = "2024-12-01", # needs to be character vector (length 1)
   description = "", # you can fill the description in later as well
-  author = c("Pooja Kumari"), # one or more authors are permitted
+  author = c("My Name"), # one or more authors are permitted
   cover_image = "pharmaverse", # chose one of the above (see line 8)
   tags = c("submission", "ADaMs", "conferences", "admiral", "xportr", "metatools", "metacore") # chose (multiple) from line 10
 )

README.md

@@ -6,20 +6,20 @@ As the CWG is a small team, we hope to make the blog development process easy en
 
 ## Spirit of a Blog Post
 
-The CWG believes that the following 4 points will help guide the creation of Blog Posts. 
+The CWG believes that the following 4 points will help guide the creation of Blog Posts.
 
 * **Short**
 * **Personalized**
 * **Reproducible**
-* **Readable**  
+* **Readable**
 
-**Short:** Posts should aim to be under a 10 minute read. We encourage longer posts to be broken up into multiple posts.  
+**Short:** Posts should aim to be under a 10 minute read. We encourage longer posts to be broken up into multiple posts.
 
 **Personalized:** Posts should have a personality! For example, a person wishing to post on a function in a package needs to differentiate the post from the documentation for function, i.e. we don't want to just recycle the documentation. How can you add your voice and experience? A bit of cheeky language is also encouraged.
 
 **Reproducible:**  Posts should work with minimal dependencies with data, packages and outside sources. Every dependency introduced in a post adds some risk to the post longevity. As package dependencies change, posts should be built in a way that they can be updated to stay relevant.
 
-**Readable:** The CWG sees this site as more of introductory site rather advanced user site. Therefore, the CWG feels that code should be introduced in a way that promotes readability over complexity. 
+**Readable:** The CWG sees this site as more of introductory site rather advanced user site. Therefore, the CWG feels that code should be introduced in a way that promotes readability over complexity.
 
 
 ## What types of posts are allowed on this site?
@@ -49,31 +49,72 @@ That is it! After that you can go wild, but we do ask that it is kept short!
 
 **Step 2:** Branch off `main`
 
-**Step 3:** Create a new Blog Post skeleton using the `create_blog_post.R` script in the `R/` folder. 
+**Step 3:** Create a new Blog Post skeleton using the `create_blog_post.R` script in the `R/` folder.
 
 - Open the `create_blogpost.R` file.
 
 - Source the script `help_create_blogpost.R` from within the `create_blogpost.R` file.
 
-- Enter your information into the `create_post` function. 
+- Enter your information into the `create_post` function.
   Please note that we do not currently allow users to specify their own categories (or `tags`),
   so you must chose (possibly several) from this list:
   `c("metadata", "submission", "qc", "ADaMs", "SDTMs", "community", "conferences",
   "admiral", "roak", "xportr", "metatools", "metacore")`.
 
 
-- Running that function will create a subfolder with a quarto file (`*.qmd`) in the `posts/` folder. 
-  Both should be named based on the supplied `post_date` and `post_name` information. 
+- Running that function will create a subfolder with a quarto file (`*.qmd`) in the `posts/` folder.
+  Both should be named based on the supplied `post_date` and `post_name` information.
 
-- Open the newly created folder and start working within the `*.qmd` file. 
+- Open the newly created folder and start working within the `*.qmd` file.
 
-**Step 4:** After you have finished your Blog Post, open the `CICD.R` file in the `R/` folder. 
-Run the script line by line to first check the spelling in your post and then to make sure your code is compatible with our code-style. 
+**Step 4:** After you have finished your Blog Post, open the `CICD.R` file in the `R/` folder.
+Run the script line by line to first check the spelling in your post and then to make sure your code is compatible with our code-style.
 
 **Step 5:** Push to your branch, create a Pull Request, and review the Spirit of the Blog Post in the Pull Request Template.
 
-**Step 6:** Poke us to do a review!  
+**Step 6:** Poke us to do a review!
 
 Most importantly:
 
 **Step 7:** Have fun :)
+
+## How to Use the `blog` Docker Image for Local Development
+
+Contributors can benefit from using the [`blog` Docker image](https://github.com/pharmaverse/blog/pkgs/container/blog) when creating their blog posts. This way, contributors don't have to install all dependencies from other blog posts and can solely focus on their own blog post and its dependencies.
+
+Here are the steps to use the blog's Docker image:
+
+1. Ensure you have [Docker Desktop](https://docs.docker.com/get-docker/) installed.
+2. Start Docker Desktop on your machine.
+3. Perform a Docker pull from the blog's GitHub registry by running this code:
+
+```bash
+docker pull ghcr.io/pharmaverse/blog:latest
+```
+
+4. Clone this `blog` repository and take note of the location of the repo in your local machine.
+5. Update the code below specifying the location of your 'blog' repository and execute the script:
+```bash
+docker run --rm -ti -e PASSWORD=yourpassword -p 8787:8787 -v <location of your blog repo>:/home/rstudio/work ghcr.io/pharmaverse/blog
+```
+
+Here's an example:
+
+```bash
+docker run --rm -ti -e PASSWORD=yourpassword -p 8787:8787 -v ~/Documents/blog:/home/rstudio/work ghcr.io/pharmaverse/blog
+```
+
+This command will run the `blog` Docker image and mount your local folder to the image.
+
+6. Open http://localhost:8787/ and you should see the RStudio welcome page.
+7. The username will be `rstudio`, and the password is `yourpassword`.
+8. Once logged in, go to the work folder, and you should see the contents of the `blog` repository.
+9. Click the `quarto-blog.Rproj` file to open the project.
+10. You can test by opening the `index.qmd` and rendering the document.
+11. Quarto should run, and you should be able to see the rendered blog locally.
+12. Develop your blog post and re-render as needed.
+13. Once complete, you can close the RStudio session, shut down the image, and push your update to the blog repo.
+
+Please note that there is no SSH or git capability in the docker image, so you can't push your update to the repo from the image directly. To push the update, you would have to do it from your local RStudio or terminal.
+
+A Dockerfile is also provided in this repo if you want to build the image locally and add more functionalities.

inst/WORDLIST.txt

@@ -121,6 +121,7 @@ CDER
 cdisc
 CDISC
 ceil
+Celine
 changelog
 ChatGPT
 cheatsheet
@@ -138,6 +139,7 @@ comms
 comparators
 compatibilities
 config
+Coretta
 cosa
 COUNTRYL
 COUNTRYN
@@ -389,6 +391,7 @@ pharmaverseadam
 pharmaversesdtm
 phuse
 PHUSE
+Piraux's
 pkglite
 pKobZqjlXChj
 png
@@ -612,10 +615,42 @@ zhu
 Zhu
 zMachine
 zxqguo
-deepdive
-feedbacks
-IoT
-JSON's
-magrittr
-NotUsed
-xport
+amongst
+enablement
+GxP
+now’
+nyone
+phar
+phriends
+PHUSE’s
+riskassessment
+yay
+ari
+farrugia
+kalappurakal
+knoph
+michael
+michaelrimler
+ross
+siggaard
+stackhouse
+sumesh
+ari
+farrugia
+kalappurakal
+knoph
+michael
+michaelrimler
+ross
+siggaard
+stackhouse
+sumesh
+atkr
+devtools
+ic
+Olo
+QKz
+scm
+ytJ
+yv
+zt

posts/2023-08-08_study_day/study_day.qmd

@@ -21,7 +21,7 @@ long_slug <- "2023-08-08_study_day"
 
 <!--------------- post begins here -----------------> 
 
-Creating `--DY` variables for your ADaMs is super easy using  [`derive_vars_dy()`](https://pharmaverse.github.io/admiral/v0.11.1/reference/derive_vars_dy.html) from the [admiral package](https://pharmaverse.github.io/admiral/).
+Creating `--DY` variables for your ADaMs is super easy using  [`derive_vars_dy()`](https://pharmaverse.github.io/admiral/reference/derive_vars_dy.html) from the [admiral package](https://pharmaverse.github.io/admiral/).
 
 
 Let's build some dummy data with 4 subjects, a start date/time for treatment (`TRTSDTM`), an analysis start date/time variable (`ASTDTM`) and an analysis end date variable (`AENDT`).