Closes #74 higher order post (#93)

* #74 higher order post * #74 spelling and syler * #74 updates following review * #74 chore: spellcheck * chore: new date to be closer to publishign * chore: fixing cosa links * chore: fix links * chore: packages for workflow --------- Co-authored-by: Ben Straub <[email protected]>
pharmaverse · Nov 27, 2023 · 04dc8b5 · 04dc8b5
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diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -35,6 +35,7 @@ jobs:
             patchwork
             here
             reactable
+            pharmaversesdtm
             
 
       - name: Install tinytex

diff --git a/inst/WORDLIST.txt b/inst/WORDLIST.txt
@@ -476,3 +476,27 @@ representable
 Representable
 resizable
 rsc
+AEDECOD
+AEs
+AESEQ
+AESEV
+AESEVN
+AESTDY
+AHIFL
+ahilofl
+ahsev
+AHSEV
+ahsevfl
+AHSEVFL
+ALOFL
+ASTDT
+modularity
+pharmaversesdtm
+preprocess
+stdy
+STUDYID
+TRTEMFL
+VSDY
+VSORRES
+VSSEQ
+VSTESTCD
diff --git a/posts/2023-06-27__hackathon_app/index.qmd b/posts/2023-06-27__hackathon_app/index.qmd
@@ -44,7 +44,7 @@ Please keep in mind that this work was done under tight time restraints.
 The [hackathon application](https://zxqguo-stefan0pascal-thoma.shinyapps.io/data_upload/?_ga=2.75919894.2036952320.1679990144-1584712930.1674550185) is still online (although data-upload is switched off) and the [GitHub repository](https://github.com/StefanThoma/hackathon_app) is publicly available.
 The application is embedded into this post right after this paragraph.
 I have also uploaded to GitHub a `.zip` file of the workspace to which hackathon participants had access via [posit cloud](https://posit.cloud).
-For more context you can watch [recordings of the hackathon-meetings](https://www.cdisc.org/events/webinar/admiral-hackathon-kickoff).
+For more context you can watch [recordings of the hackathon-meetings](https://www.cdisc.org/cosa).
 
 ```{r}
 #| echo: false

diff --git a/posts/2023-06-27_hackathon_writeup/index.qmd b/posts/2023-06-27_hackathon_writeup/index.qmd
@@ -41,7 +41,7 @@ The hackathon event was structured in two parts.
 First, we offered an *Introduction to R* for SAS programmers, a three hour workshop for R beginners to get them up to speed.
 Here we covered practical R basics, talking about how the R-workflow differs from a SAS workflow, and discussed common R functions - mostly from the tidyverse.
 This ensured that hackathon participants were familiar with core R concepts.
-The [workshop recording](https://www.cdisc.org/events/webinar/pre-admiral-hackathon-workshop-introduction-r-sas-programmers) and the [course materials](https://pharmaverse.github.io/intro-to-r-for-sas-programmers-workshop/) are available online.
+The [workshop recording](https://www.cdisc.org/cosa) and the [course materials](https://pharmaverse.github.io/intro-to-r-for-sas-programmers-workshop/) are available online.
 
 The main hackathon consisted of several ADAM data generating tasks based on a specs file and synthetic data.
 Participants were able to solve these tasks in groups at their own pace thanks to a online tool where participants could upload their task specific R scripts and they would get automatic feedback for the data-set produced by their script.
@@ -165,7 +165,7 @@ Congratulations to the winners:
 
 Although this was uncertain during the hackathon we were excited to provide a Certificate of Completion to all participants who uploaded a script to the Web Application.
 
-A recording of the hackathon readout can be found in the [CDISC Open Source Alliance Quarterly Spotlight](https://www.cdisc.org/events/webinar/cosa-quarterly-spotlight-q1-2023).
+A recording of the hackathon readout can be found in the [CDISC Open Source Alliance Quarterly Spotlight](https://www.cdisc.org/cosa).
 
 ## Conclusion
 

diff --git a/posts/2023-07-20_cross_company_dev/cross_industry_dev.qmd b/posts/2023-07-20_cross_company_dev/cross_industry_dev.qmd
@@ -84,7 +84,7 @@ If you would like to learn more about licenses for open source projects in the c
 ## Development workflow
 
 Every improvement, task, or feature we want to implement on [{admiral}](https://github.com/pharmaverse/admiral) starts as an issue on our [GitHub repository](https://github.com/pharmaverse/admiral).
-It is the centerpiece of our development workflow, along with our [developer guides](https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html) which describe in detail the strategies, conventions, and workflows used in development.
+It is the centerpiece of our development workflow, along with our [developer guides](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html) which describe in detail the strategies, conventions, and workflows used in development.
 The guides help us keep the [{admiral}](https://github.com/pharmaverse/admiral) package internally consistent (e.g. naming conventions, function logic) but also ensure that [{admiral}](https://github.com/pharmaverse/admiral) adjacent packages follow the same conventions and share the user interface.
 This is further helped by the implemented CICD pipeline which ensures styling convention and spelling (and much more).
 

diff --git a/posts/2023-11-27_higher_order/admiral.png b/posts/2023-11-27_higher_order/admiral.png
diff --git a/posts/2023-11-27_higher_order/appendix.R b/posts/2023-11-27_higher_order/appendix.R
@@ -0,0 +1,78 @@
+# markdown helpers --------------------------------------------------------
+
+markdown_appendix <- function(name, content) {
+  paste(paste("##", name, "{.appendix}"), " ", content, sep = "\n")
+}
+markdown_link <- function(text, path) {
+  paste0("[", text, "](", path, ")")
+}
+
+
+
+# worker functions --------------------------------------------------------
+
+insert_source <- function(repo_spec, name,
+                          collection = "posts",
+                          branch = "main",
+                          host = "https://github.com",
+                          text = "source code") {
+  path <- paste(
+    host,
+    repo_spec,
+    "tree",
+    branch,
+    collection,
+    name,
+    "code_sections.qmd",
+    sep = "/"
+  )
+  return(markdown_link(text, path))
+}
+
+insert_timestamp <- function(tzone = Sys.timezone()) {
+  time <- lubridate::now(tzone = tzone)
+  stamp <- as.character(time, tz = tzone, usetz = TRUE)
+  return(stamp)
+}
+
+insert_lockfile <- function(repo_spec, name,
+                            collection = "posts",
+                            branch = "main",
+                            host = "https://github.com",
+                            text = "R environment") {
+  path <- paste(
+    host,
+    repo_spec,
+    "tree",
+    branch,
+    collection,
+    name,
+    "renv.lock",
+    sep = "/"
+  )
+  return(markdown_link(text, path))
+}
+
+
+
+# top level function ------------------------------------------------------
+
+insert_appendix <- function(repo_spec, name, collection = "posts") {
+  appendices <- paste(
+    markdown_appendix(
+      name = "Last updated",
+      content = insert_timestamp()
+    ),
+    " ",
+    markdown_appendix(
+      name = "Details",
+      content = paste(
+        insert_source(repo_spec, name, collection),
+        insert_lockfile(repo_spec, name, collection),
+        sep = ", "
+      )
+    ),
+    sep = "\n"
+  )
+  knitr::asis_output(appendices)
+}