From 535170bbe4ae2bff6b054d6201cbadac4681dcd1 Mon Sep 17 00:00:00 2001 From: Ben Straub Date: Wed, 30 Oct 2024 07:53:06 -0400 Subject: [PATCH 1/4] Delete posts/2024-01-04_end_of__year__up... directory --- .../2024-01-04_end_of__year__up.../appendix.R | 73 ------------------ ..._update_from_the__pharmaverse__council.qmd | 58 -------------- .../pharmaverse.PNG | Bin 20440 -> 0 bytes 3 files changed, 131 deletions(-) delete mode 100644 posts/2024-01-04_end_of__year__up.../appendix.R delete mode 100644 posts/2024-01-04_end_of__year__up.../end_of__year__update_from_the__pharmaverse__council.qmd delete mode 100644 posts/2024-01-04_end_of__year__up.../pharmaverse.PNG diff --git a/posts/2024-01-04_end_of__year__up.../appendix.R b/posts/2024-01-04_end_of__year__up.../appendix.R deleted file mode 100644 index ac352f6a..00000000 --- a/posts/2024-01-04_end_of__year__up.../appendix.R +++ /dev/null @@ -1,73 +0,0 @@ -library(dplyr) -# 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", - file_name) { - path <- paste( - host, - repo_spec, - "tree", - branch, - collection, - name, - file_name, - 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 = "Session info") { - path <- path <- "https://pharmaverse.github.io/blog/session_info.html" - - return(markdown_link(text, path)) -} - - - -# top level function ------------------------------------------------------ - -insert_appendix <- function(repo_spec, name, collection = "posts", file_name) { - appendices <- paste( - markdown_appendix( - name = "Last updated", - content = insert_timestamp() - ), - " ", - markdown_appendix( - name = "Details", - content = paste( - insert_source(repo_spec, name, collection, file_name = file_name), - # get renv information, - insert_lockfile(repo_spec, name, collection), - sep = ", " - ) - ), - sep = "\n" - ) - knitr::asis_output(appendices) -} diff --git a/posts/2024-01-04_end_of__year__up.../end_of__year__update_from_the__pharmaverse__council.qmd b/posts/2024-01-04_end_of__year__up.../end_of__year__update_from_the__pharmaverse__council.qmd deleted file mode 100644 index ba69e2aa..00000000 --- a/posts/2024-01-04_end_of__year__up.../end_of__year__update_from_the__pharmaverse__council.qmd +++ /dev/null @@ -1,58 +0,0 @@ ---- -title: "End of Year Update from the pharmaverse Council" -author: - - name: Mike Stackhouse -description: "2023 Was a big year - let's talk about it!" -date: "2024-01-04" -# please do not use any non-default categories. -# You can find the default categories in the repository README.md -categories: [Community] -# feel free to change the image -image: "pharmaverse.PNG" - ---- - - - -```{r setup, include=FALSE} -long_slug <- "2024-01-04_end_of__year__up..." -# renv::use(lockfile = "renv.lock") -``` - - - -## 2023 Was a Big Year - -This was a big year for open-source work in clinical submissions in general. We saw Roche speak about shifting to an [open-source backbone for clinical trials](https://www.youtube.com/watch?v=nqJsLSLd39A). Novo Nordisk spoke publicly of an [R based submission to the FDA](https://www.youtube.com/watch?v=t33dS17QHuA). These are true marks of progress being made in R becoming a first class language for clinical reporting. - -Back in August, Nicholas Eugenio released a [blog post](https://pharmaverse.github.io/blog/posts/2023-10-10_pharmaverse_story/pharmaverse_story.html) on the history of pharmaverse. It's funny to think about the fact that only 3 years ago, the idea of cross organization collaboration on R packages and building a community around this in the clinical world was just a conversation between friends. Since then, we have a community of more than 1200 people on Slack, 350 on LinkedIn, interest from over 150 organizations, and over 30 packages. If 2020 through 2022 was the birth of pharmaverse, 2023 was finding our identity as a community. For the council, 2024 will be about continuing to mature and find more ways that we can continue to support the community. - -## What We Accomplished - -One of our biggest moves in 2023 was to form our partnership with [PHUSE](https://phuse.global/PHUSE_Open_Source_Technology). This latched us into an existing community with shared values and a platform that helps us continue to build the pharmaverse community. At the [PHUSE EU Connect](https://www.phuse-events.org/attend/frontend/reg/thome.csp?pageID=11403&eventID=19&traceRedir=2) we had our first opportunity to host a pharmaverse meetup and bring together pharmaverse contributors in person. Additionally, there was an excellent panel session highlighting our use and adoption of open-source across industry, including the pharmaceutical, commercial, and software perspectives. As we move forward, we'll continue to use this platform to find ways we can host events and encourage collaboration within the pharmaverse community. - -This year our community was also able to launch new platforms to share updates and knowledge throughout the industry. The [pharmaverse examples](https://pharmaverse.github.io/examples/) webpage was launched to show pharmaverse packages in action, and the [pharmaverse blog](https://pharmaverse.github.io/blog/) (which I'm using right here!) provides a platform to share updates and community news. - -## Where Next? - -Back in October, I had the opportunity to do an interview with Michael Rimler for the [PHUSE video series](https://youtu.be/F3vehIoJgdA?si=80p0pKobZqjlXChj) Open Source Technologies in Clinical Data Analytics. The last question he asked me was what I expect the state of data analytics in life science to be in 2 to 3 years. My response was that when that time comes, I hope I couldn't have predicted where we would be - because back in 2020 I could never have predicted where we are now. The progress we've made is unbelievable, and the pharmaverse community has played a huge role in getting us where we are today. For the pharmaverse community, I hope to see that progress continue as we move into next year. As a council, our goal is to continue to mature this community. How can we support and foster collaboration between our organizations? How can we leverage this platform to drive the industry forward? - -For you as an individual, there's always an opportunity to get involved - and you don't have to be a package developer to contribute. You can [join a working group](https://pharmaverse.org/contribute/wg/), write [examples](https://github.com/pharmaverse/examples), or author a [blog post](https://github.com/pharmaverse/blog). Furthermore, you can get started with the pharmaverse packages, provide feedback via issues, and advocate for their use within your own organization. The pharmaverse community doesn't exist without you, and we're happy to have you all here to help us build this together. - -## P.S. - -At PHUSE US Connect 2024 this coming February, be on the lookout for one of the keynote presentations from Michael Rimler and Ross Farrugia! We hope to see you there! - -Here's to a 2024 full of progress and collaboration! - - - -```{r, echo=FALSE, message=FALSE} -source("appendix.R") -insert_appendix( - repo_spec = "pharmaverse/blog", - name = long_slug, - # file_name should be the name of your file - file_name = list.files() %>% stringr::str_subset(".qmd") %>% first() -) -``` diff --git a/posts/2024-01-04_end_of__year__up.../pharmaverse.PNG b/posts/2024-01-04_end_of__year__up.../pharmaverse.PNG deleted file mode 100644 index 7ee40c66663af65701ffddeb9d0a21f7932056ef..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 20440 zcmeEuCT~tPKhDk;rG0s z-Vg6z@O+pH&RqNKbM{_quYIq3-Fv>NsmS6!qkIMc0Is~8%trt~l0tl_G0_pI#C<=d>IXpNwmnI~UsT3WDG^Xhl9UH4?WmR0E_p6U87oItw=|ll2 zdrWR_{`_}&IoKCXWig)r{%l&u*k^-3a6>G>jBi>IT}os4IchKt9^PQ1!=m}_M4`{g zb4utbRltxSi$1Brz$G!(+@7g=CQ{Vhq)Q^vO=7oqKt?tPBTBd z*{bZBWv=PDaEJM?9+Aoo2}ol}B|EKrDNUcd(e>)gC@p8R&3oI27h zLunc@A7#4k@?bF7;$m;Q&iiy-*Lu23n6!U$ZiY)xixDNS)E70a`!B!&JeUo 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zQ@MQK)z)cky5`EN_w?$%(9;a_yngjEJ$%cWHJ+D=Au7d!%b=joZNrC)Eqy)%6T4NEUMIN9=*q}6IB6!ZgOgjx;I=w^E4L&B6nCd6oohc+j+ham%TEfqbZ` z7Kk8WS)XepoB8mRGKtE`mp{D9H*I3MpGwZSvz_1>9>~k98uT+=jEyY%5ZfD!zNW$O zG2%e?2~r~PFZbvLwfCf0kGX`k?ngl+F%^lVtqa4@lYb+W~h>6W^aa720b-TcU? z0v#0SNV%42(6R)=+F-Le`h(Dk9>kb(hYSd7H&dHdyGri~Q{eloX?~g4y zOZEbmilvF@6t;Fme2G)d+&S~S6AOK&>2qfM95iTzr=V4HP%~1XFM)dl7%${65$}5- z!wU9d*2(YTp`sWf~4n?5nHv*wMXYhhf4m*KDe4B1`bkGA^ogR0Jz?h8|Ujq z7QZ3=GsCrlOL@YEhIL_XVCT=TJmeAPDh9k>*^4Q{Q!KD4;xo0kB2&_8284PlJMp1| zy+5v&-u<|?K*bwlFKBVDf6HYB_b+4*-1a$=a1 zadWxA{4V%bEd%a&;nD3V(!XO&#kCH5yD*Cdl{w&p2Hj+1MJby^FZ(|r%?mp@^2sIR zyod%7h==$6)0pNQlxquN@6g5v^4K<*E?Bk$>u#*l{qlRiz|I8=2Em#+8K7TMNMFui z?{VV{@?XSN-c;fqa)Eh}@o9)1+AW24aW`=cAH)Sm t1=!>eRhK(Gc5z@4<9`RoOqc!xwdr>FAi3B(2sA#(ad%(0>LW3i{tKI%Z;Jo` From a853e2f67b4bffeccd3cc9d185e6590d79669f28 Mon Sep 17 00:00:00 2001 From: bms63 Date: Wed, 30 Oct 2024 10:57:27 -0400 Subject: [PATCH 2/4] feat: #231 data blog init --- README.md | 3 +- .../zzz_DO_NOT_EDIT_data__packages/appendix.R | 73 +++++++++++++++++++ .../data__packages.qmd | 44 +++++++++++ 3 files changed, 119 insertions(+), 1 deletion(-) create mode 100644 posts/zzz_DO_NOT_EDIT_data__packages/appendix.R create mode 100644 posts/zzz_DO_NOT_EDIT_data__packages/data__packages.qmd diff --git a/README.md b/README.md index e7739111..ed6f651c 100644 --- a/README.md +++ b/README.md @@ -112,7 +112,8 @@ install.packages(c("jsonlite", "rtables", "teal", "riskmetric", - "tidyCDISC")) + "tidyCDISC", + "mirai")) ``` ## How to Use the `blog` Docker Image for Local Development diff --git a/posts/zzz_DO_NOT_EDIT_data__packages/appendix.R b/posts/zzz_DO_NOT_EDIT_data__packages/appendix.R new file mode 100644 index 00000000..c69926b0 --- /dev/null +++ b/posts/zzz_DO_NOT_EDIT_data__packages/appendix.R @@ -0,0 +1,73 @@ +suppressMessages(library(dplyr)) +# 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", + file_name) { + path <- paste( + host, + repo_spec, + "tree", + branch, + collection, + name, + file_name, + 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 = "Session info") { + path <- path <- "https://pharmaverse.github.io/blog/session_info.html" + + return(markdown_link(text, path)) +} + + + +# top level function ------------------------------------------------------ + +insert_appendix <- function(repo_spec, name, collection = "posts", file_name) { + appendices <- paste( + markdown_appendix( + name = "Last updated", + content = insert_timestamp() + ), + " ", + markdown_appendix( + name = "Details", + content = paste( + insert_source(repo_spec, name, collection, file_name = file_name), + # get renv information, + insert_lockfile(repo_spec, name, collection), + sep = ", " + ) + ), + sep = "\n" + ) + knitr::asis_output(appendices) +} diff --git a/posts/zzz_DO_NOT_EDIT_data__packages/data__packages.qmd b/posts/zzz_DO_NOT_EDIT_data__packages/data__packages.qmd new file mode 100644 index 00000000..d6b95212 --- /dev/null +++ b/posts/zzz_DO_NOT_EDIT_data__packages/data__packages.qmd @@ -0,0 +1,44 @@ +--- +title: "Data Packages" +author: + - name: My Name +description: "" +# Note that the date below will be auto-updated when the post is merged. +date: "2024-10-30" +# Please do not use any non-default categories. +# You can find the default categories in the repository README.md +categories: [Metadata, SDTM, ADaM, TLG, Shiny, Community, Conferences, Submissions, Technical] +# Feel free to change the image +image: "pharmaverse.png" + +--- + + + +```{r setup, include=FALSE} +long_slug <- "zzz_DO_NOT_EDIT_data__packages" +# renv::use(lockfile = "renv.lock") +``` + + + +## pharmaversesdtm + +## pharmaverseadam + +## meddatasets + +https://www.linkedin.com/posts/alexander-krannich_meddatasets-ugcPost-7257309409335296000-NHri?utm_source=share&utm_medium=member_ios + + + + +```{r, echo=FALSE} +source("appendix.R") +insert_appendix( + repo_spec = "pharmaverse/blog", + name = long_slug, + # file_name should be the name of your file + file_name = list.files() %>% stringr::str_subset(".qmd") %>% first() +) +``` From 52ab69221d9f28045627a8770d60b5ab642ee6f9 Mon Sep 17 00:00:00 2001 From: Ben Straub Date: Sat, 14 Dec 2024 17:40:31 +0000 Subject: [PATCH 3/4] docs: working on title and image --- .../data__packages.qmd | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/posts/zzz_DO_NOT_EDIT_data__packages/data__packages.qmd b/posts/zzz_DO_NOT_EDIT_data__packages/data__packages.qmd index d6b95212..090d4ad4 100644 --- a/posts/zzz_DO_NOT_EDIT_data__packages/data__packages.qmd +++ b/posts/zzz_DO_NOT_EDIT_data__packages/data__packages.qmd @@ -1,13 +1,13 @@ --- -title: "Data Packages" +title: "Where is the data!?!" author: - - name: My Name -description: "" + - name: Ben Straub +description: "Compilation of Data and Data Packages useful for Clinical Reporting" # Note that the date below will be auto-updated when the post is merged. -date: "2024-10-30" +date: "2024-12-30" # Please do not use any non-default categories. # You can find the default categories in the repository README.md -categories: [Metadata, SDTM, ADaM, TLG, Shiny, Community, Conferences, Submissions, Technical] +categories: [SDTM, ADaM, Community, Technical] # Feel free to change the image 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zmJM<&b$aUi5so}@Lc56(yer>aK}qw@3D^GKd(;`sYE&Af=qA0->u-nmtF$ceT`$Rh zq+`HhWf7~}5t+!@LqM~g1&IL3ZR@+4MaTO+5B~s~RjXI6IrLphVkByxJWiWzQ}Wzf z6n_TAbb?y%{Q-2=V+l+%H|MnpS6p=c*Q)E5*)&CSaQ3!oCCh0S-NCy>PCM1_v9AS$ z+e35D%6_)L8|0$iP6QHu?NWEE6y&XPn`E9yo)WgGKYmPRc*Wkbf@xTWPB*Lj_zlO| zgcl?rXf_h#d_M*``r_M!fB^8ceV Z*UQqwC4qT2 +The purpose of this blog is to maintain an ongoing list of CDISC-specific data packages or packages with CDISC data that could be useful for Clinical Reporting. The packages could have a comprehensive set of data or just small toy examples for specific functions or vignettes. + +Feel free to get in touch with me for additions or clarifications. + ## pharmaversesdtm +A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages. A CDISC Pilot was conducted somewhere between 2008 and 2010. This is that Pilot data but slowly brought up to current CDISC standards. + +Most common SDTM datasets can be found as well as some specific disease area SDTMs. + +Available on CRAN and package is actively maintained on [GitHub](https://github.com/pharmaverse/pharmaversesdtm) + ## pharmaverseadam -## meddatasets +A set of Analysis Data Model (ADaM) datasets constructed using the Study Data Tabulation Model (SDTM) datasets contained in the 'pharmaversesdtm' package and the template scripts from the {admiral} family of packages. + +Available on CRAN and package is actively maintained on [GitHub](https://github.com/pharmaverse/pharmaversesdtm) + +## admiral + +A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide. + +Limited datasets like `ADSL`, `ADLB` but the template scripts availabe in this package are used to create the ADaM data in {pharmaverseadam} + +Available on CRAN and package is actively maintained on [GitHub](https://github.com/pharmaverse/admiral) + +## random.cdisc.data + +A set of functions to create random Analysis Data Model (ADaM) datasets and cached dataset. ADaM dataset specifications are described by the Clinical Data Interchange Standards Consortium (CDISC) Analysis Data Model Team. -https://www.linkedin.com/posts/alexander-krannich_meddatasets-ugcPost-7257309409335296000-NHri?utm_source=share&utm_medium=member_ios +Available on CRAN and package is actively maintained on [GitHub](https://github.com/insightsengineering/random.cdisc.data)