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Home Page: https://pharmaverse.github.io/blog/
License: Apache License 2.0
Blogging on the latest, greatest and most spectacular stuff happening around the pharmaverse
Home Page: https://pharmaverse.github.io/blog/
License: Apache License 2.0
There are several working groups that stemmed from {admiral}, create a blog that highlights their purpose and scope.
Note on handy tools in R/CICD.R
Reference issue below
pharmaverse/admiral#1827 (comment)
Set up Google Analytics
> @pharmaverse/commswg
We have to discuss the front images and corresponding tags. The function I created here copies default images for specific tags / image parameter. We should also discuss the tags we want to use. In my opinion, writers should use as many of the predefined tags as possible. Should they be able to create their own?
No I don't think people should make their own tags - we should provide a set and create news one if needed.
Originally posted by @bms63 in #40 (comment)
A value level validation use case, where `admiral` is used to validate a small chunk of the data:
admiral::derive_param_computed
.ADEX.PARAMCD = ADPCYMG
(Actual Dose per Cycle) based on existing parameters - Actual Dose per Cycle (ADPCYMG) = Total Amount of Dose (TOTDOSE) / Number of Cycles (NUMCYC);admiral::derive_param_computed
can add a parameter computed from the analysis value of other parameters. ADEX.AVAL (where ADEX.PARAPMCD = ADPCYMG)
= ADEX.AVAL (where ADEX.PARAPMCD = TOTDOSE) / ADEX.AVAL (where ADEX.PARAPMCD = NUMCYC)
# read in data
path_ads <- "xxxx"
adex <- haven::read_sas(paste0(path_ads, "adex.sas7bdat")) %>%
select(USUBJID, PARAM, PARAMCD, AVAL)
# subset input data to PARAMCD = "TOTDOSE", "NUMCYC"
adex_TOTDOSE_NUMCYC <- adex %>% filter(PARAMCD %in% c("TOTDOSE", "NUMCYC"))
# admiral::derive_param_computed()
val <-
derive_param_computed(
adex_TOTDOSE_NUMCYC,
by_vars = exprs(USUBJID),
parameters = c("TOTDOSE", "NUMCYC"),
analysis_value = AVAL.TOTDOSE / AVAL.NUMCYC,
set_values_to = exprs(
PARAMCD = "ADPCYMG",
PARAM = "Actual Dose per Cycle (mg)"
)
)
# compare with primary
diffdf::diffdf(adex %>% filter(PARAMCD == "ADPCYMG"),
val %>% filter(PARAMCD == "ADPCYMG"),
keys = c("USUBJID", "PARAMCD"))
Originally posted by @kaz462 in #2 (comment)
use cases of convert_blanks_to_na()
What's on the website/brief tour
Discussion point:
I would like to change the name of the repo to better represent what we do here.
This is relevant because the name is featured in all URL's.
github.com/pharmaverse/blog/ would not be bad.
However, that somewhat depends on the scope: is it going to be THE pharmaverse blog?
What about the thing NEST is planning?
What do you think, @pharmaverse/commswg
Wondering if we can have a blog post for {falcon} on the pharmaver/blog site? The post has been shared on LinkedIn.
https://www.linkedin.com/pulse/harmonizing-clinical-reporting-through-falcon-initiative-vincent-shen
So it create a link to the source code for the file above the citation.
When we get a little more stable - we should start setting up the renv.lock
as this will link to R environment.
Originally posted by @bms63 in #56 (comment)
There is additional information on creating posts in Readme that is not in the Scope post.
This should be aligned and re-published.
Hi Dinakar, @cicdguy
Any chance you could help me set up a devel version of the blog site. Or point me in the right direction/hold some hands while I fumble around in the daark ????
Create a blog about the use of derive_summary_records()
I'm wondering if we have admiral loaded with admiraldev if we can just use our assertions rather than checkmate. once less depenedency.
Originally posted by @bms63 in #49 (comment)
I was thinking of writing a post about what is pharmaverse, why we should choose it, where we can find its packages, and list some useful links.
Most of those information came from Ross Farrugia presentation on R/Pharma 2022 and were the base of the slides that were shared with the Council.
Possible breakage of the derive_param_computed blog post when updated
Newcomers and using admiral and collaboration cross company
Remove CICD spelling post
derive
and compute
use_ad_template
(Ben)R-Script to run which creates a blogpost draft for new blogposts.
End result here is not a finished template, but just to set something up for now that can be adjusted later.
In this blog post, we will describe the process of reproducing the R Submissions Pilot 2 App using our in-house developed framework. We will share our stories learned, a short introduction to Rhino and how we added value by using pkglite.
Highlight the package argument in use_ad_template()
In quarto, emails are written in the format:
Person
In markdown, it is:
Person
This is an issue for the link checker, because when converting from quarto to markdown I simply change the extension.
Solution:
In R file responsible for changing extension also delete the "."
@pharmaverse/commswg - hi all
I noticed when clicking around the different posts that we don't have a button to get back to the home page.
Can anyone look into this?
Long term Strategy for Images for Posts
Maybe we can come up with a temporary tags that people can chose from to avoid too many tags.
Write out assumption, strategy and scope for blog in the Wiki
Clean out old freeze, etc files that are no longer tracked
We should write a blogpost comparing the approaches chosen by tidyverse vs admiral.
I have specifically in mind the use of exprs()
when selecting multiple variables compared to vars()
in tidyverse.
We can think about mentioning why we diverge from the tidyverse standards (need for reliability) and that we may switch to the tidyverse standard in the future.
There may be other decisions where we diverge from tidyverse standards worth mentioning but they really should have an impact on the end user (in my opinion).
I was thinking of writing a post about what is admiral, its birth (with screenshots), how was and how is the situation in terms of contributors, its extensions, and what is the modularized framework.
Most of those information came from Ross Farrugia presentation on R/Pharma 2022 and were the base of the slides that were shared with the Council.
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