Background Information

@zdz2101 @manciniedoardo labels are needed for NEST

Definition of Done

No response

Please select a category the issue is focused on?

Function Documentation

Let us know where something needs a refresh or put your idea here!

          Does "{admiral} template" refer to the templates in admiral core only or does it include the templates in the extension packages {admiralonco}, {admiralophta}, {admiralvaccines}, ...?

If it includes extension packages, we may need to add something regarding the requirements for the CI/CD workflow to process them.

Originally posted by @bundfussr in #6 (comment)

see downstream issue in scda.test insightsengineering/scda.test#134

Background Information

@manciniedoardo @bms63 any idea when installing from CRAN using install.packages() on R 4.2.2 we get:

Warning in install.packages :
  package ‘pharmaverseadam’ is not available for this version of R

Installing latest GitHub devel version works.

Definition of Done

No response

Please select a category the issue is focused on?

No response

Let us know where something needs a refresh or put your idea here!

Add badges to website as package is now available on pharmaverse.

What happened?

Just reporting issues running templates for admiral family packages :

• admiralonco :
  ad_adrs_basic.R :

Error in filter_joined(dataset, by_vars = subject_keys, order = order,  : 
  argument "dataset_add" is missing, with no default
Calls: %>% ... filter_joined -> assert_data_frame -> is.data.frame
In addition: Warning message:
The `filter` argument of `filter_joined()` is deprecated as of admiral 1.0.0.
ℹ Please use the `filter_join` argument instead.
ℹ The deprecated feature was likely used in the admiralonco package.
  Please report the issue at <https://github.com/pharmaverse/admiralonco/issues>. 
Execution halted

ad_adtr.R :

Error in derive_vars_joined(., dataset_add = adtr_sum, by_vars = exprs(USUBJID),  : 
  argument "join_type" is missing, with no default
Calls: %>% ... derive_vars_joined -> get_joined_data -> assert_character_scalar
Execution halted

• admiralvaccine :
  ad_adce.R :

Error in derive_vars_joined(adce02, dataset_add = adperiods, by_vars = exprs(STUDYID,  : 
 argument "join_type" is missing, with no default
Calls: %>% ... der

ad_adface.R

Error in derive_vars_joined(adface, dataset_add = period_ref, by_vars = exprs(STUDYID,  : 
 argument "join_type" is missing, with no default
Calls: %>% ... derive_vars_joined -> get_joined_data -> assert_character_scalar
Execution halted

• ad_adis.R

Error in derive_vars_joined(adis_crit, dataset_add = period_ref, by_vars = exprs(STUDYID,  : 
  argument "join_type" is missing, with no default
Calls: derive_var

• ad_adsl.R

Error in library(admiral.test) : 
  there is no package called ‘admiral.test’
Execution halted

(for some of them it seems just related to the use of deprecated functions and use of admiral.test that has been decommissioned )

Session Information

No response

Reproducible Example

No response

Background Information and pre-release tasks

• Release after admiral releases on week of 3rd June
• update description file and changelog
• change icon in chrome tab to package hex
• add @sadchla-codes as developer

Definition of Done

• devtools::release()

Hello,

While testing safety templates in scda.test, we found that the following variables are missing from the ADCM dataset:

• CMENRTPT
• ATIREL
• ATC1, ATC2, ATC3, ATC4

If you require any further details please let me/the SME team know.

Thanks!!

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No response

Let us know where something needs a refresh or put your idea here!

Hi,

I noticed that there are some records/values has non-compliance with the ADaM IG. Maybe I could record some issues and hope this would be useful for your work.

1. ADSL: The label of ADSL should be "Subject-Level Analysis Dataset", not "Demographics".
2. ADLB: PARAMCD in ("BASO", “LYMPH”）has two corresponding PARAM values.
3. ADPC: ATPT="Pre-dose" assigned 3 different values of ATPTN(-0.5,24,48).

Background Information

Addressing CRAN submission issue

Definition of Done

Links are working

Please select a category the issue is focused on?

No response

Let us know where something needs a refresh or put your idea here!

Could we improve the text here, similar to what we are doing in pharmaversesdtm?

I'm also seeing this is titled "Function Reference" - maybe dataset reference is better?

@kaz462 @sadchla-codes tagging you both, feel free to action as appropriate

change from remotes::install_github("pharmaverse/pharmaverseadam", ref = "devel") to
remotes::install_github("pharmaverse/pharmaverseadam", ref = "main")

same update for pharmaversesdtm

Several variables have .x and .y variables

> names(adpp)
 [1] "STUDYID"  "USUBJID"  "PPTESTCD" "PPTEST"   "PPCAT"    "PPORRES"  "PPORRESU" "PPSTRESU" "PPSPEC"   "PPRFDTC" 
[11] "TRTSDT.x" "TRTEDT.x" "DTHDT.x"  "EOSDT.x"  "TRT01P.x" "TRT01A.x" "ADT"      "ADY"      "PARAMCD"  "AVAL"    
[21] "AVALC"    "SRCDOM"   "SRCVAR"   "SRCSEQ"   "VISIT"    "VISITNUM" "AVISIT"   "AVISITN"  "TRTP"     "TRTA"    
[31] "AVALCA1N" "AVALCAT1" "SUBJID"   "RFSTDTC"  "RFENDTC"  "RFXSTDTC" "RFXENDTC" "RFICDTC"  "RFPENDTC" "DTHDTC"  
[41] "DTHFL"    "SITEID"   "AGE"      "AGEU"     "SEX"      "RACE"     "ETHNIC"   "ARMCD"    "ARM"      "ACTARMCD"
[51] "ACTARM"   "COUNTRY"  "DMDTC"    "DMDY"     "TRT01P.y" "TRT01A.y" "TRTSDTM"  "TRTSTMF"  "TRTEDTM"  "TRTETMF" 
[61] "TRTSDT.y" "TRTEDT.y" "TRTDURD"  "SCRFDT"   "EOSDT.y"  "EOSSTT"   "FRVDT"    "RANDDT"   "DTHDT.y"  "DTHADY"  
[71] "LDDTHELD" "LSTALVDT" "AGEGR1"   "SAFFL"    "RACEGR1"  "REGION1"  "LDDTHGR1" "DTH30FL"  "DTHA30FL" "DTHB30FL"

Dear maintainer

While we were testing templates using the pharmaverseadam data, we noticed that

• adpc and adpp data do not have urine data,
• avisit variable is empty
• adpp PPCAT column only has "COMPARTMENTAL", and doesn't have any other options
• AVALU is currently missing, consider to use derive this from PPORRESU

Many thanks for your consideration.

Please select a category the issue is focused on?

Other

Let us know where something needs a refresh or put your idea here!

Update the package icon to reflect pharmaverseadam

Background Information

• Prefix: admiralonco_<dataset>.
• {admiralonco} contacts: Hinal Patel, @HinalPat, Stefan Bundfuss (@bundfussr)

Definition of Done

• ADaM contents of data folder of {admiralonco}, as well as any relevant files in dev folder in copied over to same locations in {admiraldata}.
• New datasets catalogued in data.R.

Background Information

Non-ASCII characters cause NOTES to appear when running pre-release checks. We should remove any from the package to avoid any issues.

Definition of Done

• Run the following in the searchbar on github:
  repo:pharmaverse/pharmaverseadam /[^\x00-\x7F]+/
• Remove anything flagged.

rename to pharmaverseadam in all files, similar to the following PRs:
pharmaverse/pharmaversesdtm#30
pharmaverse/pharmaversesdtm#20

follow up on pharmaverse/admiralci#159

Hello again,

While testing safety templates in scda.test, we found that the following variables are missing from the ADEG and ADEX datasets:

• AVALU (missing from both ADEG and ADEX - if difficult, we could add this into our pre-processing steps)
• WORS02FL (missing from ADEG)
• PARCAT2 (missing from ADEX)

If you require any further details please let me/the SME team know.

Thanks!

adpp contains variables with suffix .x, .y
we should do a thorough check and clean up those variables @pharmaverse/admiraldata

"TRTSDT.y" "TRTEDT.y" "DTHDT.y" "EOSDT.y"  "TRT01P.y" "TRT01A.y" 
"TRTSDT.x" "TRTEDT.x" "DTHDT.x" "EOSDT.x"  "TRT01P.x" "TRT01A.x"

found this issue when I try to convert the data to .xpt file

Error: Failed to create column `TRTSDT.x`: A provided name contains an illegal character.

Background Information

Harmonize e2e examples with define/specs

Definition of Done

No response

generate a blank data-driven define-xml along with the Excel spec, so that we can -
2023Q4

• apply variable labels

In the future:

• manually enter the derivation text for each variable
• add a column for "admiral function" used in the Variable and ValueLevel sheets
• link some work from the following issue: pharmaverse/admiral#688