updated ad*.r programs to call on adam-pilot-3.xlsx in metacore object.

RConsortium · Mar 15, 2024 · 0ab0dc1 · 0ab0dc1
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diff --git a/submission/programs/adadas.r b/submission/programs/adadas.r
@@ -37,7 +37,7 @@ adsl <- convert_blanks_to_na(adsl)
 
 
 ## origin=predecessor, use metatool::build_from_derived()
-metacore <- spec_to_metacore(file.path(path$adam, "ADaM - Pilot 3.xlsx"), where_sep_sheet = FALSE)
+metacore <- spec_to_metacore(file.path(path$adam, "adam-pilot-3.xlsx"), where_sep_sheet = FALSE)
 # Get the specifications for the dataset we are currently building
 adadas_spec <- metacore %>%
   select_dataset("ADADAS")

diff --git a/submission/programs/adae.r b/submission/programs/adae.r
@@ -51,7 +51,7 @@ adsl <- convert_blanks_to_na(adsl)
 # Read in specifications from define
 #----------------------------------------------------------------------------------------
 ## placeholder for origin=predecessor, use metatool::build_from_derived()
-metacore <- spec_to_metacore(file.path(path$adam, "ADaM - Pilot 3.xlsx"), where_sep_sheet = FALSE, quiet = TRUE)
+metacore <- spec_to_metacore(file.path(path$adam, "adam-pilot-3.xlsx"), where_sep_sheet = FALSE, quiet = TRUE)
 adae_spec <- metacore %>% select_dataset("ADAE") # Get the specifications for the dataset we are currently building
 
 

diff --git a/submission/programs/adlbc.r b/submission/programs/adlbc.r
@@ -47,7 +47,7 @@ supplb <- convert_blanks_to_na(read_xpt(file.path(path$sdtm, "supplb.xpt")))
 adsl <- convert_blanks_to_na(read_xpt(file.path(path$adam, "adsl.xpt")))
 
 # create labels
-metacore <- spec_to_metacore(file.path(path$adam, "ADaM - Pilot 3.xlsx"), where_sep_sheet = FALSE, quiet = TRUE)
+metacore <- spec_to_metacore(file.path(path$adam, "adam-pilot-3.xlsx"), where_sep_sheet = FALSE, quiet = TRUE)
 
 adlbc_spec <- metacore %>%
   select_dataset("ADLBC")

diff --git a/submission/programs/adsl.r b/submission/programs/adsl.r
@@ -45,7 +45,7 @@ sc <- convert_blanks_to_na(read_xpt(file.path(path$sdtm, "sc.xpt")))
 mh <- convert_blanks_to_na(read_xpt(file.path(path$sdtm, "mh.xpt")))
 
 ## placeholder for origin=predecessor, use metatool::build_from_derived()
-metacore <- spec_to_metacore(file.path(path$adam, "ADaM - Pilot 3.xlsx"), where_sep_sheet = FALSE)
+metacore <- spec_to_metacore(file.path(path$adam, "adam-pilot-3.xlsx"), where_sep_sheet = FALSE)
 # Get the specifications for the dataset we are currently building
 adsl_spec <- metacore %>%
   select_dataset("ADSL")

diff --git a/submission/programs/adtte.r b/submission/programs/adtte.r
@@ -36,7 +36,7 @@ ds <- convert_blanks_to_na(read_xpt(file.path(path$sdtm, "ds.xpt")))
 
 ## placeholder for origin=predecessor, use metatool::build_from_derived()
 
-metacore <- spec_to_metacore(file.path(path$adam, "ADaM - Pilot 3.xlsx"), where_sep_sheet = FALSE)
+metacore <- spec_to_metacore(file.path(path$adam, "adam-pilot-3.xlsx"), where_sep_sheet = FALSE)
 
 # Get the specifications for the dataset we are currently building
 

diff --git a/vignettes/adrg.qmd b/vignettes/adrg.qmd
@@ -20,35 +20,21 @@ This document provides context for the analysis datasets and terminology that be
 
 ## Study Data Standards and Dictionary Inventory
 
-+-----------------------------+-----------------------------------------------+
 | **Standard or Dictionary**  | **Versions Used**                             |
-+=============================+===============================================+
+|-----------------------------|-----------------------------------------------|
 | SDTM                        | SDTM Implementation Guide Version 3.1.2       |
-+-----------------------------+-----------------------------------------------+
 |                             | SDTM Version 1.2                              |
-+-----------------------------+-----------------------------------------------+
 |                             |                                               |
-+-----------------------------+-----------------------------------------------+
 | SDTM Controlled Terminology | CDISC SDTM Controlled Terminology, 2022-12-16 |
-+-----------------------------+-----------------------------------------------+
 |                             |                                               |
-+-----------------------------+-----------------------------------------------+
 | ADaM                        | ADaM-IG v1.1                                  |
-+-----------------------------+-----------------------------------------------+
 |                             | ADaM v2.1                                     |
-+-----------------------------+-----------------------------------------------+
 |                             |                                               |
-+-----------------------------+-----------------------------------------------+
 | ADaM Controlled Terminology | CDISC ADaM Controlled Terminology, 2022-06-24 |
-+-----------------------------+-----------------------------------------------+
 |                             |                                               |
-+-----------------------------+-----------------------------------------------+
 | Data Definitions            | Define-XML v2.0                               |
-+-----------------------------+-----------------------------------------------+
 |                             |                                               |
-+-----------------------------+-----------------------------------------------+
 | Medical Events Dictionary   | MedDRA version 8.0                            |
-+-----------------------------+-----------------------------------------------+
 
 ## Source Data Used for Analysis Dataset Creation
 
@@ -279,11 +265,9 @@ Was define.xml evaluated?
 
 ## Issues Summary
 
-+----------+------------------------------------------------------------------------------+---------+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Check ID | Diagnostic Message                                                           | Dataset | Count (Issue Rate) | Explanation                                                                                                                                                                             |
-+==========+==============================================================================+=========+====================+=========================================================================================================================================================================================+
+|----------|------------------------------------------------------------------------------|---------|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | AD1012   | Secondary custom variable is present but its primary variable is not present | ADSL    | 1 (50.00%)         | This is a Sponsor Extension to the ADaM Model. The VISNUMEN \[End of Trt Visit (Vis 12 or Early Term.)\] variable is a integer variable which is not related to any character variable. |
-+----------+------------------------------------------------------------------------------+---------+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
 : {tbl-colwidths="\[17,22,15,22,25\]"}
 
@@ -303,19 +287,13 @@ The sponsor has provided all programs for analysis results. They are all created
 
 The following table contains the list of programs that generate the analysis datasets in Pilot 3. It shows the program file name, the analysis dataset name and the label of the analysis dataset. The recommended steps to execute the analysis results using R are described in the Appendix.
 
-+------------------+---------------------------+--------------------------------------+
 | **Program Name** | **Analysis Dataset Name** | **Analysis Dataset Label**           |
-+==================+===========================+======================================+
+|------------------|---------------------------|--------------------------------------|
 | adsl.r           | adsl.xpt                  | Subject-Level Analysis Dataset       |
-+------------------+---------------------------+--------------------------------------+
 | adadas.r         | adas.xpt                  | ADAS-Cog Analysis                    |
-+------------------+---------------------------+--------------------------------------+
 | adlbc.r          | adlb.xpt                  | Analysis Dataset Lab Blood Chemistry |
-+------------------+---------------------------+--------------------------------------+
 | adae.r           | adae.xpt                  | Adverse Events Analysis Dataset      |
-+------------------+---------------------------+--------------------------------------+
 | adtte.r          | adtte.xpt                 | AE Time to 1st Derm. Event Analysis  |
-+------------------+---------------------------+--------------------------------------+
 
 ## Analysis Output Programs
 
@@ -361,17 +339,12 @@ The following table contains a list of programs that generate outputs used in th
 
 For reference, below is a description of the analysis programs utilized and outputs generated in Pilot 1.
 
-+-------------------+-------------------------+-----------------------------------------------------------------------------------+
 | **Program Name**  | **Output Table Number** | **Title**                                                                         |
-+===================+=========================+===================================================================================+
+|-------------------|-------------------------|-----------------------------------------------------------------------------------|
 | tlf-demographic.r | Table 14-2.01           | Summary of Demographic and Baseline Characteristics                               |
-+-------------------+-------------------------+-----------------------------------------------------------------------------------+
 | tlf-primary.r     | Table 14-3.01           | Primary Endpoint Analysis: ADAS Cog (11) - Change from Baseline to Week 24 - LOCF |
-+-------------------+-------------------------+-----------------------------------------------------------------------------------+
 | tlf-efficacy.r    | Table 14-3.02           | ANCOVA of Change from Baseline at Week 20                                         |
-+-------------------+-------------------------+-----------------------------------------------------------------------------------+
 | tlf-kmplot.r      | Figure 14-1             | KM plot for Time to First Dermatologic Event: Safety population                   |
-+-------------------+-------------------------+-----------------------------------------------------------------------------------+
 
 ## Proprietary R Packages
 
@@ -569,6 +542,8 @@ To install and execute the R programs, follow all of the procedures below. Ensur
 
 In  addition, create  a  new  directory  to  hold  the  unpacked  Pilot  3  ADaM and tlf programs and files. For demonstration purposes, the procedures below assume the new directory is this location: C:\\pilot3-files, where the unpacked files are shown as the m1 and m5 directories.
 
+![](images/clipboard-641727471.png)
+
 ### Installation of R and R Studio
 
 Download and install R 4.2.3 for Windows from[ ](https://cran.r-project.org/bin/windows/base/old/4.2.1/R-4.2.1-win.exe)<https://cran.r-project.org/bin/windows/base/old/4.2.3/> . Then download and run the [R-4.2.3-win.exe](https://cran.r-project.org/bin/windows/base/old/4.2.3/R-4.2.3-win.exe) file. Also download RStudio for Windows by visiting[ ](https://www.rstudio.com/products/rstudio/download/#download)<https://dailies.rstudio.com/version/2023.03.1+446.pro1/>
@@ -585,15 +560,19 @@ Download and install R 4.2.3 for Windows from[ ](https://cran.r-project.org/bin/
 
 -   Once the location has been confirmed, click the Create Project button.
 
+-   These .Rproj files will be created.
+
+![](images/clipboard-2366076638.png)
+
 ### Installation of R Packages
 
-A minimum set of R packages are required to ensure the Pilot 3 analysis programs are successfully run and the custom package environment used for the application is replicated correctly. 
+A minimum set of R packages are required to ensure the Pilot 3 analysis programs are successfully run and the custom package environment used for the application is replicated correctly. Please follow these steps below to install these R packages.
 
-1.  The first package to install is the {remotes} package:
+1.  In the `Files` window pane, ensure that this directory `~/pilot3-files/m5/datasets/rconsortiumpilot3/analysis/adam/programs` has both the `renv-lock.txt` and `pilot3utils_0.0.2.zip` files.
 
-```         
-        install.packages("remotes")
-```
+![](images/clipboard-398207727.png)
+
+2.  In the R Studio console install the {remotes} package: `install.packages("remotes")`
 
 +-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Notes :                                                                                                                                                                                                                                                                                                                                   |
@@ -1072,21 +1051,14 @@ First 10 of 20 rows are shown in table below
 
 In pilot3, variable labels were updated per ADaM IG 1.1, which caused some discrepancies with original CDISC pilot data label.
 
-+-----------+-----------+---------------------------------+------------------------------------+
-| Dataset   | Variable  | CDISC pilot data label          | Pilot3 label                       |
-+:==========+:==========+:================================+:===================================+
-| ADAE      | ADURN     | Analysis Duration (N)           | AE Duration (N)                    |
-+-----------+-----------+---------------------------------+------------------------------------+
-|           | ADURU     | Analysis Duration Units         | AE Duration Units                  |
-+-----------+-----------+---------------------------------+------------------------------------+
-|           | AOCCFL    | 1st Occurrence of Any AE Flag   | 1st Occurrence within Subject Flag |
-+-----------+-----------+---------------------------------+------------------------------------+
-| ADADAS    | ANL01FL   | Analysis Record Flag 01         | Analysis Flag 01                   |
-+-----------+-----------+---------------------------------+------------------------------------+
-|           | ITTFL     | Intent-to-Treat Population Flag | Intent-To-Treat Population Flag    |
-+-----------+-----------+---------------------------------+------------------------------------+
-| ADTTE     | SRCDOM    | Source Data                     | Source Domain                      |
-+-----------+-----------+---------------------------------+------------------------------------+
+| Dataset | Variable | CDISC pilot data label          | Pilot3 label                       |
+|:--------|:---------|:--------------------------------|:-----------------------------------|
+| ADAE    | ADURN    | Analysis Duration (N)           | AE Duration (N)                    |
+|         | ADURU    | Analysis Duration Units         | AE Duration Units                  |
+|         | AOCCFL   | 1st Occurrence of Any AE Flag   | 1st Occurrence within Subject Flag |
+| ADADAS  | ANL01FL  | Analysis Record Flag 01         | Analysis Flag 01                   |
+|         | ITTFL    | Intent-to-Treat Population Flag | Intent-To-Treat Population Flag    |
+| ADTTE   | SRCDOM   | Source Data                     | Source Domain                      |
 
 {{< pagebreak >}}