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-|-----------------------------|-----------------------------------------------| ++=============================+===============================================+ | 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 @@ -265,9 +279,11 @@ 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="\[17,22,15,22,25\]"} @@ -287,13 +303,19 @@ 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 @@ -341,12 +363,17 @@ 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 @@ -568,6 +595,10 @@ Download and install R 4.2.3 for Windows from[ ](https://cran.r-project.org/bin/ ![](images/clipboard-2366076638.png) +::: callout-note +It is possible that the `.Rproj.user` folder may not have generated for you or or may not be visible as it is a hidden folder. If so, this is fine as it will not be necessary in order to run the analysis programs below. +::: + ### 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. Please follow these steps below to install these R packages. @@ -653,6 +684,13 @@ PACKAGES.rds' - Open the .Rprofile : C:/pilot3-files/.Rprofile and ensure these 2 lines are there : + ``` + Sys.setenv(RENV_DOWNLOAD_FILE_METHOD = "libcurl") + source("renv/activate.R") + ``` + + e.g., + ![](images/clipboard-4064866343.png) - Restart the R Session (ignoring the warning once more), then run `renv::restore()` and select `y` : @@ -666,6 +704,22 @@ The package installation procedure may take a few minutes or longer depending on 5. Upon completion of installing packages using `{renv}`, please restart your R session. +::: callout-note +After restarting the R session at this stage, running `renv::status()` will show us that the only package uninstalled is the {pilot3utils} package. + +``` +The following package(s) are used in this project, but are not installed: + + pilot3utils + +Consider installing these packages (for example, using `renv::install()`). +Then, use `renv::snapshot()` to record these packages in the lockfile. +Use `renv::dependencies()` to see where these packages appear to be used. +``` + +We may ignore this as we will be installing the {pilot3utils} package in the following steps. +::: + 6. Install the {pilot3utils} package following the steps below : - In R Studio, navigate to your `Packages` window pane, then click on `Install`. @@ -680,17 +734,21 @@ The package installation procedure may take a few minutes or longer depending on ![](images/clipboard-1218742851.png) - - In the field `Package Archive`, click on `Browse...` and navigate to this directory to point to the `{pilot3utils}` package : +::: callout-note +This drop-down option is only available on a local Windows installation, not on linux systems. +::: + +- In the field `Package Archive`, click on `Browse...` and navigate to this directory to point to the `{pilot3utils}` package : - `/m5/datasets/rconsortiumpilot3/analysis/adam/programs/pilot3utils_0.0.2.zip` +`~/pilot3-files/m5/datasets/rconsortiumpilot3/analysis/adam/programs/pilot3utils_0.0.2.zip` - ![](images/clipboard-3031640318.png) +![](images/clipboard-3031640318.png) - - In the field `Install to Library:`, you may keep this at its default setting. +- In the field `Install to Library:`, you may keep this at its default setting. - - Click `Install`. +- Click `Install`. - ![](images/clipboard-2776928439.png) + ![](images/clipboard-2776928439.png) 7. **Set the paths to run the analysis programs** @@ -709,7 +767,21 @@ OUTPUT path: to save the analysis datasets and  results, define the path variab All these paths must be defined before executing the analysis programs. You may do so by first entering the full file path directories to where the SDTM is currently stored and where the ADaMs and Outputs will be generated upon execution of the analysis programs. ::: callout-note -In the example file paths for `adam` and `output`, you will need to create these folders first, in their respective locations and set those accordingly in this path list. The reason for creating a new folder (e.g ../adam/datasets-fda) is to not overwrite the current ADaM datasets generated by the sponsor (i.e. ../adam/datasets), upon FDA reviewers' execution of the analysis programs. +Before executing the example file paths below, first navigate to the `~/pilot3-files/m5/datasets/rconsortiumpilot3/analysis` folder and do this : + +1. Create a copy of the `adam` folder in the same location and rename the new folder copy as `adam-reviewer`. The reason for creating this `adam-reviewer` folder (e.g ../adam-reviewer) is to keep the original ADaM datasets generated by the sponsor (e.g ../adam) so they will not get overwritten upon reviewers' execution of the analysis programs. + +![](images/clipboard-2507647878.png) + +![](images/clipboard-2575673838.png) + +![](images/clipboard-3211797445.png) + +2. In the same location create a new folder called `output` in order to write the outputs in this folder upon reviewers' execution of the analysis output programs. + +![](images/clipboard-3715719545.png) + +![](images/clipboard-366164445.png) ``` # Modify path to the sdtm, adam and output location @@ -717,7 +789,7 @@ In the example file paths for `adam` and `output`, you will need to create these path <- list( sdtm = "Enter full file path to the sdtm data here", - adam = "Enter full file path to where adam data should be saved and + adam = "Enter full file path to where adam data will be written and sourced here", output = "Enter full file path to where outputs should be saved here" ) @@ -725,16 +797,16 @@ path <- list( # For example path <- list( - sdtm = "~/m5/datasets/rconsortiumpilot3/tabulations/sdtm", - adam = "~/m5/datasets/rconsortiumpilot3/analysis/adam/datasets-fda", - output = "~/m5/datasets/rconsortiumpilot3/analysis/output" + sdtm = "~/pilot3-files/m5/datasets/rconsortiumpilot3/tabulations/sdtm", + adam = "~/pilot3-files/m5/datasets/rconsortiumpilot3/analysis/adam-reviewer/datasets", + output = "~/pilot3-files/m5/datasets/rconsortiumpilot3/analysis/output" ) ``` ::: 5. **Execute analysis program** -To reproduce analysis results, rerun the following programs: +To reproduce analysis results, rerun the following programs in the order below from `~/pilot3-files/m5/datasets/rconsortiumpilot3/analysis/adam-reviewer/programs` : - “adsl.r” @@ -1099,14 +1171,21 @@ 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 >}} diff --git a/vignettes/images/clipboard-1827993053.png b/vignettes/images/clipboard-1827993053.png new file mode 100644 index 0000000..496ee64 Binary files /dev/null and b/vignettes/images/clipboard-1827993053.png differ diff --git a/vignettes/images/clipboard-2507647878.png b/vignettes/images/clipboard-2507647878.png new file mode 100644 index 0000000..b32b554 Binary files /dev/null and b/vignettes/images/clipboard-2507647878.png differ diff --git a/vignettes/images/clipboard-2575673838.png b/vignettes/images/clipboard-2575673838.png new file mode 100644 index 0000000..59edc21 Binary files /dev/null and b/vignettes/images/clipboard-2575673838.png differ diff --git a/vignettes/images/clipboard-3211797445.png b/vignettes/images/clipboard-3211797445.png new file mode 100644 index 0000000..8d8b412 Binary files /dev/null and b/vignettes/images/clipboard-3211797445.png differ diff --git a/vignettes/images/clipboard-366164445.png b/vignettes/images/clipboard-366164445.png new file mode 100644 index 0000000..c9d1b63 Binary files /dev/null and b/vignettes/images/clipboard-366164445.png differ diff --git a/vignettes/images/clipboard-3715719545.png b/vignettes/images/clipboard-3715719545.png new file mode 100644 index 0000000..598b7ff Binary files /dev/null and b/vignettes/images/clipboard-3715719545.png differ