Package: metalite 0.1.4

Yujie Zhao

metalite: ADaM Metadata Structure

A metadata structure for clinical data analysis and reporting based on Analysis Data Model (ADaM) datasets. The package simplifies clinical analysis and reporting tool development by defining standardized inputs, outputs, and workflow. The package can be used to create analysis and reporting planning grid, mock table, and validated analysis and reporting results based on consistent inputs.

Authors:Yilong Zhang [aut], Yujie Zhao [aut, cre], Nan Xiao [aut], Benjamin Wang [ctb], Brian Lang [ctb], Howard Baek [ctb], Ruchitbhai Patel [ctb], Madhusudhan Ginnaram [ctb], Sarad Nepal [ctb], Venkatesh Burla [ctb], Merck Sharp & Dohme Corp [cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metalite/json (API)

# Install 'metalite' in R:
install.packages('metalite', repos = c('https://merck.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/merck/metalite/issues

Pkgdown/docs site:https://merck.github.io

On CRAN:

Conda:

cdiscclinical-trialsmetadata

8.99 score 17 stars 5 packages 86 scripts 380 downloads 36 exports 1 dependencies

Last updated from:85757ba1bf. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK151
source / vignettesOK199
linux-release-x86_64OK148
macos-release-arm64OK88
macos-oldrel-arm64OK93
windows-develOK113
windows-releaseOK106
windows-oldrelOK94
wasm-releaseOK105

Exports:adam_mappingadd_planassign_labelcollect_adam_mappingcollect_datanamecollect_n_subjectcollect_observation_indexcollect_observation_recordcollect_populationcollect_population_idcollect_population_indexcollect_population_recordcollect_titledefault_applydefine_analysisdefine_observationdefine_parameterdefine_plandefine_populationget_labelmeta_adammeta_add_totalmeta_buildmeta_examplemeta_example_explorationmeta_inheritmeta_runmeta_splitn_subjectoutdataplanspec_analysis_populationspec_call_programspec_filenamespec_titleupdate_adam_mapping

Dependencies:rlang

Collect Components
Collect ADaM mapping | Collect population | Collect population records | Collect observation record | Collect specifications
Rendered fromcomponent.Rmdusingknitr::rmarkdown

Last update: 2023-02-02
Started: 2022-04-17

Introduction to metalite
Overview | Use cases | Mental model | Example: adverse events analysis
Rendered frommetalite.Rmdusingknitr::rmarkdown

Last update: 2023-02-02
Started: 2022-04-14

Create AR Grid
Overview | Build metadata | Step 1: input the population and observation datasets | Step 2: create statistical analysis plans | Step 3: feed in the analysis plan to the existing metadata | Step 4: define the key words in the above metadata | Step 4.1: define the key words in population & observation | Step 4.2 define the key words in the analysis plans | Step 5: build the metadata | Create A&R grid
Rendered fromar-grid.Rmdusingknitr::rmarkdown

Last update: 2023-02-02
Started: 2022-08-15

Create Mockup Table Based on Metadata
Overview of the example we used | Prepare the metadata | Step 1: Define the metadata | Step 2: Define the analysis plan | Step 3: Define the keywords | Step 4: Build and review the metadata | Add components of mockup table | Create functions | Row label | Get treatment grouping order | Get the title/endnotes of TLF | Logic to create mockup table | Display the generated mockup tables
Rendered frommockup-table.Rmdusingknitr::rmarkdown

Last update: 2023-02-02
Started: 2022-08-16

Introduction to Variable Mapping
Overview | Example 1: All Participants as Treated (apat) | Base R | Tidy evaluation | Example 2: Serious adverse events (ser)
Rendered fromadam-mapping.Rmdusingknitr::rmarkdown

Last update: 2023-02-02
Started: 2022-04-14

Readme and manuals

Help Manual

Help pageTopics
Construct ADaM mappingsadam_mapping
Add additional analysis planadd_plan
A function to assign labels to a data frameassign_label
Collect 'adam_mapping' from 'meta_adam' by 'name'collect_adam_mapping
Collect specification for dataset namecollect_dataname
Collect number of subjects and its subset conditioncollect_n_subject
Collect observation record index from observation datasetcollect_observation_index
Collect observation record from observation datasetcollect_observation_record
Collect specification for population definitioncollect_population
Collect subject identifier information from population datasetcollect_population_id
Collect population record index from population datasetcollect_population_index
Collect population record from population datasetcollect_population_record
Collect specification for titlecollect_title
Apply default values to ADaM mappingsdefault_apply
Define analysis function meta information for ADaM datasetdefine_analysis
Define analysis observation meta information for ADaM datasetdefine_observation
Define analysis parameter meta information for ADaM datasetdefine_parameter
Define analysis plan meta information for ADaM datasetdefine_plan
Define analysis population meta information for ADaM datasetdefine_population
A function to get the labels of data frame columnsget_label
Create a metadata representation for ADaM data analysismeta_adam
Add duplicate data to enable a total groupmeta_add_total
Build complete meta informationmeta_build
Create an example 'meta_adam' objectmeta_example
Create a data exploration 'meta_adam' objectmeta_example_exploration
Inherit meta information by keywordsmeta_inherit
Execute analysis based on the analysis planmeta_run
Split metadata into groupsmeta_split
Count number of unique subjectsn_subject
Construct 'outdata' classoutdata
Create a analysis plan from all combination of variablesplan
Print a metadata object with its population, observation, and analysis plansprint.meta_adam
Specification for population definitionspec_analysis_population
Specification for analysis call programspec_call_program
Specification for analysis output filenamespec_filename
Specification for analysis titlespec_title
Update mapping rule in 'adam_mapping'update_adam_mapping