Package: madshapR 1.1.0

Guillaume Fabre

madshapR: Support Technical Processes Following 'Maelstrom Research' Standards

Functions to support rigorous processes in data cleaning, evaluation, and documentation across datasets from different studies based on Maelstrom Research guidelines. The package includes the core functions to evaluate and format the main inputs that define the process, diagnose errors, and summarize and evaluate datasets and their associated data dictionaries. The main outputs are clean datasets and associated metadata, and tabular and visual summary reports. As described in Maelstrom Research guidelines for rigorous retrospective data harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).

Authors:Guillaume Fabre [aut, cre], Maelstrom-research group [cph, fnd]

madshapR_1.1.0.tar.gz
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madshapR.pdf |madshapR.html✨
madshapR/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/maelstrom-research/madshapr/issues

Datasets:
  • madshapR_DEMO - Built-in material allowing the user to test the package with demo data
  • valueType_list - Built-in data frame of allowed valueType values

On CRAN:

5.88 score 2 stars 3 packages 28 scripts 249 downloads 66 exports 107 dependencies

Last updated 7 months agofrom:63d4972710. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winOKOct 27 2024
R-4.5-linuxOKOct 27 2024
R-4.4-winNOTEOct 27 2024
R-4.4-macNOTEOct 27 2024
R-4.3-winNOTEOct 27 2024
R-4.3-macNOTEOct 27 2024

Exports:as_categoryas_data_dictas_data_dict_mlstras_data_dict_shapeas_datasetas_dossieras_taxonomyas_valueTypebookdown_openbookdown_renderbookdown_templatecheck_data_dict_categoriescheck_data_dict_missing_categoriescheck_data_dict_valueTypecheck_data_dict_variablescheck_dataset_categoriescheck_dataset_valueTypecheck_dataset_variablescheck_name_standardscol_iddata_dict_applydata_dict_collapsedata_dict_evaluatedata_dict_expanddata_dict_extractdata_dict_filterdata_dict_group_bydata_dict_group_splitdata_dict_list_nestdata_dict_match_datasetdata_dict_pivot_longerdata_dict_pivot_widerdata_dict_ungroupdata_extractdataset_cat_as_labelsdataset_evaluatedataset_preprocessdataset_summarizedataset_visualizedataset_zap_data_dictdossier_createdossier_evaluatedossier_summarizedrop_categoryis_categoryis_data_dictis_data_dict_mlstris_data_dict_shapeis_datasetis_dossieris_taxonomyis_valueTypemadshapR_helpmadshapR_websiteopen_visual_reportsummary_variablessummary_variables_categoricalsummary_variables_datesummary_variables_datetimesummary_variables_numericsummary_variables_textvalueType_adjustvalueType_guessvalueType_ofvalueType_self_adjustvariable_visualize

Dependencies:askpassbase64encbitbit64bookdownbslibcachemcellrangerclicliprcolorspacecpp11crayoncredentialscrosstalkcurldescdigestdplyrDTevaluatefabRfansifarverfastmapfontawesomeforcatsfsgenericsgertggplot2ghgitcredsgluegtablehavenhighrhmshtmltoolshtmlwidgetshttpuvhttr2iniisobandjaneaustenrjanitorjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangrmarkdownrprojrootrstudioapisassscalessnakecaseSnowballCstringistringrsystibbletidyrtidyselecttidytexttimechangetinytextokenizerstzdbusethisutf8vctrsviridisLitevroomwhiskerwithrwritexlxfunyamlzip

madshapR-vignette

Rendered frommadshapR-vignette.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2024-04-30
Started: 2023-03-13

Readme and manuals

Help Manual

Help pageTopics
Validate and coerce any object as a categorical variable.as_category
Validate and coerce any object as a data dictionaryas_data_dict
Validate and coerce any object as an Opal data dictionary formatas_data_dict_mlstr
Validate and coerce any object as a workable data dictionary structureas_data_dict_shape
Validate and coerce any object as a datasetas_dataset
Validate and coerce any object as a dossier (list of dataset(s))as_dossier
Validate and coerce any object as a taxonomyas_taxonomy
Validate and coerce any object according to a given valueTypeas_valueType
Objects exported from other packagesbookdown_open
Objects exported from other packagesbookdown_render
Objects exported from other packagesbookdown_template
Assess a data dictionary for potential issues in categoriescheck_data_dict_categories
Assess categorical variables for non-Boolean values in 'missing' columncheck_data_dict_missing_categories
Assess a data dictionary for non-valid valueType valuescheck_data_dict_valueType
Assess a data dictionary for potential issues in variablescheck_data_dict_variables
Assess a data dictionary and associated dataset for category differencescheck_dataset_categories
Assess a data dictionary and associated dataset for valueType differencescheck_dataset_valueType
Assess a data dictionary and associated dataset for undeclared variablescheck_dataset_variables
Assess variable names in a data dictionary for non-standard formatscheck_name_standards
Return the id column names(s) of a datasetcol_id
Apply a data dictionary to a datasetdata_dict_apply
Transform multi-row category column(s) to single rows and join to "Variables"data_dict_collapse
Generate an assessment report for a data dictionarydata_dict_evaluate
Transform single-row category information to multiple rows as elementdata_dict_expand
Generate a data dictionary from a datasetdata_dict_extract
Subset data dictionary by row valuesdata_dict_filter
Group listed data dictionaries by specified column namesdata_dict_group_by
Split grouped data dictionaries into a named listdata_dict_group_split
Bind listed data dictionariesdata_dict_list_nest
Inner join between a dataset and its associated data dictionarydata_dict_match_dataset
Transform column(s) of a data dictionary from wide format to long formatdata_dict_pivot_longer
Transform column(s) of a data dictionary from long format to wide formatdata_dict_pivot_wider
Ungroup data dictionarydata_dict_ungroup
Create an empty dataset from a data dictionarydata_extract
Apply data dictionary category labels to the associated dataset variablesdataset_cat_as_labels
Generate an assessment report for a datasetdataset_evaluate
Generate an evaluation of all variable values in a datasetdataset_preprocess
Generate an assessment report and summary of a datasetdataset_summarize
Generate a web-based visual report for a datasetdataset_visualize
Remove labels (attributes) from a data frame, leaving its unlabelled columnsdataset_zap_data_dict
Generate a dossier from a list of one or more datasetsdossier_create
Generate an assessment report of a dossierdossier_evaluate
Generate an assessment report and summary of a dossierdossier_summarize
Validate and coerce any object as a non-categorical variable.drop_category
Test if an object is a valid datasetis_category
Test if an object is a valid data dictionaryis_data_dict
Test if an object is a valid Maelstrom data dictionaryis_data_dict_mlstr
Test if an object is a workable data dictionary structureis_data_dict_shape
Test if an object is a valid datasetis_dataset
Test if an object is a valid dossier (list of dataset(s))is_dossier
Test if an object is a valid taxonomyis_taxonomy
Test if a character object is one of the valid valueType valuesis_valueType
Built-in material allowing the user to test the package with demo datamadshapR_DEMO
Call to online documentationmadshapR_website
Provide descriptive statistics for variables in a datasetsummary_variables
Provide descriptive statistics for variables of categorical in a datasetsummary_variables_categorical
Provide descriptive statistics for variables of type 'date' in a datasetsummary_variables_date
Provide descriptive statistics for variables of type 'datetime' in a datasetsummary_variables_datetime
Provide descriptive statistics for variables of type 'numeric' in a datasetsummary_variables_numeric
Provide descriptive statistics for variables of type 'text' in a datasetsummary_variables_text
Attribute the valueType from a data dictionary to a dataset, or vice versavalueType_adjust
Guess the first possible valueType of an object (Can be a vector)valueType_guess
Built-in data frame of allowed valueType valuesvalueType_list
Return the valueType of an objectvalueType_of
Guess and attribute the valueType of a data dictionary or dataset variablevalueType_self_adjust
Generate a list of charts, figures and summary tables of a variablevariable_visualize