Package: clinpubr 1.4.0

clinpubr: Clinical Publication

Accelerate the process from clinical data to medical publication, including clinical data cleaning, significant result screening, and the generation of publish-ready tables and figures.

Authors:Yue Niu [aut, cre, cph], Keyun Wang [aut]

clinpubr_1.4.0.tar.gz
clinpubr_1.4.0.zip(r-4.7)clinpubr_1.4.0.zip(r-4.6)clinpubr_1.4.0.zip(r-4.5)
clinpubr_1.4.0.tgz(r-4.6-any)clinpubr_1.4.0.tgz(r-4.5-any)
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clinpubr_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
clinpubr/json (API)
NEWS

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

Bug tracker:https://github.com/yotasama/clinpubr/issues

On CRAN:

Conda:

6.23 score 2 stars 11 scripts 227 downloads 68 exports 160 dependencies

Last updated from:a23a1499c3. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK242
source / vignettesOK299
linux-release-x86_64OK282
macos-release-arm64OK199
macos-oldrel-arm64OK187
windows-develOK216
windows-releaseOK197
windows-oldrelOK207
wasm-releaseOK179

Exports:add_listsanswer_checkauto_encoding_repairbaseline_tablebreak_atcalc_cindexcalculate_indexchar_initial_cleaningcheck_nonnumclassif_model_comparecombine_filescombine_multichoicecommon_prefixcut_bydata_overviewdetect_outliersdf_view_nonnumemp_colorsexclusion_countextract_numfill_with_lastfilter_rcs_predictorsfirst_modeformat_pvalformula_add_covsget_samplesget_validget_valid_subsetget_var_typesimportance_plotindicate_duplicatesinteraction_p_valueinteraction_plotinteraction_scaniqr_outlierkeep_by_keywordmad_outliermax_missing_ratesmerge_by_rangemerge_by_substringmerge_ordered_vectorsna_maxna_minna2falsename2codepredictor_effect_plotqq_showrcs_plotregression_basic_resultsregression_fitregression_forestregression_scanreplace_elementsscreen_data_listsplit_multichoicestr_match_replacesubgroup_forestsubject_viewtest_normalitytime_roc_plotto_dateto_wideunit_standardizeunit_viewunmake_namesvalue_initial_cleaningvec2codezscore_outlier

Dependencies:abindaskpassbackportsbase64encbitbit64bootbroombslibcachemcarcarDatacellrangercheckmateclassclicliprclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tableDerivDescToolsdigestdoBydplyre1071evaluateExactexactRankTestsexpmfarverfastmapfBasicsfontawesomeforcatsforecastforeignforestploterFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifggtextgldgluegridExtragridtextgssgtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobandjpegjquerylibjsonliteknitrlabelinglatticelifecyclelitedownlme4lmomlmtestmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpngpolsplinepolynomprettyunitsprogressproxypurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadxlreformulasrematchrlangrmarkdownrmsrootSolverpartrstatixrstudioapiS7sandwichsassscalesSparseMspatialstablediststringistringrsurvivalsurvminersysTH.datatibbletidyrtidyselecttimeDatetimeSeriestinytextzdburcautf8vctrsviridisLitevroomwithrxfunxml2yamlzoo

Advanced Data Operations

Rendered fromadvanced-data-operations.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-05-24
Started: 2026-04-06

Creating Baseline Characteristics Tables

Rendered frombaseline-table.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-05-24
Started: 2026-04-06

Data Cleaning and Preparation

Rendered fromdata-cleaning.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-05-24
Started: 2026-04-06

Model Evaluation and Comparison

Rendered frommodel-evaluation.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-05-24
Started: 2026-04-06

Regression Analysis and Visualization

Rendered fromregression-analysis.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-05-24
Started: 2026-04-06

Readme and manuals

Help Manual

Help pageTopics
Adding lists element-wiseadd_lists
Check answers of multiple choice questionsanswer_check
Create a baseline table for a dataset.baseline_table
Generate breaks for histogrambreak_at
Calculate C-index for survival datacalc_cindex
Calculate index based on conditionscalculate_index
Check elements that are not numericcheck_nonnum
Performance comparison of classification modelsclassif_model_compare
combine multiple data files into a single data framecombine_files
Combine multi-choice columns into onecombine_multichoice
Get common prefix of a string vectorcommon_prefix
Convert Numeric to Factorcut_by
Data Overview and Quality Checkdata_overview
Detect outliers in a numeric vector.detect_outliers
Show non-numeric elements in a data framedf_view_nonnum
default color palette for 'clinpubr' plotsemp_colors
Count the number of excluded samples at each stepexclusion_count
Extract numbers from string.extract_num
Fill NA values with the last valid valuefill_with_last
Filter predictors for RCSfilter_rcs_predictors
Calculate the first modefirst_mode
Format p-value for publicationformat_pval
Add covariates to a formulaformula_add_covs
Generate a sample of values from a vector and collapse them.get_samples
Get one valid value from vector.get_valid
Get the subset that satisfies the missing rate condition.get_valid_subset
Get variable types for baseline tableget_var_types
Importance plotimportance_plot
Determine duplicate elements including their first occurrence.indicate_duplicates
Calculate interaction p-valueinteraction_p_value
Plot interactionsinteraction_plot
Scan for interactions between variablesinteraction_scan
Keep string segment by regex keyword positionkeep_by_keyword
Mark possible outliers using different methods.iqr_outlier mad_outlier zscore_outlier
Get the maximum missing rate of rows and columns.max_missing_rates
Merge Data Frames by Exact Keys and Value Rangemerge_by_range
Merge Data Frame by String Key Matchingmerge_by_substring
Merging vectors while maintaining ordermerge_ordered_vectors
Safe min and max functions that return NA if all values are NAna_max na_min
Replace NA values with FALSEna2false
Plot the effect of a predictor variablepredictor_effect_plot
QQ plotqq_show
Plot restricted cubic splinercs_plot
Basic results of logistic or Cox regression.regression_basic_results
Obtain regression resultsregression_fit
Forest plot of regression resultsregression_forest
Scan for significant regression predictorsregression_scan
Replacing elements in a vectorreplace_elements
Screen and Join Multi-Table Clinical Data by Expressionscreen_data_list
Split multi-choice data into columnssplit_multichoice
Match string and replace with corresponding valuestr_match_replace
Create subgroup forest plot.subgroup_forest
Get an overview of different subjects in data.subject_view
Test normality of a numeric variabletest_normality
Calculate and plot time-dependent ROC curvestime_roc_plot
Convert numerical or character date to date.to_date
Fast long-to-wide conversion with item selectionto_wide
Standardize units of numeric data.unit_standardize
Generate a table of conflicting units.unit_view
Unmake namesunmake_names
Preliminarily cleaning string vectorschar_initial_cleaning value_initial_cleaning
Generate code from string vectorname2code vec2code