Package: arsenal 3.6.4.0000
arsenal: An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of one or more categorical variables; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); freqlist(), a powerful frequency table across many categorical variables; comparedf(), a function for comparing data.frames; and write2(), a function to output tables to a document.
Authors:
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arsenal.pdf |arsenal.html✨
arsenal/json (API)
NEWS
# Install 'arsenal' in R: |
install.packages('arsenal', repos = c('https://mayoverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mayoverse/arsenal/issues
- mockstudy - Mock study data for examples
baseline-characteristicsdescriptive-statisticsmodelingpaired-comparisonsreportingstatisticstableone
Last updated 3 months agofrom:73f1899edd. Checks:OK: 1 NOTE: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 13 2024 |
R-4.5-win | NOTE | Nov 13 2024 |
R-4.5-linux | NOTE | Nov 13 2024 |
R-4.4-win | NOTE | Nov 13 2024 |
R-4.4-mac | NOTE | Nov 13 2024 |
R-4.3-win | NOTE | Nov 13 2024 |
R-4.3-mac | NOTE | Nov 13 2024 |
Exports:%nin%allNAas.selectallas.tbstatas.tbstat_multirowbinomCIclogcode.chunkcomparedfcomparedf.controlcountcellpctcountNcountpctcountrowpctDate.mdydiffsformulizefreq.controlfreqlistgmeangmeanCIgmeansdgsdhas_strataincludeNAiqris.Dateis.freqlistis.modelsumis.selectallis.summary.freqlistis.summary.modelsumis.summary.tablebyis.tablebyis.yamlkeep.labelslabels<-loosen.labelsmdy.DatemeanCImeanpmsdmeanpmsemeansdmeansemedianmadmedianq1q3medianrangemedSurvmedTimemodelsummodelsum.controlmodpval.tablebymuck_up_mockstudyNn.diff.obsn.diffsna.modelsumna.pairedna.tablebynegbinNeventsNeventsSurvNmissNmiss2NmisspctNmisspct2NpctNriskNriskSurvNrowpctNsigntestordinalpadjustpairedpaired.controlpctq1q3relriskreplace2rowbinomCIrowpctselectallset_attrset_labelssmart.splitsurvivaltablebytableby.controltbfmtteststol.char.bothtol.char.casetol.char.nonetol.char.trimtol.date.absolutetol.factor.labelstol.factor.levelstol.factor.nonetol.logical.nonetol.NAtol.num.absolutetol.num.pcttol.num.percenttol.other.noneverbatimwrite2write2htmlwrite2pdfwrite2wordyaml
A Few Notes on Labels
Rendered fromlabels.Rmd
usingknitr::rmarkdown
on Nov 13 2024.Last update: 2019-12-27
Started: 2017-08-02
The comparedf function
Rendered fromcomparedf.Rmd
usingknitr::rmarkdown
on Nov 13 2024.Last update: 2020-01-14
Started: 2019-03-20
The freqlist function
Rendered fromfreqlist.Rmd
usingknitr::rmarkdown
on Nov 13 2024.Last update: 2020-02-28
Started: 2016-12-13
The modelsum function
Rendered frommodelsum.Rmd
usingknitr::rmarkdown
on Nov 13 2024.Last update: 2021-05-19
Started: 2016-12-13
The paired function
Rendered frompaired.Rmd
usingknitr::rmarkdown
on Nov 13 2024.Last update: 2019-12-27
Started: 2018-07-18
The tableby function
Rendered fromtableby.Rmd
usingknitr::rmarkdown
on Nov 13 2024.Last update: 2024-05-15
Started: 2016-12-13
The write2 function
Rendered fromwrite2.Rmd
usingknitr::rmarkdown
on Nov 13 2024.Last update: 2020-10-14
Started: 2017-01-18
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Not in | %nin% nin |
An Arsenal of 'R' Functions for Large-Scale Statistical Summaries | arsenal |
'arsenal' tables with common structure | arsenal_table has_strata labels.arsenal_table labels<-.arsenal_table merge.arsenal_table merge.freqlist print.arsenal_table print.summary.arsenal_table [.arsenal_table [.tableby |
Defunct functions in 'arsenal' | arsenal-defunct |
Deprecated functions in 'arsenal' | arsenal-deprecated |
as.data.frame.freqlist | as.data.frame.freqlist |
as.data.frame.modelsum | as.data.frame.modelsum |
as.data.frame.tableby | as.data.frame.tableby |
Compare two data.frames and report differences | comparedf print.comparedf |
Control settings for 'comparedf' function | comparedf.control |
'comparedf' tolerances | comparedf.tolerances tol.char.both tol.char.case tol.char.none tol.char.trim tol.date.absolute tol.factor.labels tol.factor.levels tol.factor.none tol.logical.none tol.NA tol.num.absolute tol.num.pct tol.num.percent tol.other.none |
Extract differences | diffs diffs.comparedf diffs.summary.comparedf n.diff.obs n.diff.obs.comparedf n.diff.obs.summary.comparedf n.diffs n.diffs.comparedf n.diffs.summary.comparedf |
formulize | formulize |
Control settings for 'freqlist' function | freq.control |
freqlist | freqlist freqlist.formula freqlist.table |
Helper functions for freqlist | freqlist.internal head.summary.freqlist is.freqlist is.summary.freqlist sort.freqlist tail.summary.freqlist |
Internal Functions | internal.functions replace2 smart.split |
Keep Labels | keep.labels keep.labels.data.frame keep.labels.default loosen.labels loosen.labels.data.frame loosen.labels.default [.keep_labels [<-.keep_labels |
Labels | labels labels.data.frame labels.keep_labels labels<- labels<-.data.frame labels<-.default labels<-.keep_labels set_attr set_labels |
Convert numeric dates to Date object, and vice versa | Date.mdy is.Date mdy.Date |
Mock study data for examples | mockstudy muck_up_mockstudy |
Fit models over each of a set of independent variables with a response variable | modelsum |
Control settings for 'modelsum' function | modelsum.control |
Family functions for modelsum | clog modelsum.family negbin ordinal relrisk survival |
Helper functions for modelsum | is.modelsum is.summary.modelsum modelsum.internal na.modelsum |
Some functions to handle NAs | allNA includeNA includeNA.default includeNA.factor NA.operations |
Adjust P-values for Multiple Comparisons | padjust padjust.default padjust.summary.tableby padjust.tableby |
Summary Statistics of a Set of Independent Variables Paired Across Two Timepoints | paired |
Control settings for 'paired' function | paired.control |
Helper functions for paired | na.paired paired.internal |
Make a column for "select all" input | as.matrix.selectall as.selectall is.na.selectall is.selectall selectall [.selectall |
The summary method for a 'comparedf' object | print.summary.comparedf summary.comparedf |
summary.freqlist | as.data.frame.summary.freqlist summary.freqlist |
Summarize a 'modelsum' object. | as.data.frame.summary.modelsum summary.modelsum |
The summary method for a 'tableby' object | as.data.frame.summary.tableby summary.tableby |
Summary Statistics of a Set of Independent Variables by a Categorical Variable | tableby |
Control settings for 'tableby' function | tableby.control |
Helper functions for tableby | head.tableby is.summary.tableby is.tableby modpval.tableby na.tableby Ops.tableby sort.tableby tableby.internal tail.tableby tests tests.tableby xtfrm.tableby |
tableby Summary Statistics Functions | arsenal_max arsenal_mean arsenal_median arsenal_min arsenal_range arsenal_sd arsenal_sum arsenal_var binomCI count countcellpct countN countpct countrowpct gmean gmeanCI gmeansd gsd iqr meanCI meanpmsd meanpmse meansd meanse medianmad medianq1q3 medianrange medSurv medTime N Nevents NeventsSurv Nmiss Nmiss2 Nmisspct Nmisspct2 Npct Nrisk NriskSurv Nrowpct Nsigntest pct q1q3 rowbinomCI rowpct tableby.stats |
Internal 'tableby' functions | as.tbstat as.tbstat_multirow tableby.stats.internal tbfmt |
write2 | write2 write2.arsenal_table write2.character write2.code.chunk write2.comparedf write2.default write2.knitr_kable write2.list write2.summary.arsenal_table write2.summary.comparedf write2.verbatim write2.xtable write2.yaml |
Helper functions for 'write2' | code.chunk verbatim write2.internal |
write2word, write2html, write2pdf | write2html write2pdf write2specific write2word |
Include a YAML header in 'write2' | c.yaml is.yaml print.yaml yaml |