Package: kyotil 2024.11-01

Youyi Fong

kyotil: Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies

Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.

Authors:Youyi Fong [cre], Krisztian Sebestyen [aut], Han Sunwoo [aut], Jason Becker [ctb], Bendix Carstensen [ctb], Daryl Morris [ctb], Josh Pasek [ctb], Dennis Chao [ctb], Andri Signorell [ctb], Sue Li [ctb], Jonathan Bartlett [ctb], Christophe Dutang [ctb]

kyotil_2024.11-01.tar.gz
kyotil_2024.11-01.tar.gz(r-4.5-noble)kyotil_2024.11-01.tar.gz(r-4.4-noble)
kyotil_2024.11-01.tgz(r-4.4-emscripten)kyotil_2024.11-01.tgz(r-4.3-emscripten)
kyotil.pdf |kyotil.html
kyotil/json (API)

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

Peer review:

Uses libs:
  • openblas– Optimized BLAS
Datasets:
  • kid - Dataset from Cowling et al.

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

6.29 score 8 packages 230 scripts 1.4k downloads 1 mentions 233 exports 0 dependencies

Last updated 29 days agofrom:d7bdce6ff0. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-linux-x86_64OKNov 04 2024

Exports:.as.double%.%abline.pt.slopeabline.ptsabline.shadeabline.shade.2add.mtext.labeladdRocage_calcAR1as.binarybinarybinary2binaryloessbinom.coefbutterfly.plotcbindunevenclassification.errorcoef.auccoef.geesecoef.tpscomputeRocconcatListcontaincor.mixedcor.mixed.defaultcor.mixed.formulacor.mixed.vectorcorplotcorplot.defaultcorplot.formulacox.zph.2dberndcorbernddoublexpdec_to_binaryDemingDMHeatMapdmixnormdnorm.norm.gammaDXDempty.plotempty2naescapeUnderlineEXCHexpitf2cfastaucfileStemfill.jagged.arrayfirstIndexformatDoubleformatIntftoiget_count_from_xy_coorget.kfold.splitsget.sim.resget.splitsgetExtgetFileStemgetFixedEfgetFixedEf.coxphgetFixedEf.gamgetFixedEf.geegetFixedEf.geesegetFixedEf.glmgetFixedEf.glmerModgetFixedEf.inlagetFixedEf.lmgetFixedEf.lmegetFixedEf.logistfgetFixedEf.matrixgetFixedEf.mergetFixedEf.merModgetFixedEf.MIresultgetFixedEf.svy_vglmgetFixedEf.svycoxphgetFixedEf.svyglmgetFixedEf.tpsgetFormattedMCSummarygetFormattedSummarygetKgetMfrowgetMidPointsgetStemgetUpperRightgetVarComponentgetVarComponent.glmerModgetVarComponent.hyperpar.inlagetVarComponent.matrixgetVarComponent.mergetVarComponent.merModHhosmerleminfo.corINTinteraction.tableinterpolateiorwkeepWarningskfold.splitl.measurelastlastIndexlogDiffExplogitlogMeanExplogSumExplogSumExpFor2lpo.splitmake.latex.coef.tablemake.timedep.datasetMCsummarymeanmedmixmulti.outermutual.infomy.interaction.plotmyaggregatemyboxplotmyboxplot.data.framemyboxplot.formulamyboxplot.listmycormycor.testmydev.offmyfiguremyfisher.testmyforestplotmyhistmylegendmylinesmymatplotmypairsmypdfmyplotmyplot.cox.zphmyplot.loessmypngmypostscriptmyprintmyprint.defaultmyprint.matrixmyreshapelongmyreshapewidemysanitize.numbersmysanitize.textmysapplymyscalemysystemmytablemytapplymytexmytex.beginmytex.endmytiffmywritemywrite.csvp.adj.permpanel.corpanel.histpanel.nothingpavapdoublexppermnplotRocpredict.aucpredict.geesepredict.pccpredict.tpsprettyprintprint.aucprint.iorwqdoublexpquick.t.testran.kfold.splitrank.inv.normratioratio.aucratio.glmrbernrbidoublexprbigammarbilogisticrdoublexpread.svread.tsvrejective.samplingremove.prefixrep.data.framerep.matrixrep.matrix.blockresiduals.geeserisk.calrmixnormrnorm.arrnorm.norm.gammaroundupsample.for.cvshift.leftshift.rightsigntestsim.dat.tvarying.threesim.dat.tvarying.twoskewsmoothed.scaled.histStirling2summsummary.aucsymprodtable.casestable.cases.3table.propthin.rowsThinRowstrtrainauctrainauc.auctrainauc.glmtrimtukey.mtesttXDXtxSyunixvcov.geesevcov.logistfvcov.tpsvector.t.testVEplotVEplot.cox.zphVEplot.glmwhiskerswtd.hist

Dependencies:

Fitting Threshold Regression Models Using chngpt

Rendered fromkyotil-vignette.pdf.asisusingR.rsp::asison Nov 04 2024.

Last update: 2020-08-26
Started: 2020-08-26

Readme and manuals

Help Manual

Help pageTopics
Age Calculationage_calc
AUCauc coef.auc predict.auc print.auc ratio ratio.auc ratio.glm summary.auc trainauc trainauc.auc trainauc.glm
Some Base Functionsbinary binary2 cbinduneven f2c ftoi keepWarnings meanmed multi.outer myaggregate mycor myreshapelong myreshapewide mysapply myscale mysystem mytable mytapply read.sv read.tsv table.cases table.cases.3 table.prop unix
Using loess to Check Functional Form for Logistic Regressionbinaryloess
Test the Proportional Hazards Assumption of a Cox Regression (a slightly modified version)cox.zph.2
Cross Validation Functionsget.kfold.splits get.splits kfold.split lpo.split ran.kfold.split sample.for.cv
Fit Deming regression.coef.Deming Deming getFixedEf.Deming predict.Deming summary.Deming vcov.Deming
Better Heatmap FunctionDMHeatMap
Imaging analysis for spatial regionget_count_from_xy_coor
Read simulation resultsget.sim.res getFormattedMCSummary MCsummary
getKgetK
Causal Mediation Analysis of Cowling et al.iorw print.iorw
Dataset from Cowling et al.kid
kyotilkyotil
Create Dataset for Time-dependent Covariate Proportional Hazard Model Analaysimake.timedep.dataset
Math Functionsas.binary binom.coef expit interpolate logDiffExp logit logMeanExp logSumExp logSumExpFor2 math.functions permn Stirling2
Matrix and Array FunctionsAR1 array.functions concatList EXCH fill.jagged.array getMidPoints getUpperRight last matrix.array.functions matrix.functions mix rep.data.frame rep.matrix rep.matrix.block shift.left shift.right thin.rows ThinRows tr
Matrix Functions that May Be Faster than.as.double DXD symprod tXDX txSy
Misc Functionsdec_to_binary empty2na INT pava predict.pcc rank.inv.norm summ
Permutation-based Multitesting P Values Adjustmentp.adj.perm
Plotting Functionsabline.pt.slope abline.pts abline.shade abline.shade.2 add.mtext.label butterfly.plot corplot corplot.default corplot.formula empty.plot getMfrow my.interaction.plot myboxplot myboxplot.data.frame myboxplot.formula myboxplot.list mydev.off myfigure myforestplot myhist mylegend mylines mymatplot mypairs mypdf myplot myplot.loess mypng mypostscript mytiff panel.cor panel.hist panel.nothing smoothed.scaled.hist whiskers wtd.hist
Print FunctionsformatDouble formatInt make.latex.coef.table myprint myprint.default myprint.matrix mysanitize.numbers mysanitize.text mytex mytex.begin mytex.end mywrite mywrite.csv prettyprint roundup
Random Functionsdbern dcorbern ddoublexp dmixnorm dnorm.norm.gamma pdoublexp qdoublexp rbern rbidoublexp rbigamma rbilogistic rdoublexp rejective.sampling rmixnorm rnorm.ar rnorm.norm.gamma
Regression Model Functionscoef.geese coef.tps getFixedEf getFixedEf.coxph getFixedEf.gam getFixedEf.gee getFixedEf.geese getFixedEf.glm getFixedEf.glmerMod getFixedEf.inla getFixedEf.lm getFixedEf.lme getFixedEf.lmerMod getFixedEf.logistf getFixedEf.matrix getFixedEf.mer getFixedEf.merMod getFixedEf.MIresult getFixedEf.svycoxph getFixedEf.svyglm getFixedEf.svy_vglm getFixedEf.tps getFixedEf2 getFormattedSummary getVarComponent getVarComponent.glmerMod getVarComponent.hyperpar.inla getVarComponent.lmerMod getVarComponent.matrix getVarComponent.mer getVarComponent.merMod interaction.table predict.geese predict.tps residuals.geese risk.cal vcov.geese vcov.logistf vcov.tps
ROC and AUCaddRoc classification.error computeRoc fastauc plotRoc
Simulation Functions for Time-dependent Proportional Hazard Modelsim.dat.tvarying.three sim.dat.tvarying.two
Stat Functionscor.mixed cor.mixed.default cor.mixed.formula cor.mixed.vector H info.cor kappacor l.measure mutual.info skew stat.functions yule.y
String Functions%.% contain escapeUnderline fileStem firstIndex getExt getFileStem getStem lastIndex remove.prefix string.functions trim
Testing Functionshosmerlem mycor.test myfisher.test quick.t.test signtest tukey.mtest vector.t.test
Vaccine Efficacy Plotsmyplot.cox.zph VEplot VEplot.cox.zph VEplot.glm