Package: kyotil 2025.12-12

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]

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

# Install 'kyotil' in R:

install.packages('kyotil', repos = c('https://youyifong.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/youyifong/kyotil/issues

Uses libs:

openblas– Optimized BLAS

Datasets:

kid - Dataset from Cowling et al.

On CRAN:

openblas

7.74 score 9 packages 239 scripts 1.2k downloads 1 mentions 249 exports 0 dependencies

Last updated from:18a33802b7. Checks:11 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	ERROR	172
linux-devel-x86_64	ERROR	172
source / vignettes	OK	218
linux-release-arm64	ERROR	174
linux-release-x86_64	ERROR	155
macos-release-arm64	ERROR	133
macos-release-x86_64	ERROR	224
macos-oldrel-arm64	ERROR	119
macos-oldrel-x86_64	ERROR	274
windows-devel	ERROR	117
windows-release	ERROR	97
windows-oldrel	ERROR	96
wasm-release	OK	161

Exports:.as.double %.%abline.pt.slope abline.pts abline.shade abline.shade.2 add.mtext.label add.mtext.label.2 addRoc age_calc AR1 as.binary binary binary2 binaryloess binom.coef butterfly.plot cbinduneven classification.error coef.auc coef.geese coef.tps computeRoc concatList contain cor.mixed cor.mixed.default cor.mixed.formula cor.mixed.vector corplot corplot.default corplot.formula cox.zph.2 dbern dcorbern ddoublexp dec_to_binary Deming DMHeatMap dmixnorm dnorm.norm.gamma DXD empty.plot empty2na escape escape_latex escapeUnderline EXCH expit f2c fastauc fileStem fill.jagged.array firstIndex formatDouble formatInt formatPvalues ftoi get_count_from_xy_coor get.kfold.splits get.sim.res get.splits getExt getFileStem getFixedEf getFixedEf.coxph getFixedEf.gam getFixedEf.gee getFixedEf.geese getFixedEf.glm getFixedEf.glmerMod getFixedEf.inla getFixedEf.lm getFixedEf.lme getFixedEf.logistf getFixedEf.matrix getFixedEf.mer getFixedEf.merMod getFixedEf.MIresult getFixedEf.svy_vglm getFixedEf.svycoxph getFixedEf.svyglm getFixedEf.tps getFormattedMCSummary getFormattedSummary getK getMfrow getMidPoints getStem getUpperRight getVarComponent getVarComponent.glmerMod getVarComponent.hyperpar.inla getVarComponent.matrix getVarComponent.mer getVarComponent.merMod H hosmerlem info.cor INT interaction.table interpolate iorw keepWarnings kfold.split l.measure last lastIndex len logDiffExp logit logMeanExp logSumExp logSumExpFor2 lpo.split make.latex.coef.table make.timedep.dataset MCsummary meanmed metrics_from_preds mix multi.outer mutual.info my.interaction.plot myaggregate myboxplot myboxplot.data.frame myboxplot.formula myboxplot.list mycor mycor.test mydev.off myfigure myfisher.test myforestplot myhist mykable mylast mylegend mylines mymatplot mypairs mypdf myplot myplot.cox.zph myplot.loess mypng mypostscript myprint myprint.default myprint.matrix myreshapelong myreshapewide mysanitize.numbers mysanitize.text mysapply myscale mysystem mytable mytapply mytex mytex.begin mytex.end mytiff mywrite mywrite.csv p.adj.perm panel.cor.pearson panel.cor.spearman panel.hist panel.nothing pava pdoublexp permn plotRoc predict.auc predict.geese predict.pcc predict.tps prettyprint print.auc print.iorw qdoublexp quick.t.test quiet_library ran.kfold.split rank.inv.norm ratio ratio.auc ratio.glm rbern rbidoublexp rbigamma rbilogistic rdoublexp read.sv read.tsv reduce_margin reduce_whitespace rejective.sampling remove.prefix rep.data.frame rep.matrix rep.matrix.block residuals.geese risk.cal rmixnorm rnorm.ar rnorm.norm.gamma roundup sample.for.cv scaled.hist shift.left shift.right shrink_margin shrink_whitespace signtest sim.dat.tvarying.three sim.dat.tvarying.two skew smoothed.scaled.hist ssase Stirling2 summ summary.auc symprod table.cases table.cases.3 table.prop thin.rows ThinRows tr trainauc trainauc.auc trainauc.glm tukey.mtest tXDX txSy unix vcov.geese vcov.logistf vcov.tps vector.t.test VEplot VEplot.cox.zph VEplot.glm whiskers wtd.cor wtd.hist

Dependencies:

Fitting Threshold Regression Models Using chngpt

p.adj.perm: resampling-based approach to assessing statistical significance (Sue Li)

Rendered fromkyotil-vignette.pdf.asisusingR.rsp::asis

Last update: 2021-02-04
Started: 2021-02-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Age Calculation	age_calc
AUC	auc coef.auc predict.auc print.auc ratio ratio.auc ratio.glm summary.auc trainauc trainauc.auc trainauc.glm
Some Base Functions	binary 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 Regression	binaryloess
Test the Proportional Hazards Assumption of a Cox Regression (a slightly modified version)	cox.zph.2
Cross Validation Functions	get.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 Function	DMHeatMap
Imaging analysis for spatial region	get_count_from_xy_coor
Read simulation results	get.sim.res getFormattedMCSummary MCsummary
getK	getK
Causal Mediation Analysis of Cowling et al.	iorw print.iorw
Dataset from Cowling et al.	kid
kyotil	kyotil
Create Dataset for Time-dependent Covariate Proportional Hazard Model Analaysi	make.timedep.dataset
Math Functions	as.binary binom.coef expit interpolate logDiffExp logit logMeanExp logSumExp logSumExpFor2 math.functions permn Stirling2
Matrix and Array Functions	AR1 array.functions concatList EXCH fill.jagged.array getMidPoints getUpperRight matrix.array.functions matrix.functions mix mylast 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 Functions	dec_to_binary empty2na INT pava predict.pcc rank.inv.norm summ
Permutation-based Multitesting P Values Adjustment	p.adj.perm
Plotting Functions	abline.pt.slope abline.pts abline.shade abline.shade.2 add.mtext.label add.mtext.label.2 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 reduce_margin reduce_whitespace shrink_margin shrink_whitespace smoothed.scaled.hist whiskers wtd.hist
Print Functions	formatDouble 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 Functions	dbern dcorbern ddoublexp dmixnorm dnorm.norm.gamma pdoublexp qdoublexp rbern rbidoublexp rbigamma rbilogistic rdoublexp rejective.sampling rmixnorm rnorm.ar rnorm.norm.gamma
Regression Model Functions	coef.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 AUC	addRoc classification.error computeRoc fastauc plotRoc
Simulation Functions for Time-dependent Proportional Hazard Model	sim.dat.tvarying.three sim.dat.tvarying.two
Stat Functions	cor.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 Functions	hosmerlem mycor.test myfisher.test quick.t.test signtest tukey.mtest vector.t.test
Vaccine Efficacy Plots	myplot.cox.zph VEplot VEplot.cox.zph VEplot.glm