Package: kyotil 2024.7-31
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:
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kyotil.pdf |kyotil.html✨
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
- kid - Dataset from Cowling et al.
Last updated 10 days agofrom:8ab7a6c64c. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 10 2024 |
| R-4.5-win-x86_64 | WARNING | Sep 10 2024 |
| R-4.5-linux-x86_64 | WARNING | Sep 10 2024 |
| R-4.4-win-x86_64 | WARNING | Sep 10 2024 |
| R-4.4-mac-x86_64 | WARNING | Sep 10 2024 |
| R-4.4-mac-aarch64 | WARNING | Sep 10 2024 |
| R-4.3-win-x86_64 | WARNING | Sep 10 2024 |
| R-4.3-mac-x86_64 | WARNING | Sep 10 2024 |
| R-4.3-mac-aarch64 | WARNING | Sep 10 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:
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 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 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 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 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 |
