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

# Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies

## Documentation for package ‘kyotil’ version 2024.11-01

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

A B C D E F G H I K L M P Q R S T U V W Y misc

## -- A --

abline.pt.slope | Plotting Functions
abline.pts | Plotting Functions
abline.shade | Plotting Functions
abline.shade.2 | Plotting Functions
add.mtext.label | Plotting Functions
addRoc | ROC and AUC
age_calc | Age Calculation
AR1 | Matrix and Array Functions
array.functions | Matrix and Array Functions
as.binary | Math Functions
auc | AUC

## -- B --

binary | Some Base Functions
binary2 | Some Base Functions
binaryloess | Using loess to Check Functional Form for Logistic Regression
binom.coef | Math Functions
butterfly.plot | Plotting Functions

## -- C --

cbinduneven | Some Base Functions
classification.error | ROC and AUC
coef.auc | AUC
coef.Deming | Fit Deming regression.
coef.geese | Regression Model Functions
coef.tps | Regression Model Functions
computeRoc | ROC and AUC
concatList | Matrix and Array Functions
contain | String Functions
cor.mixed | Stat Functions
cor.mixed.default | Stat Functions
cor.mixed.formula | Stat Functions
cor.mixed.vector | Stat Functions
corplot | Plotting Functions
corplot.default | Plotting Functions
corplot.formula | Plotting Functions
cox.zph.2 | Test the Proportional Hazards Assumption of a Cox Regression (a slightly modified version)

## -- D --

dbern | Random Functions
dcorbern | Random Functions
ddoublexp | Random Functions
dec_to_binary | Misc Functions
Deming | Fit Deming regression.
DMHeatMap | Better Heatmap Function
dmixnorm | Random Functions
dnorm.norm.gamma | Random Functions
DXD | Matrix Functions that May Be Faster than

## -- E --

empty.plot | Plotting Functions
empty2na | Misc Functions
escapeUnderline | String Functions
EXCH | Matrix and Array Functions
expit | Math Functions

## -- F --

f2c | Some Base Functions
fastauc | ROC and AUC
fileStem | String Functions
fill.jagged.array | Matrix and Array Functions
firstIndex | String Functions
formatDouble | Print Functions
formatInt | Print Functions
ftoi | Some Base Functions

## -- G --

get.kfold.splits | Cross Validation Functions
get.sim.res | Read simulation results
get.splits | Cross Validation Functions
getExt | String Functions
getFileStem | String Functions
getFixedEf | Regression Model Functions
getFixedEf.coxph | Regression Model Functions
getFixedEf.Deming | Fit Deming regression.
getFixedEf.gam | Regression Model Functions
getFixedEf.gee | Regression Model Functions
getFixedEf.geese | Regression Model Functions
getFixedEf.glm | Regression Model Functions
getFixedEf.glmerMod | Regression Model Functions
getFixedEf.inla | Regression Model Functions
getFixedEf.lm | Regression Model Functions
getFixedEf.lme | Regression Model Functions
getFixedEf.lmerMod | Regression Model Functions
getFixedEf.logistf | Regression Model Functions
getFixedEf.matrix | Regression Model Functions
getFixedEf.mer | Regression Model Functions
getFixedEf.merMod | Regression Model Functions
getFixedEf.MIresult | Regression Model Functions
getFixedEf.svycoxph | Regression Model Functions
getFixedEf.svyglm | Regression Model Functions
getFixedEf.svy_vglm | Regression Model Functions
getFixedEf.tps | Regression Model Functions
getFixedEf2 | Regression Model Functions
getFormattedMCSummary | Read simulation results
getFormattedSummary | Regression Model Functions
getK | getK
getMfrow | Plotting Functions
getMidPoints | Matrix and Array Functions
getStem | String Functions
getUpperRight | Matrix and Array Functions
getVarComponent | Regression Model Functions
getVarComponent.glmerMod | Regression Model Functions
getVarComponent.hyperpar.inla | Regression Model Functions
getVarComponent.lmerMod | Regression Model Functions
getVarComponent.matrix | Regression Model Functions
getVarComponent.mer | Regression Model Functions
getVarComponent.merMod | Regression Model Functions
get_count_from_xy_coor | Imaging analysis for spatial region

## -- H --

H | Stat Functions
hosmerlem | Testing Functions

## -- I --

info.cor | Stat Functions
INT | Misc Functions
interaction.table | Regression Model Functions
interpolate | Math Functions
iorw | Causal Mediation Analysis of Cowling et al.

## -- K --

kappacor | Stat Functions
keepWarnings | Some Base Functions
kfold.split | Cross Validation Functions
kid | Dataset from Cowling et al.
kyotil | kyotil

## -- L --

l.measure | Stat Functions
last | Matrix and Array Functions
lastIndex | String Functions
logDiffExp | Math Functions
logit | Math Functions
logMeanExp | Math Functions
logSumExp | Math Functions
logSumExpFor2 | Math Functions
lpo.split | Cross Validation Functions

## -- M --

make.latex.coef.table | Print Functions
make.timedep.dataset | Create Dataset for Time-dependent Covariate Proportional Hazard Model Analaysi
math.functions | Math Functions
matrix.array.functions | Matrix and Array Functions
matrix.functions | Matrix and Array Functions
MCsummary | Read simulation results
meanmed | Some Base Functions
mix | Matrix and Array Functions
multi.outer | Some Base Functions
mutual.info | Stat Functions
my.interaction.plot | Plotting Functions
myaggregate | Some Base Functions
myboxplot | Plotting Functions
myboxplot.data.frame | Plotting Functions
myboxplot.formula | Plotting Functions
myboxplot.list | Plotting Functions
mycor | Some Base Functions
mycor.test | Testing Functions
mydev.off | Plotting Functions
myfigure | Plotting Functions
myfisher.test | Testing Functions
myforestplot | Plotting Functions
myhist | Plotting Functions
mylegend | Plotting Functions
mylines | Plotting Functions
mymatplot | Plotting Functions
mypairs | Plotting Functions
mypdf | Plotting Functions
myplot | Plotting Functions
myplot.cox.zph | Vaccine Efficacy Plots
myplot.loess | Plotting Functions
mypng | Plotting Functions
mypostscript | Plotting Functions
myprint | Print Functions
myprint.default | Print Functions
myprint.matrix | Print Functions
myreshapelong | Some Base Functions
myreshapewide | Some Base Functions
mysanitize.numbers | Print Functions
mysanitize.text | Print Functions
mysapply | Some Base Functions
myscale | Some Base Functions
mysystem | Some Base Functions
mytable | Some Base Functions
mytapply | Some Base Functions
mytex | Print Functions
mytex.begin | Print Functions
mytex.end | Print Functions
mytiff | Plotting Functions
mywrite | Print Functions
mywrite.csv | Print Functions

## -- P --

p.adj.perm | Permutation-based Multitesting P Values Adjustment
panel.cor | Plotting Functions
panel.hist | Plotting Functions
panel.nothing | Plotting Functions
pava | Misc Functions
pdoublexp | Random Functions
permn | Math Functions
plotRoc | ROC and AUC
predict.auc | AUC
predict.Deming | Fit Deming regression.
predict.geese | Regression Model Functions
predict.pcc | Misc Functions
predict.tps | Regression Model Functions
prettyprint | Print Functions
print.auc | AUC
print.iorw | Causal Mediation Analysis of Cowling et al.

## -- Q --

qdoublexp | Random Functions
quick.t.test | Testing Functions

## -- R --

ran.kfold.split | Cross Validation Functions
rank.inv.norm | Misc Functions
ratio | AUC
ratio.auc | AUC
ratio.glm | AUC
rbern | Random Functions
rbidoublexp | Random Functions
rbigamma | Random Functions
rbilogistic | Random Functions
rdoublexp | Random Functions
read.sv | Some Base Functions
read.tsv | Some Base Functions
rejective.sampling | Random Functions
remove.prefix | String Functions
rep.data.frame | Matrix and Array Functions
rep.matrix | Matrix and Array Functions
rep.matrix.block | Matrix and Array Functions
residuals.geese | Regression Model Functions
risk.cal | Regression Model Functions
rmixnorm | Random Functions
rnorm.ar | Random Functions
rnorm.norm.gamma | Random Functions
roundup | Print Functions

## -- S --

sample.for.cv | Cross Validation Functions
shift.left | Matrix and Array Functions
shift.right | Matrix and Array Functions
signtest | Testing Functions
sim.dat.tvarying.three | Simulation Functions for Time-dependent Proportional Hazard Model
sim.dat.tvarying.two | Simulation Functions for Time-dependent Proportional Hazard Model
skew | Stat Functions
smoothed.scaled.hist | Plotting Functions
stat.functions | Stat Functions
Stirling2 | Math Functions
string.functions | String Functions
summ | Misc Functions
summary.auc | AUC
summary.Deming | Fit Deming regression.
symprod | Matrix Functions that May Be Faster than

## -- T --

table.cases | Some Base Functions
table.cases.3 | Some Base Functions
table.prop | Some Base Functions
thin.rows | Matrix and Array Functions
ThinRows | Matrix and Array Functions
tr | Matrix and Array Functions
trainauc | AUC
trainauc.auc | AUC
trainauc.glm | AUC
trim | String Functions
tukey.mtest | Testing Functions
tXDX | Matrix Functions that May Be Faster than
txSy | Matrix Functions that May Be Faster than

## -- U --

unix | Some Base Functions

## -- V --

vcov.Deming | Fit Deming regression.
vcov.geese | Regression Model Functions
vcov.logistf | Regression Model Functions
vcov.tps | Regression Model Functions
vector.t.test | Testing Functions
VEplot | Vaccine Efficacy Plots
VEplot.cox.zph | Vaccine Efficacy Plots
VEplot.glm | Vaccine Efficacy Plots

## -- W --

whiskers | Plotting Functions
wtd.hist | Plotting Functions

## -- Y --

yule.y | Stat Functions

## -- misc --

%.% | String Functions
.as.double | Matrix Functions that May Be Faster than