Miscellaneous Functions from M. Kohl

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Documentation for package ‘MKmisc’ version 1.9

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

MKmisc-package	Miscellaneous Functions from M. Kohl.
AUC	Compute AUC
AUC.test	AUC-Test
binomCI	Confidence Intervals for Binomial Proportions
corDist	Correlation Distance Matrix Computation
corPlot	Plot of similarity matrix based on correlation
CV	Compute CV
cvCI	Confidence Intervals for Coefficient of Variation
fiveNS	Five-Number Summaries
glog	Compute Generalized Logarithm
glog10	Compute Generalized Logarithm
glog10_trans	New Transformations for Use with ggplot2 Package
glog2	Compute Generalized Logarithm
glog2_trans	New Transformations for Use with ggplot2 Package
glog_trans	New Transformations for Use with ggplot2 Package
heatmapCol	Generate colors for heatmaps
HLgof.test	Hosmer-Lemeshow goodness of fit tests.
hsu.t.test	Hsu Two-Sample t-Test
hsu.t.test.default	Hsu Two-Sample t-Test
hsu.t.test.formula	Hsu Two-Sample t-Test
imputeSD	Impute Standard Deviations for Changes from Baseline
inv.glog	Compute Generalized Logarithm
inv.glog10	Compute Generalized Logarithm
inv.glog2	Compute Generalized Logarithm
IQrange	The Interquartile Range
iqrCV	Compute CV
iqrSNR	Compute SNR
madCI	Confidence Intervals for Quantiles
madMatrix	Compute MAD between colums of a matrix or data.frame
madPlot	Plot of similarity matrix based on MAD
meanAD	The Mean Absolute Deviation
medCV	Compute CV
medianCI	Confidence Intervals for Quantiles
medSNR	Compute SNR
melt.long	Transform data.frame to Long Form
mi.t.test	Multiple Imputation Student's t-Test
mi.t.test.default	Multiple Imputation Student's t-Test
MKmisc	Miscellaneous Functions from M. Kohl.
mod.oneway.test	Moderated 1-Way ANOVA
mod.t.test	Moderated t-Test
neglog10_trans	New Transformations for Use with ggplot2 Package
neglog2_trans	New Transformations for Use with ggplot2 Package
neglog_breaks	New Transformations for Use with ggplot2 Package
neglog_trans	New Transformations for Use with ggplot2 Package
normCI	Confidence Intervals for Mean and Standard Deviation
normDiffCI	Confidence Intervals for Difference of Means
oneWayAnova	A function for Analysis of Variance
optCutoff	Compute the Optimal Cutoff for Binary Classification
or2rr	Transform OR to RR
pairwise.auc	Compute pairwise AUCs
pairwise.fc	Compute pairwise fold changes
pairwise.fun	Compute pairwise values for a given function
pairwise.logfc	Compute pairwise log-fold changes
pairwise.mod.t.test	Pairwise Moderated t-Tests
perfMeasures	Compute Performance Measures and Scores for Binary Classification
perfScores	Compute Performance Measures and Scores for Binary Classification
power.diagnostic.test	Power calculations for a diagnostic test
power.hsu.t.test	Power calculations for two sample Hsu t test
power.nb.test	Power calculation for comparing two negative binomial rates
power.welch.t.test	Power calculations for two sample Welch t test
predValues	Compute PPV and NPV.
print.confint	Print Method for Confidence Intervals
qboxplot	Box Plots
qboxplot.default	Box Plots
qboxplot.formula	Box Plots
qbxp.stats	Box Plot Statistics
quantileCI	Confidence Intervals for Quantiles
repMeans	Compute mean of replicated spots
risks	Compute RR, OR, etc.
rrCI	Compute Approximate Confidence Interval for RR.
scale_x_glog	New Transformations for Use with ggplot2 Package
scale_x_glog10	New Transformations for Use with ggplot2 Package
scale_x_glog2	New Transformations for Use with ggplot2 Package
scale_x_neglog	New Transformations for Use with ggplot2 Package
scale_x_neglog10	New Transformations for Use with ggplot2 Package
scale_x_neglog2	New Transformations for Use with ggplot2 Package
scale_y_glog	New Transformations for Use with ggplot2 Package
scale_y_glog10	New Transformations for Use with ggplot2 Package
scale_y_glog2	New Transformations for Use with ggplot2 Package
scale_y_neglog	New Transformations for Use with ggplot2 Package
scale_y_neglog10	New Transformations for Use with ggplot2 Package
scale_y_neglog2	New Transformations for Use with ggplot2 Package
simCorVars	Simulate correlated variables.
simPlot	Plot of a similarity matrix.
sIQR	The Interquartile Range
SNR	Compute SNR
ssize.pcc	Sample Size Planning for Developing Classifiers Using High Dimensional Data
stringDist	Function to compute distances between strings
stringSim	Function to compute similarity scores between strings
thyroid	Plot TSH, fT3 and fT4 with respect to reference range.
traceBack	Function to trace back
twoWayAnova	A function for Analysis of Variance