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RVAideMemoire (version 0.9-69-3)

Testing and Plotting Procedures for Biostatistics

Description

Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.

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Install

install.packages('RVAideMemoire')

Monthly Downloads

4,081

Version

0.9-69-3

License

GPL-2

Maintainer

Maxime Herve9

Last Published

May 14th, 2018

Functions in RVAideMemoire (0.9-69-3)

MVA.anova

Type II permutation test for constrained multivariate analyses
OR.multinom

Odds-ratio (multinomial regression)
MVA.plot

Plotting of multivariate analyses
chisq.bin.exp

Expected counts for comparison of response probabilities to given values
cond.multinom

Condition number of the Hessian matrix of a multinomial log-linear model
chisq.bintest

Pearson's Chi-squared test for binary variables
byf.qqnorm

QQ-plot for factor levels
byf.mshapiro

Shapiro-Wilk test for factor levels
PLSDA.VIP

Variable Importance in the Projection (VIP)
chisq.exp

Expected counts for comparison of proportions to given values
cochran.qtest

Cochran's Q test
cramer

Cramer's association coefficient
mqqnorm

Multivariate normality QQ-Plot
cramer.test

Cramer's association coefficient
MVA.scores

Scores of multivariate analyses
mood.medtest

Mood's median test
chisq.multcomp

Pairwise comparisons after a chi-squared goodness-of-fit test
multtest.cor

Univariate correlation test for multiple variables
MVA.scoreplot

Score plot of multivariate analyses
MVA.synt

Synthesis quality of multivariate analyses
MVA.pairplot

Paired plot of multivariate analyses
multtest.gp

Univariate comparison of groups for multiple variables
MVA.test

Significance test based on cross (model) validation
deprecated

Deprecated functions in RVAideMemoire package
pairwise.perm.t.test

Pairwise permutation t tests
pairwise.perm.var.test

Pairwise permutation F tests
RVAideMemoire-package

Testing and Plotting Procedures for Biostatistics
adonis.II

Type II permutation MANOVA using distance matrices
dummy

Dummy responses
MVA.trajplot

Trajectory plot of multivariate analyses
fp.test

Fligner-Policello test
fisher.multcomp

Pairwise comparisons using Fisher's exact test
perm.anova

Permutation Analysis of Variance
byf.shapiro

Shapiro-Wilk test for factor levels
perm.bartlett.test

Permutation Bartlett's test of homogeneity of variances
multinomial.test

Exact multinomial test
reg.ci

Confidence intervals of a simple linear regression
back.emmeans

Back-transformation of EMMeans
bootstrap

Bootstrap
byf.hist

Histogram for factor levels
cor.conf

Equality of a Pearson's linear correlation coefficient to a given value
cov.test

Significance test for the covariance between two datasets
cdf.discrete

Cumulative Distribution Function of a known discrete distribution
byf.mqqnorm

QQ-plot for factor levels
cor.multcomp

Comparison of several Pearson's linear correlation coefficients
chisq.theo.bintest

Pearson's Chi-squared test for comparison of response probabilities to given values
multinomial.theo.multcomp

Pairwise comparisons after an exact multinomial test for given probabilities
pairwise.mood.medtest

Pairwise Mood's median tests
cox.resid

Martingale residuals of a Cox model
scat.cr

"Correlation" of variables to axes in MCA or mix analyses
chisq.theo.multcomp

Pairwise comparisons after a chi-squared test for given probabilities
user.cont

User defined contrasts for EMMeans
dunn.test

Dunn's test
coord.proj

Coordinates of projected points
loc.slp

Slope of a hand-defined line
cor.2comp

Comparison of 2 Pearson's linear correlation coefficients
cv

Coefficient of variation
wald.ptheo.multinom.test

Wald tests for comparison of proportions to theoretical values
dendro.gp

Dendrogram and number of groups to be chosen
logis.fit

Graphical adujstment of a simple binary logistic regression to data
ord.rw

Re-computation of an ordination using given row weights
pairwise.perm.manova

Pairwise permutation MANOVAs
overdisp.glmer

Estimation of overdispersion with glmer models
pcor

(Semi-)Partial correlation
pcor.test

Tests for (semi-)partial association/correlation between paired samples
logis.noise

Creating a nls model for logistic regression from fitted values of a glm model
mod

Mode
perm.cor.test

Permutation Pearson's correlation test
perm.var.test

Permutation F test to compare two variances
pairwise.CDA.test

Pairwise comparisons for CDA
fisher.bintest

Fisher's exact test for binary variables
ind.contrib

Individual contributions in regression
least.rect

Least rectangles linear regression
pairwise.G.test

Pairwise comparisons for proportions using G-tests
perm.t.test

Permutation Student's t-test
plotresid

Simple analysis of model residuals
se

Standard error
seq2

Sequence generation
pairwise.to.groups

Letter summary of similarities and differences
test.multinom

Significance tests of coefficients (multinomial regression)
prop.bin.multcomp

Pairwise comparisons after a test for given probabilities
mshapiro.test

Shapiro-Wilk multivariate normality test
pairwise.var.test

Pairwise F tests
to.dudi

Synthesis quality of multivariate analyses
prop.multcomp

Pairwise comparisons after a test for given proportions
plotsurvivors

Survivor curve
stand

Standardization of a data frame based on another data frame
splitf

Divide into groups respecting relative proportions
pairwise.MVA.test

Pairwise permutation tests based on cross (model) validation
predict.CDA.cv

Predict method for cross-validated CDA submodels
multinomial.multcomp

Pairwise comparisons after an exact multinomial test
prop.multinom

Proportions and standard errors
prop.multinom.test

Wald tests for comparison of proportions
pairwise.factorfit

Pairwise comparisons of groups displayed on a factorial map
spearman.ci

Confidence interval of a Spearman's rank correlation coefficient
predict.MVA.cv

Predict method for cross-validated submodels
predict.coadisc

Predict method for CDA
spearman.cor.multcomp

Comparison of several Spearman's rank correlation coefficients
wilcox.signtest

Wilcoxon sign test
wmean

Weighted arithmetic mean
rating.emmeans

EMMeans for Cumulative Link (Mixed) Models
wilcox.paired.multcomp

Non parametric pairwise comparisons for paired data
wald.ptheo.test

Wald test for comparison of a proportion to a theoretical value
rating.prob

Observed rating frequencies
DIABLO.test

Significance test based on cross-validation
CDA.cv

Cross validation
G.bintest

G-test for binary variables
DIABLO.cv

Cross validation
CDA.test

Significance test for CDA
CvM.test

Two-sample Cramer-von Mises test
G.theo.multcomp

Pairwise comparisons after a G-test for given probabilities
G.test

G-test
G.multcomp

Pairwise comparisons after a G-test
MVA.biplot

Biplot of multivariate analyses
Anova.clm

Anova Tables for Cumulative Link (Mixed) Models
MVA.cor

Correlations of multivariate analyses
GPA.test

Significance test for GPA
MVA.cv

Cross validation
MVA.corplot

Correlation circle of multivariate analyses
MVA.loadplot

Loading plot of multivariate analyses
MVA.cmv

Cross model validation
MVA.load

Loadings of multivariate analyses