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RVAideMemoire (version 0.9-81)

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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Version

Install

install.packages('RVAideMemoire')

Monthly Downloads

4,081

Version

0.9-81

License

GPL-2

Maintainer

Maxime Herve9

Last Published

December 14th, 2021

Functions in RVAideMemoire (0.9-81)

G.theo.multcomp

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

G-test for binary variables
Anova.clm

Anova Tables for Cumulative Link (Mixed) Models
CDA.cv

Cross validation
GPA.test

Significance test for GPA
DIABLO.cv

Cross validation
CDA.test

Significance test for CDA
MVA.cmv

Cross model validation
MVA.corplot

Correlation circle of multivariate analyses
MVA.cor

Correlations of multivariate analyses
MVA.test

Significance test based on cross (model) validation
MVA.loadplot

Loading plot of multivariate analyses
MVA.cv

Cross validation
MVA.load

Loadings of multivariate analyses
MVA.synt

Synthesis quality of multivariate analyses
PLSDA.VIP

Variable Importance in the Projection (VIP)
MVA.pairplot

Paired plot of multivariate analyses
MVA.anova

Type II permutation test for constrained multivariate analyses
MVA.biplot

Biplot of multivariate analyses
chisq.exp

Expected counts for comparison of proportions to given values
cor.conf

Equality of a Pearson's linear correlation coefficient to a given value
fisher.multcomp

Pairwise comparisons using Fisher's exact test
chisq.bintest

Pearson's Chi-squared test for binary variables
cor.2comp

Comparison of 2 Pearson's linear correlation coefficients
fisher.bintest

Fisher's exact test for binary variables
MVA.scoreplot

Score plot of multivariate analyses
MVA.scores

Scores of multivariate analyses
pairwise.perm.manova

Pairwise permutation MANOVAs
MVA.plot

Plotting of multivariate analyses
chisq.theo.multcomp

Pairwise comparisons after a chi-squared test for given probabilities
dendro.gp

Dendrogram and number of groups to be chosen
byf.qqnorm

QQ-plot for factor levels
RVAideMemoire-package

Testing and Plotting Procedures for Biostatistics
byf.shapiro

Shapiro-Wilk test for factor levels
cochran.qtest

Cochran's Q test
pairwise.perm.t.test

Pairwise permutation t tests
predict.MVA.cv

Predict method for cross-validated submodels
predict.coadisc

Predict method for CDA
cond.multinom

Condition number of the Hessian matrix of a multinomial log-linear model
scat.cr

"Correlation" of variables to axes in MCA or mix analyses
MVA.trajplot

Trajectory plot of multivariate analyses
wald.ptheo.multinom.test

Wald tests for comparison of proportions to theoretical values
se

Standard error
wald.ptheo.test

Wald test for comparison of a proportion to a theoretical value
coord.proj

Coordinates of projected points
adonis.II

Type II permutation MANOVA using distance matrices
deprecated

Deprecated functions in RVAideMemoire package
logis.fit

Graphical adujstment of a simple binary logistic regression to data
logis.noise

Creating a nls model for logistic regression from fitted values of a glm model
fp.test

Fligner-Policello test
byf.hist

Histogram for factor levels
bootstrap

Bootstrap
chisq.multcomp

Pairwise comparisons after a chi-squared goodness-of-fit test
ind.contrib

Individual contributions in regression
chisq.theo.bintest

Pearson's Chi-squared test for comparison of response probabilities to given values
pcor

(Semi-)Partial correlation
pcor.test

Tests for (semi-)partial association/correlation between paired samples
pairwise.CDA.test

Pairwise comparisons for CDA
p.beta

Rescaling of a [0,1] variable into the (0,1) interval (and vice-versa)
overdisp.glmer

ord.rw

Re-computation of an ordination using given row weights
back.emmeans

Back-transformation of EMMeans
byf.mqqnorm

QQ-plot for factor levels
OR.multinom

Odds-ratio (multinomial regression)
byf.mshapiro

Shapiro-Wilk test for factor levels
cv

Coefficient of variation
mod

Mode
multinomial.theo.multcomp

Pairwise comparisons after an exact multinomial test for given probabilities
cramer.test

Cramer's association coefficient
mood.medtest

Mood's median test
perm.anova

Permutation Analysis of Variance
perm.bartlett.test

Permutation Bartlett's test of homogeneity of variances
prop.multinom

Proportions and standard errors
plotsurvivors

Survivor curve
predict.CDA.cv

Predict method for cross-validated CDA submodels
splitf

Divide into groups respecting relative proportions
reg.ci

Confidence intervals of a simple linear regression
wilcox.signtest

Wilcoxon sign test
rating.prob

Observed rating frequencies
wilcox.paired.multcomp

Non parametric pairwise comparisons for paired data
spearman.cor.multcomp

Comparison of several Spearman's rank correlation coefficients
prop.multinom.test

Wald tests for comparison of proportions
cdf.discrete

Cumulative Distribution Function of a known discrete distribution
pairwise.factorfit

Pairwise comparisons of groups displayed on a factorial map
multtest.cor

Univariate correlation test for multiple variables
stand

Standardization of a data frame based on another data frame
wmean

Weighted arithmetic mean
test.multinom

Significance tests of coefficients (multinomial regression)
dummy

Dummy responses
chisq.bin.exp

Expected counts for comparison of response probabilities to given values
loc.slp

Slope of a hand-defined line
elogis

Empirical logistic transformation
multtest.gp

Univariate comparison of groups for multiple variables
pairwise.perm.var.test

Pairwise permutation F tests
least.rect

Least rectangles linear regression
multtest.gp.bin

Univariate comparison of groups for multiple binary variables
prop.bin.multcomp

Pairwise comparisons after a test for given probabilities
pairwise.mood.medtest

Pairwise Mood's median tests
to.dudi

Synthesis quality of multivariate analyses
user.cont

User defined contrasts for EMMeans
prop.multcomp

Pairwise comparisons after a test for given proportions
pairwise.var.test

Pairwise F tests
cor.multcomp

Comparison of several Pearson's linear correlation coefficients
plotresid

Simple analysis of model residuals
perm.var.test

Permutation F test to compare two variances
quasibinomial.QAIC

QAIC(c) calculation with GLMs of the quasi- family
rating.emmeans

EMMeans for Cumulative Link (Mixed) Models
cov.test

Significance test for the covariance between two datasets
cox.resid

Martingale residuals of a Cox model
cramer

Cramer's association coefficient
mshapiro.test

Shapiro-Wilk multivariate normality test
multinomial.multcomp

Pairwise comparisons after an exact multinomial test
mqqnorm

Multivariate normality QQ-Plot
multinomial.test

Exact multinomial test
pairwise.MVA.test

Pairwise permutation tests based on cross (model) validation
pairwise.G.test

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

Permutation Pearson's correlation test
spearman.ci

Confidence interval of a Spearman's rank correlation coefficient
perm.t.test

Permutation Student's t-test
seq2

Sequence generation
DIABLO.test

Significance test based on cross-validation
G.test

G-test
G.multcomp

Pairwise comparisons after a G-test