Testing and Plotting Procedures for Biostatistics


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Documentation for package ‘RVAideMemoire’ version 0.9-79

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A B C D E F G I K L M O P R S T U W

RVAideMemoire-package Testing and Plotting Procedures for Biostatistics

-- A --

adonis.II Type II permutation MANOVA using distance matrices
Anova.clm Anova Tables for Cumulative Link (Mixed) Models
Anova.clmm Anova Tables for Cumulative Link (Mixed) Models

-- B --

back.emmeans Back-transformation of EMMeans
back.lsmeans Deprecated functions in RVAideMemoire package
bootstrap Bootstrap
byf.hist Histogram for factor levels
byf.mqqnorm QQ-plot for factor levels
byf.mshapiro Shapiro-Wilk test for factor levels
byf.normhist Deprecated functions in RVAideMemoire package
byf.qqnorm QQ-plot for factor levels
byf.shapiro Shapiro-Wilk test for factor levels

-- C --

CDA.cv Cross validation
CDA.test Significance test for CDA
cdf.discrete Cumulative Distribution Function of a known discrete distribution
chisq.bin.exp Expected counts for comparison of response probabilities to given values
chisq.bintest Pearson's Chi-squared test for binary variables
chisq.exp Expected counts for comparison of proportions to given values
chisq.multcomp Pairwise comparisons after a chi-squared goodness-of-fit test
chisq.theo.bintest Pearson's Chi-squared test for comparison of response probabilities to given values
chisq.theo.multcomp Pairwise comparisons after a chi-squared test for given probabilities
cochran.qtest Cochran's Q test
cond.multinom Condition number of the Hessian matrix of a multinomial log-linear model
coord.proj Coordinates of projected points
cor.2comp Comparison of 2 Pearson's linear correlation coefficients
cor.conf Equality of a Pearson's linear correlation coefficient to a given value
cor.multcomp Comparison of several Pearson's linear correlation coefficients
cor.sparse Deprecated functions in RVAideMemoire package
cov.test Significance test for the covariance between two datasets
cox.resid Martingale residuals of a Cox model
cramer Cramer's association coefficient
cramer.test Cramer's association coefficient
cv Coefficient of variation
CvM.test Deprecated functions in RVAideMemoire package

-- D --

DA.confusion Deprecated functions in RVAideMemoire package
DA.valid Deprecated functions in RVAideMemoire package
DA.var Deprecated functions in RVAideMemoire package
dendro.gp Dendrogram and number of groups to be chosen
DIABLO.cv Cross validation
DIABLO.test Significance test based on cross-validation
dummy Dummy responses
dunn.test Deprecated functions in RVAideMemoire package

-- E --

elogis Empirical logistic transformation

-- F --

fc.multcomp Deprecated functions in RVAideMemoire package
fisher.bintest Fisher's exact test for binary variables
fisher.multcomp Pairwise comparisons using Fisher's exact test
fp.test Fligner-Policello test
fp.test.default Fligner-Policello test
fp.test.formula Fligner-Policello test
friedman.rating.test Deprecated functions in RVAideMemoire package

-- G --

G.bintest G-test for binary variables
G.multcomp Pairwise comparisons after a G-test
G.test G-test
G.theo.multcomp Pairwise comparisons after a G-test for given probabilities
GPA.test Significance test for GPA

-- I --

ind.contrib Individual contributions in regression

-- K --

kruskal.rating.test Deprecated functions in RVAideMemoire package

-- L --

least.rect Least rectangles linear regression
loc.slp Slope of a hand-defined line
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

-- M --

mod Mode
mood.medtest Mood's median test
mood.medtest.default Mood's median test
mood.medtest.formula Mood's median test
mqqnorm Multivariate normality QQ-Plot
mshapiro.test Shapiro-Wilk multivariate normality test
multinomial.multcomp Pairwise comparisons after an exact multinomial test
multinomial.test Exact multinomial test
multinomial.theo.multcomp Pairwise comparisons after an exact multinomial test for given probabilities
multtest.cor Univariate correlation test for multiple variables
multtest.gp Univariate comparison of groups for multiple variables
multtest.gp.bin Univariate comparison of groups for multiple binary variables
MVA.anova Type II permutation test for constrained multivariate analyses
MVA.biplot Biplot of multivariate analyses
MVA.cmv Cross model validation
MVA.cor Correlations of multivariate analyses
MVA.corplot Correlation circle of multivariate analyses
MVA.cv Cross validation
MVA.load Loadings of multivariate analyses
MVA.loadplot Loading plot of multivariate analyses
MVA.pairplot Paired plot of multivariate analyses
MVA.plot Plotting of multivariate analyses
MVA.scoreplot Score plot of multivariate analyses
MVA.scores Scores of multivariate analyses
MVA.synt Synthesis quality of multivariate analyses
MVA.test Significance test based on cross (model) validation
MVA.trajplot Trajectory plot of multivariate analyses

-- O --

OR.multinom Odds-ratio (multinomial regression)
ord.rw Re-computation of an ordination using given row weights
overdisp.glmer Estimation of overdispersion with 'glmer' models

-- P --

pairwise.CDA.test Pairwise comparisons for CDA
pairwise.factorfit Pairwise comparisons of groups displayed on a factorial map
pairwise.G.test Pairwise comparisons for proportions using G-tests
pairwise.manova Deprecated functions in RVAideMemoire package
pairwise.mood.medtest Pairwise Mood's median tests
pairwise.MVA.test Pairwise permutation tests based on cross (model) validation
pairwise.perm.manova Pairwise permutation MANOVAs
pairwise.perm.t.test Pairwise permutation t tests
pairwise.perm.var.test Pairwise permutation F tests
pairwise.to.groups Deprecated functions in RVAideMemoire package
pairwise.var.test Pairwise F tests
pairwise.wilcox.rating.test Deprecated functions in RVAideMemoire package
pcor (Semi-)Partial correlation
pcor.test Tests for (semi-)partial association/correlation between paired samples
perm.anova Permutation Analysis of Variance
perm.bartlett.test Permutation Bartlett's test of homogeneity of variances
perm.cor.test Permutation Pearson's correlation test
perm.t.test Permutation Student's t-test
perm.t.test.default Permutation Student's t-test
perm.t.test.formula Permutation Student's t-test
perm.var.test Permutation F test to compare two variances
perm.var.test.default Permutation F test to compare two variances
perm.var.test.formula Permutation F test to compare two variances
plot.multtest.cor Univariate correlation test for multiple variables
plot.multtest.gp Univariate comparison of groups for multiple variables
plot.multtest.gp.bin Univariate comparison of groups for multiple binary variables
plot1comp.ind Deprecated functions in RVAideMemoire package
plot1comp.var Deprecated functions in RVAideMemoire package
plotresid Simple analysis of model residuals
plotsurvivors Survivor curve
PLSDA.ncomp Deprecated functions in RVAideMemoire package
PLSDA.test Deprecated functions in RVAideMemoire package
PLSDA.VIP Variable Importance in the Projection (VIP)
predict.CDA.cv Predict method for cross-validated CDA submodels
predict.coadisc Predict method for CDA
predict.MVA.cmv Predict method for cross-validated submodels
predict.MVA.cv Predict method for cross-validated submodels
prop.bin.multcomp Pairwise comparisons after a test for given probabilities
prop.multcomp Pairwise comparisons after a test for given proportions
prop.multinom Proportions and standard errors
prop.multinom.test Wald tests for comparison of proportions

-- R --

rating.emmeans EMMeans for Cumulative Link (Mixed) Models
rating.lsmeans Deprecated functions in RVAideMemoire package
rating.prob Observed rating frequencies
reg.ci Confidence intervals of a simple linear regression
RVAideMemoire Testing and Plotting Procedures for Biostatistics

-- S --

s.corcircle2 Deprecated functions in RVAideMemoire package
scat.cr "Correlation" of variables to axes in MCA or mix analyses
scat.mix.categorical Deprecated functions in RVAideMemoire package
scat.mix.numeric Deprecated functions in RVAideMemoire package
scatter.coa2 Deprecated functions in RVAideMemoire package
se Standard error
seq2 Sequence generation
spearman.ci Confidence interval of a Spearman's rank correlation coefficient
spearman.cor.multcomp Comparison of several Spearman's rank correlation coefficients
splitf Divide into groups respecting relative proportions
stand Standardization of a data frame based on another data frame

-- T --

test.multinom Significance tests of coefficients (multinomial regression)
to.dudi Synthesis quality of multivariate analyses

-- U --

user.cont User defined contrasts for EMMeans

-- W --

wald.ptheo.multinom.test Wald tests for comparison of proportions to theoretical values
wald.ptheo.test Wald test for comparison of a proportion to a theoretical value
wilcox.paired.multcomp Non parametric pairwise comparisons for paired data
wilcox.paired.rating.multcomp Deprecated functions in RVAideMemoire package
wilcox.rating.signtest Deprecated functions in RVAideMemoire package
wilcox.rating.test Deprecated functions in RVAideMemoire package
wilcox.signtest Wilcoxon sign test
wilcox.signtest.default Wilcoxon sign test
wilcox.signtest.formula Wilcoxon sign test
wmean Weighted arithmetic mean