R: Testing and Plotting Procedures for Biostatistics

# Testing and Plotting Procedures for Biostatistics

## Documentation for package ‘RVAideMemoire’ version 0.9-83-12

- DESCRIPTION file
- Package NEWS

## Help Pages

A B C D E F G I K L M O P Q 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 --

p.beta | Rescaling of a [0,1] variable into the (0,1) interval (and vice-versa)
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

## -- Q --

quasibinomial.QAIC | QAIC(c) calculation with GLMs of the quasi- family
quasipoisson.QAIC | QAIC(c) calculation with GLMs of the quasi- family

## -- 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