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RVAideMemoire (version 0.9-80)

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

4,870

Version

0.9-80

License

GPL-2

Maintainer

Maxime Herve9

Last Published

June 28th, 2021

Functions in RVAideMemoire (0.9-80)

Cross validation

Significance test for GPA

G-test for binary variables

Anova Tables for Cumulative Link (Mixed) Models

Significance test based on cross-validation

G.theo.multcomp

Pairwise comparisons after a G-test for given probabilities

Significance test for CDA

Cross validation

Pairwise comparisons after a G-test

Paired plot of multivariate analyses

Cross validation

Correlation circle of multivariate analyses

Type II permutation test for constrained multivariate analyses

Biplot of multivariate analyses

Loadings of multivariate analyses

Loading plot of multivariate analyses

Odds-ratio (multinomial regression)

Type II permutation MANOVA using distance matrices

Correlations of multivariate analyses

Cross model validation

Trajectory plot of multivariate analyses

Back-transformation of EMMeans

Plotting of multivariate analyses

Score plot of multivariate analyses

Pearson's Chi-squared test for binary variables

QQ-plot for factor levels

Expected counts for comparison of proportions to given values

Cochran's Q test

Cramer's association coefficient

Significance test based on cross (model) validation

chisq.theo.multcomp

Pairwise comparisons after a chi-squared test for given probabilities

Shapiro-Wilk test for factor levels

Martingale residuals of a Cox model

Synthesis quality of multivariate analyses

Dendrogram and number of groups to be chosen

Deprecated functions in RVAideMemoire package

Graphical adujstment of a simple binary logistic regression to data

Scores of multivariate analyses

Individual contributions in regression

multinomial.theo.multcomp

Pairwise comparisons after an exact multinomial test for given probabilities

Fisher's exact test for binary variables

Fligner-Policello test

fisher.multcomp

Pairwise comparisons using Fisher's exact test

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

QQ-plot for factor levels

Univariate correlation test for multiple variables

Variable Importance in the Projection (VIP)

Permutation Analysis of Variance

Proportions and standard errors

Pairwise comparisons after a test for given proportions

Simple analysis of model residuals

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

wilcox.paired.multcomp

Non parametric pairwise comparisons for paired data

Shapiro-Wilk test for factor levels

wilcox.signtest

Wilcoxon sign test

Histogram for factor levels

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

Cramer's association coefficient

Coordinates of projected points

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

pairwise.factorfit

Pairwise comparisons of groups displayed on a factorial map

pairwise.MVA.test

Pairwise permutation tests based on cross (model) validation

RVAideMemoire-package

Testing and Plotting Procedures for Biostatistics

Expected counts for comparison of response probabilities to given values

Comparison of several Pearson's linear correlation coefficients

Cumulative Distribution Function of a known discrete distribution

Multivariate normality QQ-Plot

Comparison of 2 Pearson's linear correlation coefficients

Coefficient of variation

Permutation F test to compare two variances

Sequence generation

Permutation Student's t-test

Univariate comparison of groups for multiple variables

multtest.gp.bin

Univariate comparison of groups for multiple binary variables

pairwise.CDA.test

Pairwise comparisons for CDA

pairwise.mood.medtest

Pairwise Mood's median tests

Shapiro-Wilk multivariate normality test

pairwise.G.test

Pairwise comparisons for proportions using G-tests

predict.coadisc

Predict method for CDA

prop.bin.multcomp

Pairwise comparisons after a test for given probabilities

Standardization of a data frame based on another data frame

pairwise.perm.manova

Pairwise permutation MANOVAs

Confidence interval of a Spearman's rank correlation coefficient

Significance tests of coefficients (multinomial regression)

User defined contrasts for EMMeans

Synthesis quality of multivariate analyses

Weighted arithmetic mean

multinomial.multcomp

Pairwise comparisons after an exact multinomial test

Dummy responses

Significance test for the covariance between two datasets

multinomial.test

Exact multinomial test

Empirical logistic transformation

Mood's median test

Least rectangles linear regression

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

Observed rating frequencies

Predict method for cross-validated CDA submodels

Predict method for cross-validated submodels

Confidence intervals of a simple linear regression

Estimation of overdispersion with glmer models

Re-computation of an ordination using given row weights

pairwise.var.test

Pairwise F tests

Slope of a hand-defined line

pairwise.perm.t.test

Pairwise permutation t tests

pairwise.perm.var.test

Pairwise permutation F tests

EMMeans for Cumulative Link (Mixed) Models

prop.multinom.test

Wald tests for comparison of proportions

spearman.cor.multcomp

Comparison of several Spearman's rank correlation coefficients

(Semi-)Partial correlation

Divide into groups respecting relative proportions

Permutation Pearson's correlation test

wald.ptheo.multinom.test

Wald tests for comparison of proportions to theoretical values

perm.bartlett.test

Permutation Bartlett's test of homogeneity of variances

"Correlation" of variables to axes in MCA or mix analyses

wald.ptheo.test

Wald test for comparison of a proportion to a theoretical value