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RVAideMemoire (version 0.9-83-7)

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

4,000

Version

0.9-83-7

License

GPL-2

Maintainer

Maxime Herve9

Last Published

November 6th, 2023

Functions in RVAideMemoire (0.9-83-7)

Correlations of multivariate analyses

Plotting of multivariate analyses

Correlation circle of multivariate analyses

Type II permutation test for constrained multivariate analyses

Biplot of multivariate analyses

Cross model validation

Cross validation

Loadings of multivariate analyses

Paired plot of multivariate analyses

Loading plot of multivariate analyses

Variable Importance in the Projection (VIP)

RVAideMemoire-package

Testing and Plotting Procedures for Biostatistics

Scores of multivariate analyses

Synthesis quality of multivariate analyses

Odds-ratio (multinomial regression)

Type II permutation MANOVA using distance matrices

Trajectory plot of multivariate analyses

Score plot of multivariate analyses

Back-transformation of EMMeans

Significance test based on cross (model) validation

QQ-plot for factor levels

Pearson's Chi-squared test for binary variables

Cumulative Distribution Function of a known discrete distribution

Shapiro-Wilk test for factor levels

Expected counts for comparison of proportions to given values

chisq.theo.multcomp

Pairwise comparisons after a chi-squared test for given probabilities

Cochran's Q test

Comparison of 2 Pearson's linear correlation coefficients

Expected counts for comparison of response probabilities to given values

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

Coordinates of projected points

QQ-plot for factor levels

Shapiro-Wilk test for factor levels

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

Dummy responses

Empirical logistic transformation

Least rectangles linear regression

Slope of a hand-defined line

Significance test for the covariance between two datasets

Fisher's exact test for binary variables

Comparison of several Pearson's linear correlation coefficients

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

Martingale residuals of a Cox model

Histogram for factor levels

Dendrogram and number of groups to be chosen

Deprecated functions in RVAideMemoire package

Mood's median test

Cramer's association coefficient

Multivariate normality QQ-Plot

Shapiro-Wilk multivariate normality test

Re-computation of an ordination using given row weights

Univariate comparison of groups for multiple variables

Graphical adujstment of a simple binary logistic regression to data

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

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

multtest.gp.bin

Univariate comparison of groups for multiple binary variables

pairwise.perm.t.test

Pairwise permutation t tests

pairwise.perm.manova

Pairwise permutation MANOVAs

pairwise.MVA.test

Pairwise permutation tests based on cross (model) validation

Estimation of overdispersion with glmer models

pairwise.G.test

Pairwise comparisons for proportions using G-tests

multinomial.test

Exact multinomial test

multinomial.multcomp

Pairwise comparisons after an exact multinomial test

(Semi-)Partial correlation

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

pairwise.CDA.test

Pairwise comparisons for CDA

Simple analysis of model residuals

Permutation F test to compare two variances

Univariate correlation test for multiple variables

Fligner-Policello test

Individual contributions in regression

multinomial.theo.multcomp

Pairwise comparisons after an exact multinomial test for given probabilities

pairwise.perm.var.test

Pairwise permutation F tests

Coefficient of variation

Cramer's association coefficient

Predict method for cross-validated submodels

predict.coadisc

Predict method for CDA

pairwise.factorfit

Pairwise comparisons of groups displayed on a factorial map

Observed rating frequencies

pairwise.var.test

Pairwise F tests

Permutation Analysis of Variance

Permutation Pearson's correlation test

pairwise.mood.medtest

Pairwise Mood's median tests

prop.bin.multcomp

Pairwise comparisons after a test for given probabilities

Permutation Student's t-test

Sequence generation

Pairwise comparisons after a test for given proportions

Confidence intervals of a simple linear regression

Synthesis quality of multivariate analyses

User defined contrasts for EMMeans

Predict method for cross-validated CDA submodels

prop.multinom.test

Wald tests for comparison of proportions

Proportions and standard errors

wald.ptheo.test

Wald test for comparison of a proportion to a theoretical value

wald.ptheo.multinom.test

Wald tests for comparison of proportions to theoretical values

perm.bartlett.test

Permutation Bartlett's test of homogeneity of variances

quasibinomial.QAIC

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

Standardization of a data frame based on another data frame

EMMeans for Cumulative Link (Mixed) Models

Significance tests of coefficients (multinomial regression)

wilcox.signtest

Wilcoxon sign test

wilcox.paired.multcomp

Non parametric pairwise comparisons for paired data

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

spearman.cor.multcomp

Comparison of several Spearman's rank correlation coefficients

Confidence interval of a Spearman's rank correlation coefficient

Weighted arithmetic mean

Divide into groups respecting relative proportions

G-test for binary variables

Significance test for CDA

Pairwise comparisons after a G-test

Significance test based on cross-validation

Anova Tables for Cumulative Link (Mixed) Models

Cross validation

Cross validation

G.theo.multcomp

Pairwise comparisons after a G-test for given probabilities

Significance test for GPA