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RVAideMemoire (version 0.9-81-2)

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

4,000

Version

0.9-81-2

License

GPL-2

Maintainer

Maxime Herve9

Last Published

February 21st, 2022

Functions in RVAideMemoire (0.9-81-2)

Pairwise comparisons after a G-test

G.theo.multcomp

Pairwise comparisons after a G-test for given probabilities

Anova Tables for Cumulative Link (Mixed) Models

Significance test based on cross-validation

Significance test for CDA

G-test for binary variables

Significance test for GPA

Cross validation

Cross validation

Loadings of multivariate analyses

Paired plot of multivariate analyses

Biplot of multivariate analyses

Type II permutation test for constrained multivariate analyses

Cross model validation

Correlations of multivariate analyses

RVAideMemoire-package

Testing and Plotting Procedures for Biostatistics

Variable Importance in the Projection (VIP)

Synthesis quality of multivariate analyses

QQ-plot for factor levels

Significance test based on cross (model) validation

Shapiro-Wilk test for factor levels

Scores of multivariate analyses

Cumulative Distribution Function of a known discrete distribution

Score plot of multivariate analyses

Martingale residuals of a Cox model

Plotting of multivariate analyses

Expected counts for comparison of response probabilities to given values

Pearson's Chi-squared test for binary variables

Trajectory plot of multivariate analyses

Expected counts for comparison of proportions to given values

Odds-ratio (multinomial regression)

Significance test for the covariance between two datasets

Cramer's association coefficient

Loading plot of multivariate analyses

Comparison of several Pearson's linear correlation coefficients

Least rectangles linear regression

Slope of a hand-defined line

Coordinates of projected points

pairwise.perm.manova

Pairwise permutation MANOVAs

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

Fisher's exact test for binary variables

Univariate correlation test for multiple variables

multinomial.theo.multcomp

Pairwise comparisons after an exact multinomial test for given probabilities

pairwise.G.test

Pairwise comparisons for proportions using G-tests

pairwise.MVA.test

Pairwise permutation tests based on cross (model) validation

Predict method for cross-validated CDA submodels

QQ-plot for factor levels

Pairwise comparisons after a test for given proportions

prop.bin.multcomp

Pairwise comparisons after a test for given probabilities

pairwise.perm.t.test

Pairwise permutation t tests

Simple analysis of model residuals

Permutation F test to compare two variances

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

Standardization of a data frame based on another data frame

Shapiro-Wilk test for factor levels

Pairwise comparisons after a chi-squared goodness-of-fit test

chisq.theo.multcomp

Pairwise comparisons after a chi-squared test for given probabilities

Cochran's Q test

chisq.theo.bintest

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

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

Graphical adujstment of a simple binary logistic regression to data

fisher.multcomp

Pairwise comparisons using Fisher's exact test

Univariate comparison of groups for multiple variables

Significance tests of coefficients (multinomial regression)

Empirical logistic transformation

Fligner-Policello test

Dummy responses

Individual contributions in regression

multinomial.multcomp

Pairwise comparisons after an exact multinomial test

Correlation circle of multivariate analyses

Cramer's association coefficient

Coefficient of variation

Multivariate normality QQ-Plot

Shapiro-Wilk multivariate normality test

Synthesis quality of multivariate analyses

Predict method for cross-validated submodels

multinomial.test

Exact multinomial test

predict.coadisc

Predict method for CDA

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

Cross validation

quasibinomial.QAIC

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

EMMeans for Cumulative Link (Mixed) Models

Divide into groups respecting relative proportions

spearman.cor.multcomp

Comparison of several Spearman's rank correlation coefficients

pairwise.CDA.test

Pairwise comparisons for CDA

Weighted arithmetic mean

User defined contrasts for EMMeans

(Semi-)Partial correlation

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

Back-transformation of EMMeans

Type II permutation MANOVA using distance matrices

Confidence intervals of a simple linear regression

Observed rating frequencies

wilcox.paired.multcomp

Non parametric pairwise comparisons for paired data

Histogram for factor levels

pairwise.factorfit

Pairwise comparisons of groups displayed on a factorial map

multtest.gp.bin

Univariate comparison of groups for multiple binary variables

wilcox.signtest

Wilcoxon sign test

Permutation Student's t-test

Permutation Pearson's correlation test

pairwise.mood.medtest

Pairwise Mood's median tests

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

Comparison of 2 Pearson's linear correlation coefficients

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

Dendrogram and number of groups to be chosen

Deprecated functions in RVAideMemoire package

Mood's median test

Re-computation of an ordination using given row weights

Estimation of overdispersion with glmer models

pairwise.perm.var.test

Pairwise permutation F tests

pairwise.var.test

Pairwise F tests

perm.bartlett.test

Permutation Bartlett's test of homogeneity of variances

Permutation Analysis of Variance

Proportions and standard errors

prop.multinom.test

Wald tests for comparison of proportions

Confidence interval of a Spearman's rank correlation coefficient

Sequence generation