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ade4 (version 1.7-4)

Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

Description

Multivariate data analysis and graphical display.

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Version

Install

install.packages('ade4')

Monthly Downloads

57,496

Version

1.7-4

License

GPL (>= 2)

Homepage

http://pbil.univ-lyon1.fr/ADE-4

Maintainer

Aurélie Siberchicot

Last Published

March 1st, 2016

Functions in ade4 (1.7-4)

banque

Table of Factors

Amount of Evolutionary History

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

African Estuary Fishes

coleo

Table of Fuzzy Biological Traits

as.taxo

Taxonomy

dudi.mix

Ordination of Tables mixing quantitative variables and factors

RVdist.randtest

Tests of randomization on the correlation between two distance matrices (in R).

ggtortoises

Microsatellites of Galapagos tortoises populations

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

amova

Analysis of molecular variance

fuzzygenet

Reading a table of genetic data (diploid individuals)

carni19

Phylogeny and quantative trait of carnivora

avijons

Bird species distribution

bsetal97

Ecological and Biological Traits

bacteria

Genomes of 43 Bacteria

fission

Fission pattern and heritable morphological traits

discrimin

Linear Discriminant Analysis (descriptive statistic)

cailliez

Transformation to make Euclidean a distance matrix

dudi.pco

Principal Coordinates Analysis

ade4-package

The ade4 package

dist.genet

Genetic distances from gene frequencies

add.scatter

Add graphics to an existing plot

bwca.dpcoa

Between- and within-class double principal coordinate analysis

mafragh

Phyto-Ecological Survey

ade4toR

Format Change Utility

dist.ktab

Mixed-variables coefficient of distance

aravo

Distribution of Alpine plants in Aravo (Valloire, France)

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

costatis

STATIS and Co-Inertia : Analysis of a series of paired ecological tables

deug

Exam marks for some students

kdist2ktab

Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab')

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

kcponds

Ponds in a nature reserve

ecg

Electrocardiogram data

julliot

Seed dispersal

chatcat

Qualitative Weighted Variables

euro123

Triangular Data

pcw

Distribution of of tropical trees along the Panama canal

costatis.randtest

Monte-Carlo test on a Costatis analysis (in C).

PI2newick

Import data files from Phylogenetic Independance Package

bordeaux

Wine Tasting

chickenk

Veterinary epidemiological study to assess the risk factors for losses in broiler chickens

atlas

Small Ecological Dataset

bf88

Cubic Ecological Data

aviurba

Ecological Tables Triplet

dudi.nsc

Non symmetric correspondence analysis

dpcoa

Double principal coordinate analysis

ardeche

Fauna Table with double (row and column) partitioning

buech

Buech basin

acacia

Spatial pattern analysis in plant communities

arrival

Arrivals at an intensive care unit

chats

Pair of Variables

cnc2003

Frequenting movie theaters in France in 2003

abouheif.eg

Phylogenies and quantitative traits from Abouheif

ichtyo

Point sampling of fish community

bca

Between-Class Analysis

foucart

K-tables Correspondence Analysis with the same rows and the same columns

capitales

Road Distances

cca

Canonical Correspondence Analysis

jv73

K-tables Multi-Regions

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

dist.dudi

Computation of the Distance Matrix from a Statistical Triplet

kplot.statis

Multiple Graphs of a STATIS Analysis

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

butterfly

Genetics-Ecology-Environment Triple

elec88

Electoral Data

ktab.match2ktabs

STATIS and Co-Inertia : Analysis of a series of paired ecological tables

Deprecated functions

Deprecated functions in ade4

disc

Rao's dissimilarity coefficient

dudi

Duality Diagram

RV.rtest

Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in R).

atya

Genetic variability of Cacadors

escopage

K-tables of wine-tasting

casitas

Enzymatic polymorphism in Mus musculus

hdpg

Genetic Variation In Human Populations

randboot.multiblock

Bootstraped simulations for multiblock methods

aminoacyl

Codon usage

apqe

Apportionment of Quadratic Entropy

rhone

Physico-Chemistry Data

ade4-internal

Internal ade4 functions

dudi.coa

Correspondence Analysis

dotcircle

Representation of n values on a circle

dudi.acm

Multiple Correspondence Analysis

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

irishdata

Geary's Irish Data

bicenter.wt

Double Weighted Centring

avimedi

Fauna Table for Constrained Ordinations

mcoa

Multiple CO-inertia Analysis

macroloire

Assemblages of Macroinvertebrates in the Loire River (France)

bca.rlq

Between-Class RLQ analysis

lingoes

Transformation of a Distance Matrix for becoming Euclidean

divc

Rao's diversity coefficient also called quadratic entropy

area.plot

Graphical Display of Areas

lascaux

Genetic/Environment and types of variables

discrimin.coa

Discriminant Correspondence Analysis

mfa

Multiple Factorial Analysis

carni70

Phylogeny and quantitative traits of carnivora

chevaine

Enzymatic polymorphism in Leuciscus cephalus

Computation of the Distance Matrix associated to a Neighbouring Graph

dist.binary

Computation of Distance Matrices for Binary Data

Functions to compute the fourth-corner statistic

Phylogeny and trait of bacteria

piosphere

Plant traits response to grazing

scalewt

Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)

A class of data: tables of populations and alleles

nipals

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

dist.prop

Computation of Distance Matrices of Percentage Data

orthobasis

Orthonormal basis for orthonormal transform

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

dudi.dec

Decentred Correspondence Analysis

meau

Ecological Data : sites-variables, sites-species, where and when

mstree

Minimal Spanning Tree

rhizobium

Genetic structure of two nitrogen fixing bacteria influenced by geographical isolation and host specialization

dudi.fca

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

macon

Wine Tasting

sarcelles

Array of Recapture of Rings

krandtest

Class of the Permutation Tests (in C).

olympic

Olympic Decathlon

mantel.rtest

Mantel test (correlation between two distance matrices (in R).)

withincoinertia

Within-class coinertia analysis

maples

Phylogeny and quantitative traits of flowers

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

lizards

Phylogeny and quantitative traits of lizards

dunedata

Dune Meadow Data

multispati

Multivariate spatial analysis

macaca

Landmarks

pcaiv

Principal component analysis with respect to instrumental variables

toxicity

Homogeneous Table

ktab

the class of objects 'ktab' (K-tables)

procella

Phylogeny and quantitative traits of birds

newick2phylog

Create phylogeny

s.class

Plot of factorial maps with representation of point classes

bca.coinertia

Between-class coinertia analysis

scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis

divcmax

Maximal value of Rao's diversity coefficient also called quadratic entropy

dist.quant

Computation of Distance Matrices on Quantitative Variables

doubs

Pair of Ecological Tables

ktab.within

Process to go from a Within Analysis to a K-tables

mollusc

Faunistic Communities and Sampling Experiment

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

skulls

Morphometric Evolution

ktab.list.df

Creating a K-tables from a list of data frames.

ktab.list.dudi

Creation of a K-tables from a list of duality diagrams

inertia.dudi

Statistics of inertia in a one-table analysis

sepan

Separated Analyses in a K-tables

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

westafrica

Freshwater fish zoogeography in west Africa

randtest.amova

Permutation tests on an analysis of molecular variance (in C).

pcoscaled

Simplified Analysis in Principal Coordinates

presid2002

Results of the French presidential elections of 2002

gearymoran

Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation

microsatt

Genetic Relationships between cattle breeds with microsatellites

dudi.pca

Principal Component Analysis

gridrowcol

Complete regular grid analysis

ecomor

Ecomorphological Convergence

is.euclid

Is a Distance Matrix Euclidean ?

score.coa

Reciprocal scaling after a correspondence analysis

mld

Multi Level Decomposition of unidimensional data

niche

Method to Analyse a pair of tables : Environmental and Faunistic Data

Global State of the World in 1984

orthogram

Orthonormal decomposition of variance

originality

Originality of a species

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

woangers

Plant assemblages in woodlands of the conurbation of Angers (France)

variance.phylog

The phylogenetic ANOVA

s.kde2d

Scatter Plot with Kernel Density Estimate

mbpls

Multiblock partial least squares

Multivariate spatial autocorrelation test

newick.eg

Phylogenetic trees in Newick format

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

multiblock

Display and summarize multiblock objects

s.image

Graph of a variable using image and contour

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

humDNAm

human mitochondrial DNA restriction data

palm

Phylogenetic and quantitative traits of amazonian palm trees

optimEH

Nee and May's optimizing process

mbpcaiv

Multiblock principal component analysis with instrumental variables

s.hist

Display of a scatterplot and its two marginal histograms

kdist

the class of objects 'kdist' (K distance matrices)

randboot

Bootstrap simulations

sco.gauss

Relationships between one score and qualitative variables

pta

Partial Triadic Analysis of a K-tables

quasieuclid

Transformation of a distance matrice to a Euclidean one

ours

A table of Qualitative Variables

s.multinom

Graph of frequency profiles (useful for instance in genetic)

scatter.coa

Plot of the factorial maps for a correspondence analysis

ktab.data.frame

Creation of K-tables from a data frame

s.match

Plot of Paired Coordinates

table.dist

Graph Display for Distance Matrices

procuste.rtest

Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R).

randxval

Two-fold cross-validation

perthi02

Contingency Table with a partition in Molecular Biology

rtest.discrimin

Monte-Carlo Test on a Discriminant Analysis (in R).

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

kdisteuclid

a way to obtain Euclidean distance matrices

randtest.coinertia

Monte-Carlo test on a Co-inertia analysis (in C).

pap

Taxonomy and quantitative traits of carnivora

s.arrow

Plot of the factorial maps for the projection of a vector basis

testdim.multiblock

Selection of the number of dimension by two-fold cross-validation for multiblock methods

mariages

Correspondence Analysis Table

orisaved

Maximal or minimal amount of originality saved under optimal conditions

s.traject

Trajectory Plot

procuste

Simple Procruste Rotation between two sets of points

rtest.between

Monte-Carlo Test on the between-groups inertia percentage (in R).

sco.match

1D plot of a pair of numeric scores with labels

procuste.randtest

Monte-Carlo Test on the sum of the singular values of a procustean rotation (in C).

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

sco.boxplot

Representation of the link between a variable and a set of qualitative variables

meaudret

Ecological Data : sites-variables, sites-species, where and when

randtest.between

Monte-Carlo Test on the between-groups inertia percentage (in C).

statico.krandtest

Monte-Carlo test on a Statico analysis (in C).

table.phylog

Plot arrays in front of a phylogenetic tree

between

Between-Class Analysis

within

Within-Class Analysis

randtest

Class of the Permutation Tests (in C).

mantel.randtest

Mantel test (correlation between two distance matrices (in C).)

tortues

Morphological Study of the Painted Turtle

scatterutil

Graphical utility functions

table.paint

Plot of the arrays by grey levels

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

uniquewt.df

Elimination of Duplicated Rows in a Array

veuvage

Example for Centring in PCA

multispati.randtest

Multivariate spatial autocorrelation test (in C)

mjrochet

Phylogeny and quantitative traits of teleos fishes

s.value

Representation of a value in a graph

wca.rlq

Within-Class RLQ analysis

randtest.pcaiv

Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia

s.corcircle

Plot of the factorial maps of a correlation circle

scatter.dudi

Plot of the Factorial Maps

Projections of Supplementary Rows

witwit.coa

Internal Correspondence Analysis

sco.class

1D plot of a numeric score and a factor with labels

s.chull

Plot of the factorial maps with polygons of contour by level of a factor

santacatalina

Indirect Ordination

rpjdl

Avifauna and Vegetation

mdpcoa

Multiple Double Principal Coordinate Analysis

s.label

Scatter Plot

reconst

Reconstitution of Data from a Duality Diagram

phylog

Phylogeny

supcol

Projections of Supplementary Columns

syndicats

Two Questions asked on a Sample of 1000 Respondents

s.logo

Representation of an object in a graph by a picture

table.cont

Plot of Contingency Tables

s.distri

Plot of a frequency distribution

testdim

Function to perform a test of dimensionality

randEH

Nee and May's random process

taxo.eg

Examples of taxonomy

scatter

Graphical representation of the outputs of a multivariate analysis

randtest.discrimin

Monte-Carlo Test on a Discriminant Analysis (in C).

worksurv

French Worker Survey (1970)

score.pca

Graphs to Analyse a factor in PCA

tarentaise

Mountain Avifauna

seconde

Students and Subjects

sco.distri

Representation by mean- standard deviation of a set of weight distributions on a numeric score

randtest.dpcoa

Permutation test for double principal coordinate analysis (DPCoA)

sco.label

1D plot of a numeric score with labels

tithonia

Phylogeny and quantitative traits of flowers

vegtf

Vegetation in Trois-Fontaines

steppe

Transect in the Vegetation

trichometeo

Pair of Ecological Data

zealand

Road distances in New-Zealand

t3012

Average temperatures of 30 French cities

ungulates

Phylogeny and quantitative traits of ungulates.

rtest

Class of the Permutation Tests (in R).

tintoodiel

Tinto and Odiel estuary geochemistry

s.match.class

Scatterplot of two sets of coordinates and a partionning into classes

wca

Within-Class Analysis

score.mix

Graphs to Analyse a factor in a Mixed Analysis

score

Graphs for One Dimension

statis

STATIS, a method for analysing K-tables

withinpca

Normed within principal component analysis

triangle.class

Triangular Representation and Groups of points

statico

STATIS and Co-Inertia : Analysis of a series of paired ecological tables

yanomama

Distance Matrices