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ade4 (version 1.7-5)

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

38,204

Version

1.7-5

License

GPL (>= 2)

Homepage

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

Maintainer

Aurélie Siberchicot

Last Published

December 13th, 2016

Functions in ade4 (1.7-5)

Deprecated functions

Deprecated functions in ade4

abouheif.eg

Phylogenies and quantitative traits from Abouheif

amova

Analysis of molecular variance

aminoacyl

Codon usage

ade4toR

Format Change Utility

ade4-package

The ade4 package

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

add.scatter

Add graphics to an existing plot

acacia

Spatial pattern analysis in plant communities

ade4-internal

Internal ade4 functions

ardeche

Fauna Table with double (row and column) partitioning

aravo

Distribution of Alpine plants in Aravo (Valloire, France)

avijons

Bird species distribution

atlas

Small Ecological Dataset

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

area.plot

Graphical Display of Areas

arrival

Arrivals at an intensive care unit

apqe

Apportionment of Quadratic Entropy

as.taxo

Taxonomy

atya

Genetic variability of Cacadors

aviurba

Ecological Tables Triplet

bca.coinertia

Between-class coinertia analysis

baran95

African Estuary Fishes

bca.rlq

Between-Class RLQ analysis

avimedi

Fauna Table for Constrained Ordinations

bacteria

Genomes of 43 Bacteria

bca

Between-Class Analysis

bf88

Cubic Ecological Data

banque

Table of Factors

bicenter.wt

Double Weighted Centring

butterfly

Genetics-Ecology-Environment Triple

bsetal97

Ecological and Biological Traits

carni70

Phylogeny and quantitative traits of carnivora

carni19

Phylogeny and quantative trait of carnivora

Between- and within-class double principal coordinate analysis

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

cailliez

Transformation to make Euclidean a distance matrix

chatcat

Qualitative Weighted Variables

chats

Pair of Variables

casitas

Enzymatic polymorphism in Mus musculus

cca

Canonical Correspondence Analysis

coinertia

Coinertia Analysis

coleo

Table of Fuzzy Biological Traits

clementines

Fruit Production

cnc2003

Frequenting movie theaters in France in 2003

chevaine

Enzymatic polymorphism in Leuciscus cephalus

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

dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph

dist.quant

Computation of Distance Matrices on Quantitative Variables

disc

Rao's dissimilarity coefficient

discrimin.coa

Discriminant Correspondence Analysis

divc

Rao's diversity coefficient also called quadratic entropy

divcmax

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

dist.dudi

Computation of the Distance Matrix from a Statistical Triplet

discrimin

Linear Discriminant Analysis (descriptive statistic)

dist.genet

Genetic distances from gene frequencies

dist.ktab

Mixed-variables coefficient of distance

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

dudi

Duality Diagram

Amount of Evolutionary History

costatis.randtest

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

ecomor

Ecomorphological Convergence

deug

Exam marks for some students

dpcoa

Double principal coordinate analysis

doubs

Pair of Ecological Tables

dudi.acm

Multiple Correspondence Analysis

dudi.coa

Correspondence Analysis

genet

A class of data: tables of populations and alleles

ggtortoises

Microsatellites of Galapagos tortoises populations

ktab.list.df

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

ktab

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

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

dotcircle

Representation of n values on a circle

dudi.fca

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

dudi.dec

Decentred Correspondence Analysis

elec88

Electoral Data

escopage

K-tables of wine-tasting

fuzzygenet

Reading a table of genetic data (diploid individuals)

gearymoran

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

kdist2ktab

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

kdist

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

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

euro123

Triangular Data

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

fission

Fission pattern and heritable morphological traits

granulo

Granulometric Curves

gridrowcol

Complete regular grid analysis

inertia.dudi

Decomposition of inertia (i.e. contributions) in multivariate methods

irishdata

Geary's Irish Data

kdisteuclid

a way to obtain Euclidean distance matrices

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

humDNAm

human mitochondrial DNA restriction data

ichtyo

Point sampling of fish community

ktab.data.frame

Creation of K-tables from a data frame

krandtest

Class of the Permutation Tests (in C).

maples

Phylogeny and quantitative traits of flowers

mariages

Correspondence Analysis Table

mjrochet

Phylogeny and quantitative traits of teleos fishes

perthi02

Contingency Table with a partition in Molecular Biology

mld

Multi Level Decomposition of unidimensional data

phylog

Phylogeny

dudi.pca

Principal Component Analysis

dudi.pco

Principal Coordinates Analysis

foucart

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

fourthcorner

Functions to compute the fourth-corner statistic

K-tables Multi-Regions

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

kcponds

Ponds in a nature reserve

dunedata

Dune Meadow Data

dudi.nsc

Non symmetric correspondence analysis

dudi.mix

Ordination of Tables mixing quantitative variables and factors

ecg

Electrocardiogram data

hdpg

Genetic Variation In Human Populations

housetasks

Contingency Table

is.euclid

Is a Distance Matrix Euclidean?

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

julliot

Seed dispersal

procuste

Simple Procruste Rotation between two sets of points

procella

Phylogeny and quantitative traits of birds

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

randtest.pcaiv

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

randtest

Class of the Permutation Tests (in C).

rhone

Physico-Chemistry Data

Array of Recapture of Rings

s.logo

Representation of an object in a graph by a picture

scalewt

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

lizards

Phylogeny and quantitative traits of lizards

lingoes

Transformation of a Distance Matrix for becoming Euclidean

macroloire

Assemblages of Macroinvertebrates in the Loire River (France)

mafragh

Phyto-Ecological Survey

multiblock

Display and summarize multiblock objects

neig

Neighbourhood Graphs

multispati

Multivariate spatial analysis

newick.eg

Phylogenetic trees in Newick format

kplot.statis

Multiple Graphs of a STATIS Analysis

originality

Originality of a species

oribatid

Oribatid mite

ktab.within

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

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

lascaux

Genetic/Environment and types of variables

mcoa

Multiple CO-inertia Analysis

mdpcoa

Multiple Double Principal Coordinate Analysis

mollusc

Faunistic Communities and Sampling Experiment

monde84

Global State of the World in 1984

nipals

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

sco.match

1D plot of a pair of numeric scores with labels

sco.label

1D plot of a numeric score with labels

njplot

Phylogeny and trait of bacteria

statico

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

skulls

Morphometric Evolution

syndicats

Two Questions asked on a Sample of 1000 Respondents

taxo.eg

Examples of taxonomy

t3012

Average temperatures of 30 French cities

testdim

Function to perform a test of dimensionality

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

mantel.randtest

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

pcaiv

Principal component analysis with respect to instrumental variables

optimEH

Nee and May's optimizing process

olympic

Olympic Decathlon

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

randEH

Nee and May's random process

meau

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

meaudret

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

mstree

Minimal Spanning Tree

morphosport

Athletes' Morphology

multispati.randtest

Multivariate spatial autocorrelation test (in C)

multispati.rtest

Multivariate spatial autocorrelation test

orisaved

Maximal or minimal amount of originality saved under optimal conditions

orthobasis

Orthonormal basis for orthonormal transform

between

Between-Class Analysis

plot.phylog

Plot phylogenies

randtest.amova

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

randtest.dpcoa

Permutation test for double principal coordinate analysis (DPCoA)

randtest.discrimin

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

rpjdl

Avifauna and Vegetation

s.match

Plot of Paired Coordinates

s.match.class

Scatterplot of two sets of coordinates and a partionning into classes

rtest.between

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

santacatalina

Indirect Ordination

s.value

Representation of a value in a graph

within

Within-Class Analysis

presid2002

Results of the French presidential elections of 2002

randxval

Two-fold cross-validation

rankrock

Ordination Table

rtest

Class of the Permutation Tests (in R).

rtest.discrimin

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

sco.boxplot

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

sco.class

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

statico.krandtest

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

statis

STATIS, a method for analysing K-tables

procuste.randtest

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

RV.rtest

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

procuste.rtest

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

RVdist.randtest

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

s.kde2d

Scatter Plot with Kernel Density Estimate

s.image

Graph of a variable using image and contour

s.multinom

Graph of frequency profiles (useful for instance in genetic)

sco.distri

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

s.traject

Trajectory Plot

sco.gauss

Relationships between one score and qualitative variables

orthogram

Orthonormal decomposition of variance

ours

A table of Qualitative Variables

pcoscaled

Simplified Analysis in Principal Coordinates

pcw

Distribution of of tropical trees along the Panama canal

randboot.multiblock

Bootstraped simulations for multiblock methods

randboot

Bootstrap simulations

randtest.coinertia

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

randtest.between

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

ktab.list.dudi

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

s.hist

Display of a scatterplot and its two marginal histograms

s.distri

Plot of a frequency distribution

ktab.match2ktabs

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

mfa

Multiple Factorial Analysis

microsatt

Genetic Relationships between cattle breeds with microsatellites

newick2phylog

Create phylogeny

niche

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

pap

Taxonomy and quantitative traits of carnivora

palm

Phylogenetic and quantitative traits of amazonian palm trees

score.mix

Graphs to Analyse a factor in a Mixed Analysis

piosphere

Plant traits response to grazing

PI2newick

Import data files from Phylogenetic Independance Package

score.pca

Graphs to Analyse a factor in PCA

table.cont

Plot of Contingency Tables

table.dist

Graph Display for Distance Matrices

woangers

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

vegtf

Vegetation in Trois-Fontaines

witwit.coa

Internal Correspondence Analysis

tarentaise

Mountain Avifauna

variance.phylog

The phylogenetic ANOVA

table.value

Plot of the Arrays

suprow

Projections of Supplementary Rows

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

testdim.multiblock

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

tintoodiel

Tinto and Odiel estuary geochemistry

pta

Partial Triadic Analysis of a K-tables

withinpca

Normed within principal component analysis

withincoinertia

Within-class coinertia analysis

westafrica

Freshwater fish zoogeography in west Africa

wca

Within-Class Analysis

reconst

Reconstitution of Data from a Duality Diagram

quasieuclid

Transformation of a distance matrice to a Euclidean one

s.arrow

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

rhizobium

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

s.chull

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

s.corcircle

Plot of the factorial maps of a correlation circle

scatter.dudi

Plot of the Factorial Maps

s.class

Plot of factorial maps with representation of point classes

scatter.coa

Plot of the factorial maps for a correspondence analysis

scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

score.coa

Reciprocal scaling after a correspondence analysis

score

Graphs for One Dimension

supcol

Projections of Supplementary Columns

steppe

Transect in the Vegetation

triangle.class

Triangular Representation and Groups of points

toxicity

Homogeneous Table

veuvage

Example for Centring in PCA

worksurv

French Worker Survey (1970)

wca.rlq

Within-Class RLQ analysis

yanomama

Distance Matrices

table.paint

Plot of the arrays by grey levels

table.phylog

Plot arrays in front of a phylogenetic tree

tortues

Morphological Study of the Painted Turtle

tithonia

Phylogeny and quantitative traits of flowers

uniquewt.df

Elimination of Duplicated Rows in a Array

ungulates

Phylogeny and quantitative traits of ungulates.

seconde

Students and Subjects

scatterutil

Graphical utility functions

scatter

Graphical representation of the outputs of a multivariate analysis

sepan

Separated Analyses in a K-tables

triangle.plot

Triangular Plotting

trichometeo

Pair of Ecological Data

zealand

Road distances in New-Zealand