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ade4 (version 1.4-16)

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

1.4-16

License

GPL (>= 2)

Homepage

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

Maintainer

Simon Penel

Last Published

August 19th, 2010

Functions in ade4 (1.4-16)

costatis

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

newick2phylog

Create phylogeny

scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis

bordeaux

Wine Tasting

between

Between-Class Analysis

testdim

Function to perform a test of dimensionality

dudi.acm

Multiple Correspondence Analysis

betweencoinertia

Between-class coinertia analysis

carni70

Phylogeny and quantitative traits of carnivora

avimedi

Fauna Table for Constrained Ordinations

dist.prop

Computation of Distance Matrices of Percentage Data

capitales

Road Distances

aviurba

Ecological Tables Triplet

RV.rtest

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

area.plot

Graphical Display of Areas

ade4-package

The ade4 package

arrival

Arrivals at an intensive care unit

add.scatter

Add graphics to an existing plot

dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph

dudi.coa

Correspondence Analysis

dudi

Duality Diagram

ade4toR

Format Change Utility

butterfly

Genetics-Ecology-Environment Triple

acacia

Spatial pattern analysis in plant communities

abouheif.eg

Phylogenies and quantitative traits from Abouheif

deug

Exam marks for some students

aminoacyl

Codon usage

RVdist.randtest

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

baran95

African Estuary Fishes

cca

Canonical Correspondence Analysis

corvus

Corvus morphology

dudi.fca

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

PI2newick

Import data files from Phylogenetic Independance Package

banque

Table of Factors

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

as.taxo

Taxonomy

foucart

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

K-tables Multi-Regions

dudi.dec

Decentred Correspondence Analysis

kplot.statis

Multiple Graphs of a STATIS Analysis

amova

Analysis of molecular variance

dist.ktab

Mixed-variables coefficient of distance

disc

Rao's dissimilarity coefficient

ktab.match2ktabs

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

Amount of Evolutionary History

lingoes

Transformation of a Distance Matrix for becoming Euclidean

buech

Buech basin

atya

Genetic variability of Cacadors

atlas

Small Ecological Dataset

originality

Originality of a species

dist.genet

Genetic distances from gene frequencies

ktab.data.frame

Creation of K-tables from a data frame

chatcat

Qualitative Weighted Variables

dudi.pca

Principal Component Analysis

bicenter.wt

Double Weighted Centring

cailliez

Transformation to make Euclidean a distance matrix

ardeche

Fauna Table with double (row and column) partitioning

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

chazeb

Charolais-Zebus

discrimin

Linear Discriminant Analysis (descriptive statistic)

ichtyo

Point sampling of fish community

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

divc

Rao's diversity coefficient also called quadratic entropy

ktab.within

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

chevaine

Enzymatic polymorphism in Leuciscus cephalus

chats

Pair of Variables

dist.dudi

Computation of the Distance Matrix from a Statistical Triplet

procuste.randtest

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

divcmax

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

casitas

Enzymatic polymorphism in Mus musculus

bf88

Cubic Ecological Data

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

meau

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

dotcircle

Representation of n values on a circle

cnc2003

Frequenting movie theaters in France in 2003

apqe

Apportionment of Quadratic Entropy

discrimin.coa

Discriminant Correspondence Analysis

macon

Wine Tasting

krandtest

Class of the Permutation Tests (in C).

fuzzygenet

Reading a table of genetic data (diploid individuals)

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

coleo

Table of Fuzzy Biological Traits

kcponds

Ponds in a nature reserve

randtest.pcaiv

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

dist.binary

Computation of Distance Matrices for Binary Data

s.corcircle

Plot of the factorial maps of a correlation circle

multispati.randtest

Multivariate spatial autocorrelation test (in C)

carni19

Phylogeny and quantative trait of carnivora

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

dist.quant

Computation of Distance Matrices on Quantitative Variables

fission

Fission pattern and heritable morphological traits

mantel.randtest

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

granulo

Granulometric Curves

ktab.list.df

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

microsatt

Genetic Relationships between cattle breeds with microsatellites

ecg

Electrocardiogram data

dudi.pco

Principal Coordinates Analysis

dpcoa

Double principal coordinate analysis

mcoa

Multiple CO-inertia Analysis

morphosport

Athletes' Morphology

mjrochet

Phylogeny and quantitative traits of teleos fishes

friday87

Faunistic K-tables

mld

Multi Level Decomposition of unidimensional data

inertia.dudi

Statistics of inertia in a one-table analysis

euro123

Triangular Data

optimEH

Nee and May's optimizing process

ktab

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

scatter

Scatter Plot

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

julliot

Seed dispersal

rhizobium

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

dudi.nsc

Non symmetric correspondence analysis

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

lascaux

Genetic/Environment and types of variables

avijons

Bird species distribution

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

oribatid

Oribatid mite

kdist

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

rpjdl

Avifauna and Vegetation

supcol

Projections of Supplementary Columns

score.mix

Graphs to Analyse a factor in a Mixed Analysis

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

bacteria

Genomes of 43 Bacteria

doubs

Pair of Ecological Tables

bsetal97

Ecological and Biological Traits

ecomor

Ecomorphological Convergence

kdisteuclid

a way to obtain Euclidean distance matrices

mollusc

Faunistic Communities and Sampling Experiment

fruits

Pair of Tables

randtest.between

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

orisaved

Maximal or minimal amount of originality saved under optimal conditions

elec88

Electoral Data

dudi.mix

Ordination of Tables mixing quantitative variables and factors

Phylogeny and quantitative traits of lizards

monde84

Global State of the World in 1984

mstree

Minimal Spanning Tree

mafragh

Phyto-Ecological Survey

neig

Neighbourhood Graphs

table.cont

Plot of Contingency Tables

mantel.rtest

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

irishdata

Geary's Irish Data

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

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

gridrowcol

Complete regular grid analysis

palm

Phylogenetic and quantitative traits of amazonian palm trees

escopage

K-tables of wine-tasting

randEH

Nee and May's random process

mfa

Multiple Factorial Analysis

is.euclid

Is a Distance Matrix Euclidean ?

gearymoran

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

sco.gauss

Relationships between one score and qualitative variables

mdpcoa

Multiple Double Principal Coordinate Analysis

s.logo

Representation of an object in a graph by a picture

macroloire

Assemblages of Macroinvertebrates in the Loire River (France)

ktab.list.dudi

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

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

skulls

Morphometric Evolution

mariages

Correspondence Analysis Table

Partial Triadic Analysis of a K-tables

statico

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

meaudret

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

phylog

Phylogeny

s.distri

Plot of a frequency distribution

newick.eg

Phylogenetic trees in Newick format

s.multinom

Graph of frequency profiles (useful for instance in genetic)

sco.match

1D plot of a pair of numeric scores with labels

s.label

Scatter Plot

humDNAm

human mitochondrial DNA restriction data

Graphs to Analyse a factor in PCA

scalewt

Centring and Scaling a Matrix of Any Weighting

genet

A class of data: tables of populations and alleles

olympic

Olympic Decathlon

scatter.coa

Plot of the factorial maps for a correspondence analysis

sepan

Separated Analyses in a K-tables

rhone

Physico-Chemistry Data

procuste

Simple Procruste Rotation between two sets of points

s.class

Plot of factorial maps with representation of point classes

hdpg

Genetic Variation In Human Populations

orthobasis

Orthonormal basis for orthonormal transform

reconst

Reconstitution of Data from a Duality Diagram

randtest-internal

Internal Permutation Tests functions (in C).

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

njplot

Phylogeny and trait of bacteria

randtest

Class of the Permutation Tests (in C).

pcaiv

Principal component analysis with respect to instrumental variables

maples

Phylogeny and quantitative traits of flowers

procuste.rtest

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

procella

Phylogeny and quantitative traits of birds

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

ours

A table of Qualitative Variables

multispati.rtest

Multivariate spatial autocorrelation test

rtest

Class of the Permutation Tests (in R).

s.traject

Trajectory Plot

s.kde2d

Scatter Plot with Kernel Density Estimate

table.dist

Graph Display for Distance Matrices

s.match.class

Scatterplot of two sets of coordinates and a partionning into classes

score.coa

Reciprocal scaling after a correspondence analysis

triangle.plot

Triangular Plotting

s.arrow

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

orthogram

Orthonormal decomposition of variance

tarentaise

Mountain Avifauna

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

presid2002

Results of the French presidential elections of 2002

multispati

Multivariate spatial analysis

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

pcoscaled

Simplified Analysis in Principal Coordinates

s.hist

Display of a scatterplot and its two marginal histograms

pap

Taxonomy and quantitative traits of carnivora

scatter.dudi

Plot of the Factorial Maps

tithonia

Phylogeny and quantitative traits of flowers

s.match

Plot of Paired Coordinates

randtest.amova

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

suprow

Projections of Supplementary Rows

scatterutil

Graphical utility functions

tortues

Morphological Study of the Painted Turtle

quasieuclid

Transformation of a distance matrice to a Euclidean one

ggtortoises

Microsatellites of Galapagos tortoises populations

niche

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

perthi02

Contingency Table with a partition in Molecular Biology

fourthcorner

Functions to compute the fourth-corner statistic

rtest.discrimin

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

steppe

Transect in the Vegetation

score

Graphs for One Dimension

sco.label

1D plot of a numeric score with labels

randtest.coinertia

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

nipals

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

statis

STATIS, a method for analysing K-tables

rtest.between

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

randtest.discrimin

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

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

seconde

Students and Subjects

table.value

Plot of the Arrays

s.image

Graph of a variable using image and contour

table.phylog

Plot arrays in front of a phylogenetic tree

syndicats

Two Questions asked on a Sample of 1000 Respondents

sco.distri

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

worksurv

French Worker Survey (1970)

sarcelles

Array of Recapture of Rings

s.value

Representation of a value in a graph

taxo.eg

Examples of taxonomy

triangle.class

Triangular Representation and Groups of points

woangers

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

vegtf

Vegetation in Trois-Fontaines

withinpca

Normed within Principal Component Analysis

table.paint

Plot of the arrays by grey levels

tintoodiel

Tinto and Odiel estuary geochemistry

witwit.coa

Internal Correspondence Analysis

t3012

Average temperatures of 30 French cities

s.chull

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

within

Within Analyses

withincoinertia

Within-class coinertia analysis

trichometeo

Pair of Ecological Data

ungulates

Phylogeny and quantitative traits of ungulates.

yanomama

Distance Matrices

veuvage

Example for Centring in PCA

uniquewt.df

Elimination of Duplicated Rows in a Array

variance.phylog

The phylogenetic ANOVA

westafrica

Freshwater fish zoogeography in west Africa

zealand

Road distances in New-Zealand