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ade4 (version 1.5-0)

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

64,558

Version

1.5-0

License

GPL (>= 2)

Homepage

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

Maintainer

Simon Penel

Last Published

April 24th, 2012

Functions in ade4 (1.5-0)

bsetal97

Ecological and Biological Traits

bca

Between-Class Analysis

housetasks

Contingency Table

ktab.list.df

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

bicenter.wt

Double Weighted Centring

bca.rlq

Between-Class RLQ analysis

optimEH

Nee and May's optimizing process

banque

Table of Factors

divc

Rao's diversity coefficient also called quadratic entropy

palm

Phylogenetic and quantitative traits of amazonian palm trees

plot.phylog

Plot phylogenies

RV.rtest

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

arrival

Arrivals at an intensive care unit

ade4toR

Format Change Utility

casitas

Enzymatic polymorphism in Mus musculus

costatis

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

add.scatter

Add graphics to an existing plot

discrimin.coa

Discriminant Correspondence Analysis

atya

Genetic variability of Cacadors

dudi.coa

Correspondence Analysis

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

cca

Canonical Correspondence Analysis

dist.binary

Computation of Distance Matrices for Binary Data

avijons

Bird species distribution

buech

Buech basin

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

lingoes

Transformation of a Distance Matrix for becoming Euclidean

PI2newick

Import data files from Phylogenetic Independance Package

dist.quant

Computation of Distance Matrices on Quantitative Variables

butterfly

Genetics-Ecology-Environment Triple

cailliez

Transformation to make Euclidean a distance matrix

foucart

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

Amount of Evolutionary History

apqe

Apportionment of Quadratic Entropy

pcaiv

Principal component analysis with respect to instrumental variables

kdisteuclid

a way to obtain Euclidean distance matrices

dpcoa

Double principal coordinate analysis

RVdist.randtest

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

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

kcponds

Ponds in a nature reserve

bf88

Cubic Ecological Data

bordeaux

Wine Tasting

dist.genet

Genetic distances from gene frequencies

pta

Partial Triadic Analysis of a K-tables

genet

A class of data: tables of populations and alleles

ecomor

Ecomorphological Convergence

irishdata

Geary's Irish Data

chevaine

Enzymatic polymorphism in Leuciscus cephalus

dudi.dec

Decentred Correspondence Analysis

euro123

Triangular Data

atlas

Small Ecological Dataset

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

is.euclid

Is a Distance Matrix Euclidean ?

inertia.dudi

Statistics of inertia in a one-table analysis

discrimin

Linear Discriminant Analysis (descriptive statistic)

abouheif.eg

Phylogenies and quantitative traits from Abouheif

dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph

kplot.statis

Multiple Graphs of a STATIS Analysis

Phylogeny and quantitative traits of flowers

ichtyo

Point sampling of fish community

divcmax

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

granulo

Granulometric Curves

carni70

Phylogeny and quantitative traits of carnivora

presid2002

Results of the French presidential elections of 2002

dudi

Duality Diagram

randEH

Nee and May's random process

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

Fauna Table for Constrained Ordinations

fourthcorner

Functions to compute the fourth-corner statistic

meaudret

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

procella

Phylogeny and quantitative traits of birds

ktab

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

rpjdl

Avifauna and Vegetation

monde84

Global State of the World in 1984

pap

Taxonomy and quantitative traits of carnivora

olympic

Olympic Decathlon

tortues

Morphological Study of the Painted Turtle

s.traject

Trajectory Plot

mollusc

Faunistic Communities and Sampling Experiment

oribatid

Oribatid mite

mfa

Multiple Factorial Analysis

niche

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

cnc2003

Frequenting movie theaters in France in 2003

statis

STATIS, a method for analysing K-tables

macroloire

Assemblages of Macroinvertebrates in the Loire River (France)

randtest.amova

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

aviurba

Ecological Tables Triplet

bacteria

Genomes of 43 Bacteria

score.pca

Graphs to Analyse a factor in PCA

acacia

Spatial pattern analysis in plant communities

randtest.pcaiv

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

newick.eg

Phylogenetic trees in Newick format

rhone

Physico-Chemistry Data

sco.label

1D plot of a numeric score with labels

pcoscaled

Simplified Analysis in Principal Coordinates

coleo

Table of Fuzzy Biological Traits

elec88

Electoral Data

dudi.mix

Ordination of Tables mixing quantitative variables and factors

Scatter Plot with Kernel Density Estimate

mafragh

Phyto-Ecological Survey

ardeche

Fauna Table with double (row and column) partitioning

chatcat

Qualitative Weighted Variables

dudi.acm

Multiple Correspondence Analysis

testdim

Function to perform a test of dimensionality

Class of the Permutation Tests (in C).

carni19

Phylogeny and quantative trait of carnivora

multispati.rtest

Multivariate spatial autocorrelation test

fuzzygenet

Reading a table of genetic data (diploid individuals)

friday87

Faunistic K-tables

ktab.data.frame

Creation of K-tables from a data frame

santacatalina

Indirect Ordination

statico

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

fission

Fission pattern and heritable morphological traits

worksurv

French Worker Survey (1970)

rtest.discrimin

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

table.phylog

Plot arrays in front of a phylogenetic tree

dudi.pca

Principal Component Analysis

sco.distri

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

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

capitales

Road Distances

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

macaca

Landmarks

nipals

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

dist.prop

Computation of Distance Matrices of Percentage Data

clementines

Fruit Production

procuste.rtest

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

jv73

K-tables Multi-Regions

ecg

Electrocardiogram data

s.value

Representation of a value in a graph

doubs

Pair of Ecological Tables

microsatt

Genetic Relationships between cattle breeds with microsatellites

steppe

Transect in the Vegetation

dudi.fca

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

variance.phylog

The phylogenetic ANOVA

s.multinom

Graph of frequency profiles (useful for instance in genetic)

tithonia

Phylogeny and quantitative traits of flowers

dotcircle

Representation of n values on a circle

trichometeo

Pair of Ecological Data

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

newick2phylog

Create phylogeny

randtest.between

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

dudi.nsc

Non symmetric correspondence analysis

originality

Originality of a species

syndicats

Two Questions asked on a Sample of 1000 Respondents

deug

Exam marks for some students

mdpcoa

Multiple Double Principal Coordinate Analysis

orthogram

Orthonormal decomposition of variance

rankrock

Ordination Table

sco.match

1D plot of a pair of numeric scores with labels

table.paint

Plot of the arrays by grey levels

gridrowcol

Complete regular grid analysis

s.match.class

Scatterplot of two sets of coordinates and a partionning into classes

disc

Rao's dissimilarity coefficient

tintoodiel

Tinto and Odiel estuary geochemistry

lascaux

Genetic/Environment and types of variables

triangle.plot

Triangular Plotting

score.mix

Graphs to Analyse a factor in a Mixed Analysis

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

Ordination of Tables mixing quantitative variables and factors

humDNAm

human mitochondrial DNA restriction data

uniquewt.df

Elimination of Duplicated Rows in a Array

taxo.eg

Examples of taxonomy

s.distri

Plot of a frequency distribution

s.class

Plot of factorial maps with representation of point classes

orisaved

Maximal or minimal amount of originality saved under optimal conditions

s.corcircle

Plot of the factorial maps of a correlation circle

quasieuclid

Transformation of a distance matrice to a Euclidean one

within

Within-Class Analysis

amova

Analysis of molecular variance

scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis

mjrochet

Phylogeny and quantitative traits of teleos fishes

morphosport

Athletes' Morphology

dudi.pco

Principal Coordinates Analysis

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

wca.rlq

Within-Class RLQ analysis

ktab.list.dudi

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

mld

Multi Level Decomposition of unidimensional data

as.taxo

Taxonomy

table.dist

Graph Display for Distance Matrices

sarcelles

Array of Recapture of Rings

skulls

Morphometric Evolution

bca.coinertia

Between-class coinertia analysis

rhizobium

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

s.match

Plot of Paired Coordinates

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

mantel.randtest

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

sco.gauss

Relationships between one score and qualitative variables

lizards

Phylogeny and quantitative traits of lizards

wca

Within-Class Analysis

mantel.rtest

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

vegtf

Vegetation in Trois-Fontaines

s.image

Graph of a variable using image and contour

meau

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

tarentaise

Mountain Avifauna

mstree

Minimal Spanning Tree

perthi02

Contingency Table with a partition in Molecular Biology

njplot

Phylogeny and trait of bacteria

escopage

K-tables of wine-tasting

randtest.discrimin

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

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

between

Between-Class Analysis

kdist2ktab

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

procuste

Simple Procruste Rotation between two sets of points

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

s.chull

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

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

multispati.randtest

Multivariate spatial autocorrelation test (in C)

neig

Neighbourhood Graphs

orthobasis

Orthonormal basis for orthonormal transform

multispati

Multivariate spatial analysis

reconst

Reconstitution of Data from a Duality Diagram

s.label

Scatter Plot

ktab.match2ktabs

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

score

Graphs for One Dimension

randtest

Class of the Permutation Tests (in C).

scatterutil

Graphical utility functions

score.coa

Reciprocal scaling after a correspondence analysis

phylog

Phylogeny

sco.boxplot

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

ours

A table of Qualitative Variables

piosphere

Plant traits response to grazing

scatter

Graphical representation of the outputs of a multivariate analysis

s.hist

Display of a scatterplot and its two marginal histograms

randtest-internal

Internal Permutation Tests functions (in C).

veuvage

Example for Centring in PCA

seconde

Students and Subjects

s.logo

Representation of an object in a graph by a picture

s.arrow

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

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

scatter.dudi

Plot of the Factorial Maps

suprow

Projections of Supplementary Rows

hdpg

Genetic Variation In Human Populations

area.plot

Graphical Display of Areas

yanomama

Distance Matrices

rtest.between

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

scatter.coa

Plot of the factorial maps for a correspondence analysis

ggtortoises

Microsatellites of Galapagos tortoises populations

t3012

Average temperatures of 30 French cities

supcol

Projections of Supplementary Columns

westafrica

Freshwater fish zoogeography in west Africa

withinpca

Normed within principal component analysis

withincoinertia

Within-class coinertia analysis

dist.dudi

Computation of the Distance Matrix from a Statistical Triplet

dist.ktab

Mixed-variables coefficient of distance

scalewt

Centring and Scaling a Matrix of Any Weighting

rtest

Class of the Permutation Tests (in R).

randtest.coinertia

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

kdist

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

ungulates

Phylogeny and quantitative traits of ungulates.

sepan

Separated Analyses in a K-tables

table.cont

Plot of Contingency Tables

woangers

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

rlq

RLQ analysis

ktab.within

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

triangle.class

Triangular Representation and Groups of points

zealand

Road distances in New-Zealand

mcoa

Multiple CO-inertia Analysis

mariages

Correspondence Analysis Table

procuste.randtest

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

sco.class

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

baran95

African Estuary Fishes

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

witwit.coa

Internal Correspondence Analysis