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ade4 (version 1.6-2)

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

47,387

Version

1.6-2

License

GPL (>= 2)

Homepage

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

Maintainer

Simon Penel

Last Published

November 20th, 2013

Functions in ade4 (1.6-2)

avijons

Bird species distribution

neig

Neighbourhood Graphs

dotcircle

Representation of n values on a circle

pcaiv

Principal component analysis with respect to instrumental variables

table.value

Plot of the Arrays

Amount of Evolutionary History

banque

Table of Factors

ardeche

Fauna Table with double (row and column) partitioning

costatis

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

add.scatter

Add graphics to an existing plot

acacia

Spatial pattern analysis in plant communities

bca.rlq

Between-Class RLQ analysis

dudi.nsc

Non symmetric correspondence analysis

disc

Rao's dissimilarity coefficient

is.euclid

Is a Distance Matrix Euclidean ?

RV.rtest

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

PI2newick

Import data files from Phylogenetic Independance Package

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

foucart

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

atlas

Small Ecological Dataset

butterfly

Genetics-Ecology-Environment Triple

divc

Rao's diversity coefficient also called quadratic entropy

aviurba

Ecological Tables Triplet

bordeaux

Wine Tasting

atya

Genetic variability of Cacadors

genet

A class of data: tables of populations and alleles

coinertia

Coinertia Analysis

cailliez

Transformation to make Euclidean a distance matrix

discrimin

Linear Discriminant Analysis (descriptive statistic)

dudi.pco

Principal Coordinates Analysis

clementines

Fruit Production

divcmax

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

avimedi

Fauna Table for Constrained Ordinations

fruits

Pair of Tables

discrimin.coa

Discriminant Correspondence Analysis

cca

Canonical Correspondence Analysis

Deprecated functions

Deprecated functions in ade4

fission

Fission pattern and heritable morphological traits

deug

Exam marks for some students

randtest.pcaiv

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

dudi.acm

Multiple Correspondence Analysis

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

casitas

Enzymatic polymorphism in Mus musculus

ktab.list.df

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

buech

Buech basin

dist.dudi

Computation of the Distance Matrix from a Statistical Triplet

mld

Multi Level Decomposition of unidimensional data

ade4-internal

Internal ade4 functions

macaca

Landmarks

abouheif.eg

Phylogenies and quantitative traits from Abouheif

dist.prop

Computation of Distance Matrices of Percentage Data

between

Between-Class Analysis

dist.ktab

Mixed-variables coefficient of distance

mariages

Correspondence Analysis Table

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

jv73

K-tables Multi-Regions

dudi

Duality Diagram

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

olympic

Olympic Decathlon

mcoa

Multiple CO-inertia Analysis

carni19

Phylogeny and quantative trait of carnivora

meaudret

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

mantel.randtest

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

fuzzygenet

Reading a table of genetic data (diploid individuals)

inertia.dudi

Statistics of inertia in a one-table analysis

perthi02

Contingency Table with a partition in Molecular Biology

kdist2ktab

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

hdpg

Genetic Variation In Human Populations

escopage

K-tables of wine-tasting

gridrowcol

Complete regular grid analysis

bsetal97

Ecological and Biological Traits

Ordination of Tables mixing quantitative variables and factors

ktab.within

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

morphosport

Athletes' Morphology

scatter.dudi

Plot of the Factorial Maps

ecomor

Ecomorphological Convergence

amova

Analysis of molecular variance

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

bca

Between-Class Analysis

Genetic distances from gene frequencies

aravo

Distribution of Alpine plants in Aravo (Valloire, France)

baran95

African Estuary Fishes

chatcat

Qualitative Weighted Variables

bca.coinertia

Between-class coinertia analysis

dist.quant

Computation of Distance Matrices on Quantitative Variables

kcponds

Ponds in a nature reserve

dudi.fca

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

gearymoran

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

coleo

Table of Fuzzy Biological Traits

cnc2003

Frequenting movie theaters in France in 2003

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

apqe

Apportionment of Quadratic Entropy

dudi.coa

Correspondence Analysis

ktab.match2ktabs

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

ade4-package

The ade4 package

mdpcoa

Multiple Double Principal Coordinate Analysis

humDNAm

human mitochondrial DNA restriction data

macon

Wine Tasting

dudi.pca

Principal Component Analysis

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

ade4toR

Format Change Utility

Arrivals at an intensive care unit

bacteria

Genomes of 43 Bacteria

Pair of Ecological Data

chevaine

Enzymatic polymorphism in Leuciscus cephalus

area.plot

Graphical Display of Areas

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

bicenter.wt

Double Weighted Centring

bf88

Cubic Ecological Data

elec88

Electoral Data

multispati.randtest

Multivariate spatial autocorrelation test (in C)

nipals

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

irishdata

Geary's Irish Data

procella

Phylogeny and quantitative traits of birds

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

palm

Phylogenetic and quantitative traits of amazonian palm trees

score.coa

Reciprocal scaling after a correspondence analysis

veuvage

Example for Centring in PCA

scatter.coa

Plot of the factorial maps for a correspondence analysis

randtest.between

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

s.logo

Representation of an object in a graph by a picture

euro123

Triangular Data

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

s.arrow

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

carni70

Phylogeny and quantitative traits of carnivora

s.chull

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

rtest

Class of the Permutation Tests (in R).

ecg

Electrocardiogram data

oribatid

Oribatid mite

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

s.match

Plot of Paired Coordinates

randtest.coinertia

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

procuste.randtest

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

kdisteuclid

a way to obtain Euclidean distance matrices

dpcoa

Double principal coordinate analysis

table.cont

Plot of Contingency Tables

randtest.discrimin

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

kplot.statis

Multiple Graphs of a STATIS Analysis

orthogram

Orthonormal decomposition of variance

dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph

pta

Partial Triadic Analysis of a K-tables

tortues

Morphological Study of the Painted Turtle

multispati.rtest

Multivariate spatial autocorrelation test

yanomama

Distance Matrices

pap

Taxonomy and quantitative traits of carnivora

fourthcorner

Functions to compute the fourth-corner statistic

sco.distri

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

maples

Phylogeny and quantitative traits of flowers

withincoinertia

Within-class coinertia analysis

within

Within-Class Analysis

monde84

Global State of the World in 1984

presid2002

Results of the French presidential elections of 2002

niche

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

statico

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

variance.phylog

The phylogenetic ANOVA

s.kde2d

Scatter Plot with Kernel Density Estimate

ours

A table of Qualitative Variables

score

Graphs for One Dimension

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

s.label

Scatter Plot

table.paint

Plot of the arrays by grey levels

randtest.amova

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

s.corcircle

Plot of the factorial maps of a correlation circle

rlq

RLQ analysis

krandtest

Class of the Permutation Tests (in C).

rtest.discrimin

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

table.phylog

Plot arrays in front of a phylogenetic tree

suprow

Projections of Supplementary Rows

granulo

Granulometric Curves

mfa

Multiple Factorial Analysis

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

lascaux

Genetic/Environment and types of variables

ichtyo

Point sampling of fish community

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

lingoes

Transformation of a Distance Matrix for becoming Euclidean

phylog

Phylogeny

sco.label

1D plot of a numeric score with labels

mjrochet

Phylogeny and quantitative traits of teleos fishes

rtest.between

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

scatter

Graphical representation of the outputs of a multivariate analysis

mstree

Minimal Spanning Tree

dist.binary

Computation of Distance Matrices for Binary Data

taxo.eg

Examples of taxonomy

s.distri

Plot of a frequency distribution

multispati

Multivariate spatial analysis

s.hist

Display of a scatterplot and its two marginal histograms

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

rhone

Physico-Chemistry Data

kdist

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

julliot

Seed dispersal

ktab.data.frame

Creation of K-tables from a data frame

newick.eg

Phylogenetic trees in Newick format

withinpca

Normed within principal component analysis

orisaved

Maximal or minimal amount of originality saved under optimal conditions

orthobasis

Orthonormal basis for orthonormal transform

pcoscaled

Simplified Analysis in Principal Coordinates

ktab

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

mafragh

Phyto-Ecological Survey

s.value

Representation of a value in a graph

sco.boxplot

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

doubs

Pair of Ecological Tables

piosphere

Plant traits response to grazing

t3012

Average temperatures of 30 French cities

triangle.plot

Triangular Plotting

skulls

Morphometric Evolution

testdim

Function to perform a test of dimensionality

scalewt

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

mantel.rtest

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

dudi.dec

Decentred Correspondence Analysis

sco.class

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

ggtortoises

Microsatellites of Galapagos tortoises populations

originality

Originality of a species

s.class

Plot of factorial maps with representation of point classes

lizards

Phylogeny and quantitative traits of lizards

wca.rlq

Within-Class RLQ analysis

supcol

Projections of Supplementary Columns

randtest

Class of the Permutation Tests (in C).

s.match.class

Scatterplot of two sets of coordinates and a partionning into classes

sco.gauss

Relationships between one score and qualitative variables

s.multinom

Graph of frequency profiles (useful for instance in genetic)

seconde

Students and Subjects

westafrica

Freshwater fish zoogeography in west Africa

score.pca

Graphs to Analyse a factor in PCA

tarentaise

Mountain Avifauna

uniquewt.df

Elimination of Duplicated Rows in a Array

witwit.coa

Internal Correspondence Analysis

njplot

Phylogeny and trait of bacteria

procuste

Simple Procruste Rotation between two sets of points

macroloire

Assemblages of Macroinvertebrates in the Loire River (France)

rpjdl

Avifauna and Vegetation

s.traject

Trajectory Plot

steppe

Transect in the Vegetation

vegtf

Vegetation in Trois-Fontaines

procuste.rtest

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

scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis

randEH

Nee and May's random process

wca

Within-Class Analysis

rhizobium

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

tithonia

Phylogeny and quantitative traits of flowers

triangle.class

Triangular Representation and Groups of points

table.dist

Graph Display for Distance Matrices

sco.match

1D plot of a pair of numeric scores with labels

sepan

Separated Analyses in a K-tables

woangers

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

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

ungulates

Phylogeny and quantitative traits of ungulates.

ktab.list.dudi

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

zealand

Road distances in New-Zealand

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

corvus

Corvus morphology

worksurv

French Worker Survey (1970)

reconst

Reconstitution of Data from a Duality Diagram

meau

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

syndicats

Two Questions asked on a Sample of 1000 Respondents

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

optimEH

Nee and May's optimizing process

quasieuclid

Transformation of a distance matrice to a Euclidean one

microsatt

Genetic Relationships between cattle breeds with microsatellites

tintoodiel

Tinto and Odiel estuary geochemistry

mollusc

Faunistic Communities and Sampling Experiment

Graph of a variable using image and contour

scatterutil

Graphical utility functions

statis

STATIS, a method for analysing K-tables

score.mix

Graphs to Analyse a factor in a Mixed Analysis

santacatalina

Indirect Ordination

sarcelles

Array of Recapture of Rings