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ade4 (version 1.5-2)

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

51,023

Version

1.5-2

License

GPL (>= 2)

Homepage

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

Maintainer

Simon Penel

Last Published

April 11th, 2013

Functions in ade4 (1.5-2)

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Amount of Evolutionary History

Representation of many quantitative variables in front of a phylogenetic tree

acacia

Spatial pattern analysis in plant communities

friday87

Faunistic K-tables

hdpg

Genetic Variation In Human Populations

bf88

Cubic Ecological Data

apqe

Apportionment of Quadratic Entropy

gridrowcol

Complete regular grid analysis

add.scatter

Add graphics to an existing plot

carni19

Phylogeny and quantative trait of carnivora

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

pcoscaled

Simplified Analysis in Principal Coordinates

humDNAm

human mitochondrial DNA restriction data

doubs

Pair of Ecological Tables

macon

Wine Tasting

aviurba

Ecological Tables Triplet

baran95

African Estuary Fishes

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

ecomor

Ecomorphological Convergence

ade4toR

Format Change Utility

bca.coinertia

Between-class coinertia analysis

bca

Between-Class Analysis

as.taxo

Taxonomy

divc

Rao's diversity coefficient also called quadratic entropy

bsetal97

Ecological and Biological Traits

RV.rtest

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

banque

Table of Factors

dudi.pca

Principal Component Analysis

costatis

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

Enzymatic polymorphism in Leuciscus cephalus

disc

Rao's dissimilarity coefficient

amova

Analysis of molecular variance

chatcat

Qualitative Weighted Variables

abouheif.eg

Phylogenies and quantitative traits from Abouheif

kplot.statis

Multiple Graphs of a STATIS Analysis

coleo

Table of Fuzzy Biological Traits

Tests of randomization between distances applied to 'kdist' objetcs

mantel.rtest

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

escopage

K-tables of wine-tasting

ardeche

Fauna Table with double (row and column) partitioning

RVdist.randtest

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

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

casitas

Enzymatic polymorphism in Mus musculus

mjrochet

Phylogeny and quantitative traits of teleos fishes

mcoa

Multiple CO-inertia Analysis

randtest

Class of the Permutation Tests (in C).

inertia.dudi

Statistics of inertia in a one-table analysis

dudi

Duality Diagram

ktab.data.frame

Creation of K-tables from a data frame

Deprecated functions

Deprecated functions in ade4

mdpcoa

Multiple Double Principal Coordinate Analysis

dudi.nsc

Non symmetric correspondence analysis

randtest.pcaiv

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

multispati.randtest

Multivariate spatial autocorrelation test (in C)

maples

Phylogeny and quantitative traits of flowers

lingoes

Transformation of a Distance Matrix for becoming Euclidean

genet

A class of data: tables of populations and alleles

arrival

Arrivals at an intensive care unit

chazeb

Charolais-Zebus

mstree

Minimal Spanning Tree

meaudret

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

bca.rlq

Between-Class RLQ analysis

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

newick.eg

Phylogenetic trees in Newick format

cnc2003

Frequenting movie theaters in France in 2003

woangers

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

njplot

Phylogeny and trait of bacteria

withincoinertia

Within-class coinertia analysis

rpjdl

Avifauna and Vegetation

dist.binary

Computation of Distance Matrices for Binary Data

within

Within-Class Analysis

dudi.acm

Multiple Correspondence Analysis

pap

Taxonomy and quantitative traits of carnivora

trichometeo

Pair of Ecological Data

rhone

Physico-Chemistry Data

randtest.amova

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

neig

Neighbourhood Graphs

suprow

Projections of Supplementary Rows

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

foucart

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

elec88

Electoral Data

dudi.mix

Ordination of Tables mixing quantitative variables and factors

dudi.fca

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

orthobasis

Orthonormal basis for orthonormal transform

dunedata

Dune Meadow Data

dotcircle

Representation of n values on a circle

sco.match

1D plot of a pair of numeric scores with labels

macroloire

Assemblages of Macroinvertebrates in the Loire River (France)

niche

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

randtest-internal

Internal Permutation Tests functions (in C).

mollusc

Faunistic Communities and Sampling Experiment

mantel.randtest

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

presid2002

Results of the French presidential elections of 2002

randtest.coinertia

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

discrimin.coa

Discriminant Correspondence Analysis

Allelic frequencies in ten honeybees populations at eight microsatellites loci

avimedi

Fauna Table for Constrained Ordinations

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

ktab.list.dudi

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

mld

Multi Level Decomposition of unidimensional data

rtest.discrimin

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

cailliez

Transformation to make Euclidean a distance matrix

pta

Partial Triadic Analysis of a K-tables

meau

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

sco.distri

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

sarcelles

Array of Recapture of Rings

optimEH

Nee and May's optimizing process

ungulates

Phylogeny and quantitative traits of ungulates.

rtest.between

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

taxo.eg

Examples of taxonomy

bacteria

Genomes of 43 Bacteria

table.paint

Plot of the arrays by grey levels

butterfly

Genetics-Ecology-Environment Triple

cca

Canonical Correspondence Analysis

housetasks

Contingency Table

dist.dudi

Computation of the Distance Matrix from a Statistical Triplet

atya

Genetic variability of Cacadors

carni70

Phylogeny and quantitative traits of carnivora

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

dudi.dec

Decentred Correspondence Analysis

dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

scatterutil

Graphical utility functions

kdist2ktab

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

s.arrow

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

ktab.match2ktabs

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

ktab.within

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

t3012

Average temperatures of 30 French cities

worksurv

French Worker Survey (1970)

dpcoa

Double principal coordinate analysis

ours

A table of Qualitative Variables

originality

Originality of a species

Import data files from Phylogenetic Independance Package

procella

Phylogeny and quantitative traits of birds

s.kde2d

Scatter Plot with Kernel Density Estimate

gearymoran

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

procuste.randtest

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

randEH

Nee and May's random process

yanomama

Distance Matrices

between

Between-Class Analysis

lizards

Phylogeny and quantitative traits of lizards

ggtortoises

Microsatellites of Galapagos tortoises populations

kdisteuclid

a way to obtain Euclidean distance matrices

toxicity

Homogeneous Table

lascaux

Genetic/Environment and types of variables

krandtest

Class of the Permutation Tests (in C).

s.match.class

Scatterplot of two sets of coordinates and a partionning into classes

procuste

Simple Procruste Rotation between two sets of points

sco.boxplot

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

dist.prop

Computation of Distance Matrices of Percentage Data

westafrica

Freshwater fish zoogeography in west Africa

santacatalina

Indirect Ordination

s.image

Graph of a variable using image and contour

Phylogenetic and quantitative traits of amazonian palm trees

randtest.between

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

seconde

Students and Subjects

table.phylog

Plot arrays in front of a phylogenetic tree

score

Graphs for One Dimension

deug

Exam marks for some students

tithonia

Phylogeny and quantitative traits of flowers

syndicats

Two Questions asked on a Sample of 1000 Respondents

s.logo

Representation of an object in a graph by a picture

tintoodiel

Tinto and Odiel estuary geochemistry

divcmax

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

rankrock

Ordination Table

is.euclid

Is a Distance Matrix Euclidean ?

scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

mfa

Multiple Factorial Analysis

orisaved

Maximal or minimal amount of originality saved under optimal conditions

s.distri

Plot of a frequency distribution

variance.phylog

The phylogenetic ANOVA

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

supcol

Projections of Supplementary Columns

scatter.coa

Plot of the factorial maps for a correspondence analysis

multispati.rtest

Multivariate spatial autocorrelation test

dudi.pco

Principal Coordinates Analysis

quasieuclid

Transformation of a distance matrice to a Euclidean one

triangle.class

Triangular Representation and Groups of points

testdim

Function to perform a test of dimensionality

witwit.coa

Internal Correspondence Analysis

granulo

Granulometric Curves

s.hist

Display of a scatterplot and its two marginal histograms

microsatt

Genetic Relationships between cattle breeds with microsatellites

sco.gauss

Relationships between one score and qualitative variables

fuzzygenet

Reading a table of genetic data (diploid individuals)

jv73

K-tables Multi-Regions

orthogram

Orthonormal decomposition of variance

procuste.rtest

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

scatter.dudi

Plot of the Factorial Maps

score.mix

Graphs to Analyse a factor in a Mixed Analysis

plot.phylog

Plot phylogenies

steppe

Transect in the Vegetation

scatter

Graphical representation of the outputs of a multivariate analysis

ecg

Electrocardiogram data

sepan

Separated Analyses in a K-tables

s.class

Plot of factorial maps with representation of point classes

statis

STATIS, a method for analysing K-tables

kdist

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

s.multinom

Graph of frequency profiles (useful for instance in genetic)

score.pca

Graphs to Analyse a factor in PCA

morphosport

Athletes' Morphology

ktab.list.df

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

s.traject

Trajectory Plot

nipals

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

s.value

Representation of a value in a graph

Reconstitution of Data from a Duality Diagram

statico

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

vegtf

Vegetation in Trois-Fontaines

table.dist

Graph Display for Distance Matrices

pcaiv

Principal component analysis with respect to instrumental variables

scalewt

Centring and Scaling a Matrix of Any Weighting

ichtyo

Point sampling of fish community

mafragh

Phyto-Ecological Survey

sco.label

1D plot of a numeric score with labels

table.cont

Plot of Contingency Tables

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

s.chull

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

atlas

Small Ecological Dataset

withinpca

Normed within principal component analysis

mariages

Correspondence Analysis Table

wca.rlq

Within-Class RLQ analysis

score.coa

Reciprocal scaling after a correspondence analysis

olympic

Olympic Decathlon

skulls

Morphometric Evolution

Morphological Study of the Painted Turtle

rhizobium

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

zealand

Road distances in New-Zealand

s.match

Plot of Paired Coordinates

uniquewt.df

Elimination of Duplicated Rows in a Array

aminoacyl

Codon usage

avijons

Bird species distribution

bicenter.wt

Double Weighted Centring

buech

Buech basin

discrimin

Linear Discriminant Analysis (descriptive statistic)

dist.quant

Computation of Distance Matrices on Quantitative Variables

dist.ktab

Mixed-variables coefficient of distance

fourthcorner

Functions to compute the fourth-corner statistic

area.plot

Graphical Display of Areas

kcponds

Ponds in a nature reserve

ktab

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

multispati

Multivariate spatial analysis

coinertia

Coinertia Analysis

sco.class

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

corvus

Corvus morphology

dist.genet

Genetic distances from gene frequencies

dudi.coa

Correspondence Analysis

fission

Fission pattern and heritable morphological traits

monde84

Global State of the World in 1984

piosphere

Plant traits response to grazing

randtest.discrimin

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

perthi02

Contingency Table with a partition in Molecular Biology

rtest

Class of the Permutation Tests (in R).

s.corcircle

Plot of the factorial maps of a correlation circle

triangle.plot

Triangular Plotting

wca

Within-Class Analysis

veuvage

Example for Centring in PCA