Ajout des aides

ProcMod.Rproj

@@ -18,4 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette

man/.gitignore

-*.Rd

man/AIC.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{AIC.pm}
+\alias{AIC.pm}
+\title{Compute the Akaike Information criterion (AIC) for a procruste model.}
+\usage{
+\method{AIC}{pm}(object, ..., k = length(object$coefficients))
+}
+\description{
+Compute the Akaike Information criterion (AIC) for a procruste model.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/BIC.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{BIC.pm}
+\alias{BIC.pm}
+\title{Compute the Bayesian Information criterion (BIC) for a procruste model.}
+\usage{
+\method{BIC}{pm}(object, ..., k = length(object$coefficients))
+}
+\description{
+Compute the Bayesian Information criterion (BIC) for a procruste model.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/as.procmod.frame.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/procmod.frame.R
+\name{as.procmod.frame}
+\alias{as.procmod.frame}
+\title{Coerce to a ProcMod Frame.}
+\usage{
+as.procmod.frame(data, ...)
+}
+\description{
+Coerce to a ProcMod Frame.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/as.procmod.frame.array.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/procmod.frame.R
+\name{as.procmod.frame.array}
+\alias{as.procmod.frame.array}
+\title{Coerce to a ProcMod Frame.}
+\usage{
+\method{as.procmod.frame}{array}(data, ...)
+}
+\description{
+Coerce to a ProcMod Frame.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/as.procmod.frame.list.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/procmod.frame.R
+\name{as.procmod.frame.list}
+\alias{as.procmod.frame.list}
+\title{Coerce to a ProcMod Frame.}
+\usage{
+\method{as.procmod.frame}{list}(data, ...)
+}
+\description{
+Coerce to a ProcMod Frame.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/as.procmod.frame.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/procmod.frame.R
+\name{as.procmod.frame.pm}
+\alias{as.procmod.frame.pm}
+\title{Coerce to a ProcMod Frame.}
+\usage{
+\method{as.procmod.frame}{pm}(data, ...)
+}
+\description{
+Coerce to a ProcMod Frame.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/as.procmod.frame.procmod.frame.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/procmod.frame.R
+\name{as.procmod.frame.procmod.frame}
+\alias{as.procmod.frame.procmod.frame}
+\title{Coerce to a ProcMod Frame.}
+\usage{
+\method{as.procmod.frame}{procmod.frame}(data, ...)
+}
+\description{
+Coerce to a ProcMod Frame.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/bicenter.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/multivariate.R
+\name{bicenter}
+\alias{bicenter}
+\title{Double centering of a matrix.}
+\usage{
+bicenter(m)
+}
+\description{
+colSums and rowSums of the returned matrix are all equal to zero.
+}
+\details{
+Inspired from the algorithm described in stackoverflow
+\url{https://stackoverflow.com/questions/43639063/double-centering-in-r}
+}

man/deviance.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{deviance.pm}
+\alias{deviance.pm}
+\title{Model Deviance for the procruste model.}
+\usage{
+\method{deviance}{pm}(object, ...)
+}
+\value{
+The value of the deviance extracted from the object object.
+}
+\description{
+Returns the deviance of a fitted model object.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/dim.procmod.frame.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/procmod.frame.R
+\name{dim.procmod.frame}
+\alias{dim.procmod.frame}
+\title{Dimensions of a Matrix Frame.}
+\usage{
+\method{dim}{procmod.frame}(x)
+}
+\description{
+Dimensions of a Matrix Frame.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/dist2orthospace.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/multivariate.R
+\name{dist2orthospace}
+\alias{dist2orthospace}
+\title{Project a distance matrix in a euclidean space.}
+\usage{
+dist2orthospace(distances, tol = 1e-07)
+}
+\description{
+Project a set of points defined by a distance matrix in
+an eucleadean space. If the used distance is a metric,
+this is done using the \code{\link[ProcMod]{pcoa}} function,
+otherwise the \code{\link[ProcMod]{nmds}} is used.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/extractAIC.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{extractAIC.pm}
+\alias{extractAIC.pm}
+\title{Compute the Akaike Information criterion (AIC) for a procruste model.}
+\usage{
+\method{extractAIC}{pm}(fit, scale, k = 2, ...)
+}
+\description{
+Compute the Akaike Information criterion (AIC) for a procruste model.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/formula.procmod.frame.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/formula.procmod.frame.R
+\name{formula.procmod.frame}
+\alias{formula.procmod.frame}
+\title{Build a formula from a procmod.frame.}
+\usage{
+\method{formula}{procmod.frame}(x, ...)
+}
+\description{
+Build a formula from a procmod.frame.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/getPermuteMatrix.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/anova.pm.R
+\name{getPermuteMatrix}
+\alias{getPermuteMatrix}
+\title{Generate permutation matrix according to a schema.}
+\usage{
+getPermuteMatrix(perm, N, strata = NULL)
+}
+\description{
+The permutation schema is defined using the `how` function.
+The implementation of this function is currectly extraced 
+from the VEGAN package and just copied pasted here to avoid
+dependency on an hidden vegan function.
+}

man/is.euclid.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/multivariate.R
+\name{is.euclid}
+\alias{is.euclid}
+\title{Test if the distance matrix is euclidean.}
+\usage{
+is.euclid(distances, tol = 1e-07)
+}
+\description{
+Actually a simplified version of the ADE4 implementation
+(\code{\link[ade4]{is.euclid}}).
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/is.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{is.pm}
+\alias{is.pm}
+\title{Tests that the object is as `pm` instance.}
+\usage{
+is.pm(obj)
+}
+\description{
+Tests that the object is as `pm` instance.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/is.procmod.frame.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/procmod.frame.R
+\name{is.procmod.frame}
+\alias{is.procmod.frame}
+\title{Check if an object is a Matrix Frame.}
+\usage{
+is.procmod.frame(x)
+}
+\description{
+Check if an object is a Matrix Frame.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/mcor.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mcov.R
+\name{mcor}
+\alias{mcor}
+\title{Compute the person correlation matrix of K coordinate matrices}
+\usage{
+mcor(...)
+}
+\description{
+Compute the person correlation matrix of K coordinate matrices
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/mcor.partial.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mcov.R
+\name{mcor.partial}
+\alias{mcor.partial}
+\title{Compute the person partial correlation matrix of K coordinate matrices}
+\usage{
+mcor.partial(...)
+}
+\description{
+Compute the person partial correlation matrix of K coordinate matrices
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/mvar.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mcov.R
+\name{mvar}
+\alias{mvar}
+\title{Compute the variance, covariance matrix of K coordinate matrices.}
+\usage{
+mvar(...)
+}
+\arguments{
+\item{...}{the set of matrices}
+}
+\description{
+Covariance between two matrices is defined as the sum of the
+sigular values of the X'Y matrix. All the matrices must have
+the same number of rows.
+}
+\examples{
+   # Build Three matrices of 3 rows.
+   A <- matrix(1:9,nrow=3)
+   B <- matrix(10:15,nrow=3)
+   C <- matrix(20:31,nrow=3)
+   # compute the variance covariance matrix
+   mvar(A,B,C)
+   mvar(A=A,B=B,C=C)
+
+}
+\author{
+Eric Coissac & Christelle Gonindard-Melodelima
+}

man/nmds.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/multivariate.R
+\name{nmds}
+\alias{nmds}
+\title{Project a distance matrix in a euclidean space (NMDS).}
+\usage{
+nmds(distances, maxit = 50, trace = TRUE, tol = 0.001, p = 2)
+}
+\description{
+Project a set of points defined by a distance matrix in
+an eucleadean space using the Kruskal's Non-metric
+Multidimensional Scaling. This function is mainly a simplified
+interface on the \code{\link[MASS]{isoMDS}} function using as
+much as possible dimensionsto limit the stress. The aims of this
+NDMS being only to project point in an orthogonal space therefore
+without any correlation between axis. Because a non-metric method
+is used no condition is required on the used distance.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/pca.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/multivariate.R
+\name{pca}
+\alias{pca}
+\title{Project a set of points in a euclidean space (PCA).}
+\usage{
+pca(data, scale = FALSE)
+}
+\description{
+Project a set of points in a euclidean space (PCA).
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/pcoa.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/multivariate.R
+\name{pcoa}
+\alias{pcoa}
+\title{Project a distance matrix in a euclidean space (PCOA).}
+\usage{
+pcoa(distances)
+}
+\description{
+Project a set of points defined by a distance matrix in
+an eucleadean space using the Principal Coordinates Analysis
+method. This function is mainly a simplified
+interface on the \code{\link[stats]{cmdscale}} function using as
+much as possible dimensions for the projection. The aims of this
+PCoA being only to project point in an orthogonal space therefore
+without any correlation between axis. Because a metric method
+is used the used distance must be euclidean
+(cf \code{\link[ProcMod]{is.euclid}}).
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/plot.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.pm.R
+\name{plot.pm}
+\alias{plot.pm}
+\title{Default plot function for `pm` objects.}
+\usage{
+\method{plot}{pm}(m, points.cex = 0.6, labels.cex = 0.6,
+  arrow.length = 0.05, asp = 1, ...)
+}
+\description{
+Default plot function for `pm` objects.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{pm}
+\alias{pm}
+\title{Performs a procruste model on a set of coordinate matrices}
+\usage{
+pm(formula, data, subset, weights, na.action, method = "qr",
+  singular.ok = TRUE, tol = 1e-07, model = TRUE, x = TRUE, y = TRUE,
+  A = TRUE)
+}
+\description{
+Performs a procruste model on a set of coordinate matrices
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/print.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{print.pm}
+\alias{print.pm}
+\title{Default display function for `pm` objects.}
+\usage{
+\method{print}{pm}(m, ...)
+}
+\description{
+Default display function for `pm` objects.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/procmod.frame.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/procmod.frame.R
+\name{procmod.frame}
+\alias{procmod.frame}
+\title{Build a procmod.frame data structure.}
+\usage{
+procmod.frame(..., row.names = NULL, check.rows = FALSE,
+  check.names = TRUE, reorder.rows = FALSE)
+}
+\description{
+Build a procmod.frame data structure.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/residuals.pm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{residuals.pm}
+\alias{residuals.pm}
+\title{Extract Model Residuals.}
+\usage{
+\method{residuals}{pm}(object, type = c("working", "response", "deviance",
+  "pearson", "partial"), ...)
+}
+\arguments{
+\item{type}{the type of residuals which should be returned.
+Can be abbreviated.}
+
+\item{obj}{R object of class `pm`}
+}
+\value{
+Numeric matrix of n rows, where n is the number
+        of observations.
+}
+\description{
+residuals is a generic function which extracts model
+             residuals from objects returned by modeling functions.
+             The abbreviated form resid is an alias for residuals.
+             It is intended to encourage users to access object
+             components through an accessor function rather than by
+             directly referencing an object slot.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/vars.procmod.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/model.procmod.R
+\name{vars.procmod}
+\alias{vars.procmod}
+\title{Plays the role of model.matrix in classical lm}
+\usage{
+vars.procmod(object, data = environment(object), xlev = NULL, ...)
+}
+\description{
+Plays the role of model.matrix in classical lm
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

man/weighted.residuals.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mprocuste.R
+\name{weighted.residuals}
+\alias{weighted.residuals}
+\title{Compute Weighted Residuals.}
+\usage{
+weighted.residuals(obj, drop0 = TRUE)
+}
+\arguments{
+\item{obj}{R object of class `pm`}
+
+\item{drop0}{logical. If `TRUE``, drop all cases with `weights` == 0.}
+}
+\value{
+Numeric matrix of n' rows, where n' is the number
+        of of non-0 weights (drop0 = TRUE) or
+        the number of observations, otherwise.
+}
+\description{
+Computed weighted residuals from a procrustean model fit.
+}
+\author{
+Eric Coissac
+
+Christelle Gonindard-Melodelima
+}

vignettes/Principes-francais.R

+## ----setup, include = FALSE----------------------------------------------
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+
+## ------------------------------------------------------------------------
+library(ProcMod)
+
+## ------------------------------------------------------------------------
+data("eukaryotes")
+data("bacteria")
+
+## ------------------------------------------------------------------------
+data("soil")
+data("climat")
+data("geography")
+
+## ------------------------------------------------------------------------
+library(vegan)
+
+bac.hellinger = decostand(bacteria,method ="hellinger")
+euk.hellinger = decostand(eukaryotes,method ="hellinger")
+
+## ------------------------------------------------------------------------
+bac.bray = vegdist(bac.hellinger,method = "bray")
+euk.bray = vegdist(euk.hellinger,method = "bray")
+
+## ------------------------------------------------------------------------
+soil.rescaled   = scale(soil,   center = TRUE, scale = TRUE)
+climat.rescaled = scale(climat, center = TRUE, scale = TRUE)
+
+## ------------------------------------------------------------------------
+data = procmod.frame(euk       = euk.bray,
+                     bac       = bac.bray,
+                     climat    = climat,
+                     soil      = soil,
+                     geography = geography)
+
+## ------------------------------------------------------------------------
+euk.pm = pm(formula = euk ~ soil + climat + geography, data = data)
+euk.pm
+
+## ------------------------------------------------------------------------
+plot(euk.pm)
+
+## ------------------------------------------------------------------------
+anova(euk.pm)
+