procmod_frame.Rd 2.5 KB
 Eric Coissac committed Jul 06, 2018 1 % Generated by roxygen2: do not edit by hand  Eric Coissac committed Apr 30, 2019 2 % Please edit documentation in R/procmod_frame.R  Eric Coissac committed Oct 01, 2019 3 4 5 \name{procmod_frame} \alias{procmod_frame} \title{The procmod_frame data structure.}  Eric Coissac committed Jul 06, 2018 6 \usage{  Eric Coissac committed Oct 01, 2019 7 procmod_frame(..., row.names = NULL, check.rows = TRUE,  Eric Coissac committed Oct 01, 2019 8 9 10 11  reorder.rows = TRUE, contrasts.arg = NULL) } \arguments{ \item{...}{a set of objects to aggregate into a  Eric Coissac committed Oct 01, 2019 12 \code{procmod_frame}. These objects can be  Eric Coissac committed Oct 01, 2019 13 14 15 16 17 numeric matrices, or dist objects. Every objects must have the same number of row.} \item{row.names}{a character vector containing names associated to each row.}  Eric Coissac committed Jul 09, 2018 18   Eric Coissac committed Oct 01, 2019 19 20 \item{check.rows}{a logical value. When set to \code{TRUE}, its default value, the number of row of every elements of the  Eric Coissac committed Oct 01, 2019 21 \code{procmod_frame} are tested for equality. Otherwise no  Eric Coissac committed Oct 01, 2019 22 check is done.}  Eric Coissac committed Jul 09, 2018 23   Eric Coissac committed Oct 01, 2019 24 25 \item{reorder.rows}{a logical value. When set to \code{TRUE}, its default value, every elements of the  Eric Coissac committed Oct 01, 2019 26 \code{procmod_frame} are reordered according to the \code{row.names}  Eric Coissac committed Oct 01, 2019 27 28 29 30 31 32 33 34 35 order. Otherwise nothing is done.} \item{contrasts.arg}{A list, whose entries are values (numeric matrices or character strings naming functions) to be used as replacement values for the contrasts replacement function and whose names are the names of columns of data containing factors.} } \value{  Eric Coissac committed Oct 01, 2019 36 a \code{procmod_frame} instance.  Eric Coissac committed Jul 06, 2018 37 38 } \description{  Eric Coissac committed Oct 01, 2019 39 40 A \code{procmod_frame} can be considered as the analog of a \code{data.frame} for vector data. In a \code{procmod_frame}  Eric Coissac committed Sep 12, 2019 41 42 43 44 45 each element, equivalent to a column in a \code{data.frame} is a numeric matrix or a distance matrix object (\code{dist}). Every element must describe the same number of individuals. Therefore every numeric matrix must have the same number of row (\code{nrow}) and every distance matrix must have the same size  Eric Coissac committed Oct 01, 2019 46 (\code{attr(d,"Size")}). A \code{procmod_frame} can simultaneously  Eric Coissac committed Sep 12, 2019 47 48 49 50 51 52 53 contain both types of data, numeric and distance matrix. } \examples{ library(vegan) data(bacteria) data(eukaryotes) data(soil)  Eric Coissac committed Jul 09, 2018 54   Eric Coissac committed Oct 01, 2019 55 dataset <- procmod_frame(euk = vegdist(decostand(eukaryotes,  Eric Coissac committed Sep 12, 2019 56 57 58 59 60 61 62 63 64 65 66 67  method = "hellinger"), method = "euclidean"), bac = vegdist(decostand(bacteria, method = "hellinger"), method = "euclidean"), soil = scale(soil, center = TRUE, scale = TRUE)) length(dataset) nrow(dataset) ncol(dataset) dataset\$euk  Eric Coissac committed Jul 09, 2018 68   Eric Coissac committed Jul 06, 2018 69 70 71 72 73 74 } \author{ Eric Coissac Christelle Gonindard-Melodelima }