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# Author: Babak Naimi, naimi.b@gmail.com
# Date : June 2014
# Version 1.0
# Licence GPL v3
setMethod ('show' , 'singleSpecies',
function ( object ) {
cat('class :' , class(object), '\n')
cat('===========================================================','\n')
cat('species name : ' , object@train@Occurrence@species.name , '\n')
cat('number of fearures : ' , if (!is.null(object@train@Features)) length(object@train@Features@featureNames) else NA, '\n')
cat('fearure names : ' , if (!is.null(object@train@Features)) {
if (length(object@train@Features@featureNames) > 3) paste(c(object@train@Features@featureNames[1:3],'...'),collapse=', ') else paste(object@train@Features@featureNames,collapse=', ')
} else NA, '\n')
cat('type : ' , if (object@train@Occurrence@presence.only) 'presence-only' else 'presence-absence', '\n')
cat('number of observations (train) : ', length(object@train@Occurrence@Occurrence),'\n')
cat('has independet test data? : ' , !is.null(object@test), '\n')
if (!is.null(object@test))
cat('number of observations (test) : ', length(object@test@Occurrence@Occurrence),'\n' )
cat('has Coordinates? : ' , !is.null(object@train@coordinates) , '\n')
}
)
setMethod ('show' , 'multipleSpecies',
function ( object ) {
cat('class :' , class(object), '\n')
cat('===========================================================','\n')
cat('number of species : ' , length(object@train@Occurrence@species.names), '\n')
cat('species names : ' , if (length(object@train@Occurrence@species.names) > 3) paste(c(object@train@Occurrence@species.names[1:3],'...'),collapse=', ') else paste(object@train@Occurrence@species.names,collapse=', ') , '\n')
cat('number of fearures : ' , if (!is.null(object@train@Features)) length(object@train@Features@featureNames) else NA, '\n')
cat('fearure names : ' , if (!is.null(object@train@Features)) {
if (length(object@train@Features@featureNames) > 3) paste(c(object@train@Features@featureNames[1:3],'...'),collapse=', ') else paste(object@train@Features@featureNames,collapse=', ')
} else NA, '\n')
cat('type : ' ,
if (all(object@train@Occurrence@presence.only)) 'presence-only'
else if (all(!object@train@Occurrence@presence.only)) 'presence-absence'
else 'presence-absence AND presence-only', '\n')
cat('number of observations (train) : ', nrow(object@train@Occurrence@Occurrence),'\n')
cat('has independet test data? : ' , if (is.null(object@test)) FALSE
else if (all(unlist(lapply(object@train@Occurrence@species.names,function(x) {x %in% object@test@Occurrence@species.names})))) TRUE
else paste('Only ',length(object@test@Occurrence@species.names),' species have test data!',sep=''),'\n' )
if (!is.null(object@test))
cat('number of observations (test) : ', nrow(object@test@Occurrence@Occurrence),'\n' )
cat('has Coordinates? : ' , !is.null(object@train@coordinates) , '\n')
}
)
#-------------
setMethod ('show' , 'SpeciesDataList',
function ( object ) {
cat('class :' , class(object), '\n')
cat('===========================================================','\n')
cat('number of species : ' , length(object@train@species.names), '\n')
cat('species names : ' , if (length(object@train@species.names) > 3) paste(c(object@train@species.names[1:3],'...'),collapse=', ') else paste(object@train@species.names,collapse=', ') , '\n')
cat('number of fearures : ' , if (!is.null(object@train@SpeciesDataList[[1]]@Features)) length(object@train@SpeciesDataList[[1]]@Features@featureNames) else NA, '\n')
cat('fearure names : ' , if (!is.null(object@train@SpeciesDataList[[1]]@Features)) {
if (length(object@train@SpeciesDataList[[1]]@Features@featureNames) > 3) paste(c(object@train@SpeciesDataList[[1]]@Features@featureNames[1:3],'...'),collapse=', ') else paste(object@train@SpeciesDataList[[1]]@Features@featureNames,collapse=', ')
} else NA, '\n')
cat('type : ' ,
if (all(unlist(lapply(object@train@SpeciesDataList,function(x) {x@Occurrence@presence.only})))) 'presence-only'
else if (all(!unlist(lapply(object@train@SpeciesDataList,function(x) {x@Occurrence@presence.only})))) 'presence-absence'
else 'presence-absence AND presence-only', '\n')
cat('number of observations (train) : ', if (length(object@train@species.names) > 6) paste(c(unlist(lapply(object@train@SpeciesDataList,function(x) {length(x@Occurrence@Occurrence)}))[1:6],'...'),collapse=', ')
else paste(unlist(lapply(object@train@SpeciesDataList,function(x) {length(x@Occurrence@Occurrence)})),collapse=', ') ,'\n')
cat('has independet test data? : ' , if (is.null(object@test)) FALSE
else if (all(unlist(lapply(object@train@species.names,function(x) {x %in% object@test@species.names})))) TRUE
else paste('Only ',length(object@test@species.names),' species have test data!',sep=''),'\n' )
if (!is.null(object@test))
cat('number of observations (test) : ', nrow(object@test@Occurrence@Occurrence),'\n' )
cat('has Coordinates? : ' , !is.null(object@train@SpeciesDataList[[1]]@coordinates) , '\n')
}
)
#---------
setMethod ('show' , 'sdmSettings',
function (object) {
cv.n <- 1
r.n <- 1
r <- 1
cat('class :' , class(object), '\n')
cat('========================================================','\n')
cat('modelling methods : ' , paste(object@methods,collapse=', '), '\n')
sn <- strsplit(as.character(object@basicSettings@formula[2]),'\\+')[[1]]
cat('species names : ' , if (length(sn) > 3) paste(length(sn),'species including:',paste(c(sn,'...'),collapse=', ')) else paste(sn,collapse=', '), '\n')
cat('feature names : ' , if (length(object@basicSettings@featureNames) > 3) paste(length(object@basicSettings@featureNames),'variables including:',paste(c(object@basicSettings@featureNames[1:3],'...'),collapse=', ')) else paste(object@basicSettings@featureNames,collapse=', '), '\n')
cat('feature types : ' , paste(.ftype_names(object@basicSettings@feature.types),collapse=', '), '\n')
if (!is.null(object@basicSettings@replicates)) {
r.n <- length(object@basicSettings@replicates@method)
r <- object@basicSettings@replicates@n.replicates
cat('replicate.methods (data partitioning) : ' , paste(object@basicSettings@replicates@method,collapse=','), '\n')
cat('test percentage : ' , object@basicSettings@test.percentage, '\n')
cat('number of replicates (each method) : ' , r, '\n')
if ("cross-validation" %in% object@basicSettings@replicates@method) {
cv.n <- length(unique(object@basicSettings@replicates@fold$'cross-validation'))
cat('n.folds in cross-validation : ' ,cv.n , '\n')
}
}
n <- r * (r.n-1+cv.n)
cat('------------------------------------------\n')
cat('number of runs : ' , paste(n,' for each model, ',n*length(object@methods),' in total... (per species)' ,sep=''), '\n')
}
)
#---------------------
setMethod ('show' , 'sdmModel',
function (object) {
cv.n <- 1
r.n <- 1
r <- 1
nn <- names(object@data)
cat('class :' , class(object), '\n')
cat('========================================================','\n')
cat('number of species : ' , length(nn), '\n')
cat('number of modelling methods : ' , length(object@settings@methods), '\n')
cat('names of modelling methods : ' , paste(object@settings@methods,collapse=', '), '\n')
if (!is.null(object@settings@basicSettings@replicates)) {
r.n <- length(object@settings@basicSettings@replicates@method)
r <- object@settings@basicSettings@replicates@n.replicates
if ("cross-validation" %in% object@settings@basicSettings@replicates@method) {
cv.n <- length(unique(object@settings@basicSettings@replicates@fold$'cross-validation'))
#cat('n.folds in cross-validation : ' ,cv.n , '\n')
}
n <- r * (r.n-1+cv.n)
cat('number of simulations per model : ' , paste(n,'(per species)'), '\n')
cat('replicate.methods (data partitioning) : ' , paste(object@settings@basicSettings@replicates@method,collapse=','), '\n')
cat('number of replicates (each method) : ' , r, '\n')
cat('test percentage : ' , object@settings@basicSettings@test.percentage, '\n')
cat('---------------------------------------\n')
cat('run success percentage (all species) :\n')
cat('---------------------------------------\n')
p2 <- function(x) {
o <- rep(NA,length(nn))
for (i in seq_along(nn)) {
o[i] <- (length(which(object@models@multiModelList[[nn[i]]]@modelList[[x]]@run.success))/n)*100
}
o
}
for (i in seq_along(object@settings@methods)) {
cat(paste(object@settings@methods[i],paste(rep(' ',8 - length(unlist(strsplit(object@settings@methods[i],'')))),collapse=''),' : ',paste(rep(' ',10),collapse=''),sep='') , mean(p2(object@settings@methods[i])), '%\n')
}
}
if (!is.null(object@models@multiModelList[[1]]@modelList[[1]]@modelObjectList) || !is.null(object@models@multiModelList[[1]]@modelList[[1]]@independent.evaluationList)) {
cat('---------------------------------------\n')
cat('average performance (all species) :\n')
cat('---------------------------------------\n')
p <- function(x,n) {
apply(.getPerformance(object,x,species = n)[[1]],2,function(x) mean(x,na.rm=TRUE))
}
#o <- data.frame(matrix(ncol=4,nrow=length(object@settings@methods)))
#colnames(o) <- c('method',)
cat(paste('methods',paste(rep(' ',3),collapse=''),' : ',paste(rep(' ',3),collapse=''),sep='') , paste(c('AUC','COR','TSS'),collapse=' | '), '\n')
cat('------------------------------------------\n')
for (i in seq_along(object@settings@methods)) {
o <- rep(0,3)
k <- 0
for (j in seq_along(nn)) {
w <- try(p(object@settings@methods[i],nn[j]),silent=TRUE)
if (!inherits(w,'try-error')) {
o <- o + w
k <- k + 1
}
}
if (k > 0) {
o <- o / k
cat(paste(object@settings@methods[i],paste(rep(' ',10 - length(unlist(strsplit(object@settings@methods[i],'')))),collapse=''),' : ',paste(rep(' ',3),collapse=''),sep='') , paste(round(o,3),collapse=' | '), '\n')
} else {
cat(paste(object@settings@methods[i],paste(rep(' ',10 - length(unlist(strsplit(object@settings@methods[i],'')))),collapse=''),' : ',paste(rep(' ',3),collapse=''),sep='') , paste(rep('---',3),collapse=' | '), '\n')
}
}
}
}
)
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