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# Author: Babak Naimi, naimi.b@gmail.com
# Date : June 2014
# Version 2.1
# Licence GPL v3
setClassUnion("vectorORnull", c("vector", "NULL"))
setClassUnion("characterORnull", c("character", "NULL"))
setClassUnion("CRSorNULL", c("CRS", "NULL"))
setClassUnion("formulaORnull", c("formula", "NULL"))
setClassUnion("numericORnull", c("numeric", "NULL"))
setClassUnion("characterORmissing", c("character", "missing"))
setClassUnion("listORnull", c("list", "NULL"))
setClass(".Index",
representation(
index.name = 'character',
ID='numeric',
time='vectorORnull'
),
prototype(
index.name = '',
ID=c(),
time=NULL
),
validity = function(object) {
return(TRUE)
}
)
#-------
setClass(".Occurrence",
representation(
species.name = 'character',
Occurrence='vector',
index='.Index',
presence.only='logical',
pseudo.absense.index='numericORnull',
pseudo.absense.replicates='numericORnull',
pseudo.absence.method='characterORnull' # if length=1, the same method used for all replicates, otherwise, the first item is for first replicate, and so on
),
prototype(
species.name = '',
pseudo.absense.index=NULL,
pseudo.absense.replicates=NULL,
pseudo.absence.method=NULL
),
validity = function(object) {
return(length(object@Occurrence) == length(object@index@ID))
}
)
#-------
setClass(".multipleOccurrence",
representation(
species.names = 'character',
Occurrence='matrix',
index='.Index',
time='vectorORnull',
presence.only='logical',
pseudo.absense.index='numericORnull',
pseudo.absense.replicates='numericORnull',
pseudo.absence.method='characterORnull'
),
prototype(
time=NULL,
pseudo.absense.index=NULL,
pseudo.absense.replicates=NULL,
pseudo.absence.method=NULL
),
validity = function(object) {
return(nrow(object@Occurrence) == length(object@index@ID))
}
)
#-------
setClass(".Features",
representation(
featureNames = 'character',
factors='characterORnull',
features='data.frame',
index='.Index'
),
prototype(
featureNames = '',
factors=NULL
),
validity = function(object) {
v1 <- ncol(object@features) == length(object@featureNames)
v2 <- nrow(object@features) == length(object@index@ID)
v3 <- TRUE
if (!is.null(object@factors)) v3 <- all(unlist(lapply(object@factors,function(x) {is.factor(object@features[,x])})))
return(v1 & v2 & v3)
}
)
#-------------
setClass(".coords",
representation(
coords = 'matrix',
index='.Index',
crs='CRSorNULL'
),
prototype(
crs=NULL
),
validity = function(object) {
return(nrow(object@coords) == length(object@index@ID))
}
)
#-------
setClassUnion(".IndexORnull", c(".Index", "NULL"))
setClassUnion(".coordsORnull", c(".coords", "NULL"))
setClassUnion(".FeaturesORnull", c(".Features", "NULL"))
setClass(".singleSpeciesData",
representation(
Occurrence='.Occurrence',
Features='.FeaturesORnull',
coordinates='.coordsORnull'
),
prototype(
Features=NULL,
coordinates=NULL
),
validity = function(object) {
v1 <- v2 <- TRUE
if (!is.null(object@Features)) v1 <- validObject(object@Features)
if(!is.null(object@coordinates)) v2 <- validObject(object@coordinates)
return(validObject(object@Occurrence) & v1 & v2)
}
)
#-------
setClass(".multipleSpeciesData",
representation(
Occurrence='.multipleOccurrence',
Features='.FeaturesORnull',
coordinates='.coordsORnull'
),
prototype(
Features=NULL,
coordinates=NULL
),
validity = function(object) {
v1 <- v2 <- TRUE
if (!is.null(object@Features)) v1 <- validObject(object@Features)
if(!is.null(object@coordinates)) v2 <- validObject(object@coordinates)
return(validObject(object@Occurrence) & v1 & v2)
}
)
#--------------
setClass(".SpeciesDataList",
representation(
species.names='character',
SpeciesDataList='list'
),
validity = function(object) {
return(TRUE)
}
)
#-----------
setClass(".FileSDMdata",
representation(
name='character',
keepRasters='logical',
RasterFile='character'
),
prototype(
name='',
keepRasters=FALSE,
RasterFile=''
)
)
#--------
setClassUnion(".singleSpeciesDataORnull", c(".singleSpeciesData", "NULL"))
setClassUnion(".multipleSpeciesDataORnull", c(".multipleSpeciesData", "NULL"))
setClassUnion(".SpeciesDataListORnull", c(".SpeciesDataList", "NULL"))
#-------
setClass("singleSpecies",
representation(
train='.singleSpeciesData',
test='.singleSpeciesDataORnull'
),
prototype(
test=NULL
),
validity = function(object) {
v1 <- TRUE
if (!is.null(object@test)) v1 <- validObject(object@test)
return(validObject(object@train) & v1)
}
)
#--------
setClass("multipleSpecies",
representation(
train='.multipleSpeciesData',
test='.multipleSpeciesDataORnull'
),
prototype(
test=NULL
),
validity = function(object) {
v1 <- TRUE
if (!is.null(object@test)) v1 <- validObject(object@test)
return(validObject(object@train) & v1)
}
)
#--------
setClass("SpeciesDataList",
representation(
train='.SpeciesDataList',
test='.SpeciesDataListORnull'
),
prototype(
test=NULL
),
validity = function(object) {
v1 <- TRUE
if (!is.null(object@test)) v1 <- validObject(object@test)
return(validObject(object@train) & v1)
}
)
setClassUnion("speciesData", c("singleSpecies", "multipleSpecies", "SpeciesDataList"))
#---------
#############
#------------
# setClass(".modelSettings",
# representation(
# models='character',
# modelSettings='list'
# ),
# prototype(
# models=c(),
# modelSettings=list()
# ),
# validity=function(object) {
# return(sort(models) == sort(names(modelSettings) ))
# }
# )
#---------
#
# setClass(".featureSettings",
# representation(
# featureNames='character',
# feature.types='character',
# interaction.depth='numeric',
# formula='formulaORnull'
# ),
# prototype(
# featureNames=c(),
# feature.types='auto',
# interaction.depth=1,
# formula=NULL
# ),
# validity=function(object) {
# return(TRUE)
# }
# )
# #-----
# setClassUnion(".featureSettingsORnull", c(".featureSettings", "NULL"))
#------
setClass(".pseudo.absence",
representation(
method = 'character',
n.replicates='numeric',
featureNames='character',
coord.names='character',
pseudo.absence='list'
),
validity = function(object) {
return(TRUE)
}
)
#---------
setClass(".replicates",
representation(
method = 'character',
n.replicates='numeric',
fold='list',
index.name='character',
row.index='list'
),
validity = function(object) {
return(TRUE)
}
)
setClassUnion(".replicatesORnull", c(".replicates", "NULL"))
#------
setClass(".basicSettings",
representation(
featureNames='character',
feature.types='listORnull',
interaction.depth='numeric',
formula='formulaORnull',
replicates='.replicatesORnull',
test.percentage='numericORnull',
pseudo.absence.method='characterORnull',
pseudo.absence.number='numericORnull',
variable.importance='logical',
variable.selection='characterORnull'
),
prototype(
featureNames=c(),
feature.types=NULL,
interaction.depth=1,
formula=NULL,
replicates=NULL,
test.percentage=NULL,
pseudo.absence.method=NULL,
pseudo.absence.number=NULL,
variable.importance=TRUE,
variable.selection=NULL
),
validity=function(object) {
return(TRUE)
}
)
setClassUnion(".basicSettingsORnull", c(".basicSettings", "NULL"))
setClass("sdmSettings",
representation(
methods='character',
basicSettings='.basicSettingsORnull',
modelSettings='list'
),
prototype(
basicSettings=NULL,
modelSettings=list()
),
validity=function(object) {
v1 <- TRUE
if (length(object@methods) > 0) v1 <- all(sort(object@methods) == sort(names(object@modelSettings)))
return(v1)
}
)
#-----
##################################
setClass(".glmSettings",
representation(
basicSettings='.basicSettingsORnull',
family="ANY",
otherSettings='list',
predictSettings='list'
),
prototype(
basicSettings=NULL,
family=binomial(link='logit'),
otherSettings=list(),
predictSettings=list(type='response')
),
validity=function(object) {
return(TRUE)
}
)
#------
setClass(".brtSettings",
representation(
basicSettings='.basicSettingsORnull',
distribution = "character",
n.trees = "numeric",
interaction.depth = "numeric",
n.minobsinnode = "numeric",
shrinkage = "numeric",
bag.fraction = "numeric",
train.fraction = "numeric",
cv.folds="numeric",
otherSettings='list',
predictSettings='list'
),
prototype(
basicSettings=NULL,
distribution = "bernoulli",
n.trees = 1000,
interaction.depth = 1,
n.minobsinnode = 10,
shrinkage = 0.001,
bag.fraction = 0.5,
train.fraction = 1.0,
cv.folds=0,
otherSettings=list(),
predictSettings=list(n.trees=1000,type='response')
),
validity=function(object) {
return(TRUE)
}
)
#--------
setClass(".rfSettings",
representation(
basicSettings='.basicSettingsORnull',
ntree='numeric',
importance='logical',
otherSettings='list',
predictSettings='list'
),
prototype(
basicSettings=NULL,
ntree=1000,
importance=FALSE,
otherSettings=list(),
predictSettings=list(type='response')
),
validity=function(object) {
return(TRUE)
}
)
#-----------
setClass(".svmSettings",
representation(
basicSettings='.basicSettingsORnull',
type="character",
otherSettings='list',
predictSettings='list'
),
prototype(
basicSettings=NULL,
type="eps-svr",
otherSettings=list(),
predictSettings=list(type='response')
),
validity=function(object) {
return(TRUE)
}
)
#-------
setClass(".gamSettings",
representation(
basicSettings='.basicSettingsORnull',
family='ANY',
otherSettings='list',
predictSettings='list'
),
prototype(
basicSettings=NULL,
family=binomial,
otherSettings=list(),
predictSettings=list(type='response')
),
validity=function(object) {
return(TRUE)
}
)
#-----------
setClass(".maxentSettings",
representation(
basicSettings='.basicSettingsORnull',
factors = "characterORnull",
args = "characterORnull",
removeDuplicates = "logical",
path = "characterORnull",
otherSettings='list',
predictSettings='list'
)
)
###############
setClass("sdmEvaluate",
representation(
observed='numeric',
predicted='numeric',
prevalence='numeric',
AUC='numeric',
COR='numeric',
threshod_based='data.frame'
),
validity=function(object) {
return(TRUE)
}
)
#------------
setClass("sdmEvaluates",
representation(
model='character',
n.run='numeric',
scenarios='data.frame',
evaluationList='list'
),
validity=function(object) {
return(TRUE)
}
)
#----------
setClass(".sdmModels",
representation(
model='character',
n.run='integer',
run.index='integer',
run.success='logical',
scenarios='data.frame',
modelObjectList='list',
evaluation='sdmEvaluates'
),
prototype(
n.run=as.integer(0),
run.index=as.integer(0),
run.success=logical(),
modelObjectList=list(),
evaluation=new('sdmEvaluates')
),
validity=function(object) {
return(TRUE)
}
)
#----
setClass(".sdmMultiModel",
representation(
species.name='character',
modelList='list'
),
validity=function(object) {
return(TRUE)
}
)
#-----------
setClass(".sdmMultiModelList",
representation(
species.names='character',
multiModelList='list'
),
prototype(
species.names=character(),
multiModelList=list()
),
validity=function(object) {
return(length(object@species.names) == length(object@multiModelList))
}
)
setClass("sdmModel",
representation(
data='speciesData',
settings='sdmSettings',
models='.sdmMultiModelList'
),
validity=function(object) {
return(TRUE)
}
)
#------
#------
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