Nothing
# Author: Babak Naimi, naimi.b@gmail.com
# Date (last update): Feb. 2024
# Version 2.4
# Licence GPL v3
.newFormulaFunction <- function(cls,name,args,setFrame=NULL,getFeature=NULL) {
new('.formulaFunction',cls=cls,name=name,args=args,setFrame=setFrame,getFeature=getFeature)
}
# adding the classes of formula functions into the corresponding container:
# for each function, a specific class is defined in which the name of feature,
# and its arguments as well as the function to generate the feature from dataset is specified
.sdmFormulaFuncs <- new('.formulaFunctions')
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.auto',
representation(x='character',
features='character',
stat='characterORnull',
term='call'
))),
name=c('auto','Auto'),args=c('x','features','stat')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.hinge',
representation(x='character',
k='numericORnull',
thresholds='numericORnull',
feature.name='characterORnull',
term='call'
),
prototype(
k=20
))),
name=c('hinge','h','H','Hinge','hing','Hing'),
args=c('x','k'),
setFrame = function(x,param) {
x@thresholds <- seq(param$min,param$max,length=x@k)
x@feature.name <- c(paste0(x@x,'_hi_',x@thresholds[-length(x@thresholds)]),paste0(x@x,'_hd_',x@thresholds[-1]))
x
},
getFeature = function(x,.var) {
k <- x@thresholds
h1 <- as.data.frame(lapply(k[-length(k)],function(th,x,...) {
.hinge(.var,th)
},x=.var))
#----
h2 <- as.data.frame(lapply(k[-1],function(th,x,...) {
.invhinge(x,th)
},x=.var))
d <- cbind(h1,h2)
colnames(d) <- x@feature.name
d
}))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.quad',
representation(x='character',
feature.name='characterORnull',
term='call'
))),
name=c('quad','q','Q','Quad','quadratic','Quadratic'),args=c('x'),
getFeature = function(x) {
x * x
}))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.cubic',
representation(x='character',
feature.name='characterORnull',
term='call'
))),
name=c('cubic','c','C','Cubic'),args=c('x')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.factor',
representation(x='character',
levels='character',
feature.name='characterORnull',
term='call'
))),
name=c('factor','f','F','Factor','fact','Fact'),args=c('x')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.threshold',
representation(x='character',
k='numeric',
thresholds='numericORnull',
feature.name='characterORnull',
term='call'
),
prototype(
k=20
))),
name=c('threshold','th','Th','thereshold','thresh','Thresh'),args=c('x','k')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.poly',
representation(x='character',
degree='numeric',
raw='logical',
feature.name='characterORnull',
term='call'
),
prototype(
degree=3,
raw=TRUE
))),
name=c('poly','Po','po','Poly'),args=c('x','degree','raw')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.interaction',
representation(x='character',
depth='numeric',
feature.name='characterORnull',
term='call'
),
prototype(
depth=1
))),
name=c('int','interaction','in','In','Int','INT'),args=c('x','depth')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.product',
representation(x='character',
feature.name='characterORnull',
term='call'
))),
name=c('product','p','P','Product','prod','Prod','pr'),args=c('x')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.func',
representation(x='call',
varName='characterORnull',
feature.name='characterORnull',
term='call'
))),
name=c('I'),args=c('x')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.simple.func',
representation(x='name',
varName='characterORnull',
feature.name='characterORnull',
term='call'
))),
name=c('FUN'),args=c('x')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.log',
representation(x='character',
feature.name='characterORnull',
term='call'
))),
name=c('log'),args=c('x')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.log10',
representation(x='character',
feature.name='characterORnull',
term='call'
))),
name=c('log10'),args=c('x')))
.sdmFormulaFuncs$add(.newFormulaFunction(cls=quote(setClass('.exp',
representation(x='character',
feature.name='characterORnull',
term='call'
))),
name=c('exp'),args=c('x')))
.sdmFormulaFuncs$setClasses() # set the classes
#
########################################################
#------ split a formula (f) based on the sep
.split.formula <- function(f,sep='~') {
# based on split_formula in the package Formula by Achim Zeileis
o <- list()
if (length(f) > 2) {
while (length(f) > 2 && f[[1]] == sep) {
o <- c(f[[3]],o)
f <- f[[2]]
}
c(f,o)
} else if (length(f) == 2) {
o[[1]] <- f[[2]]
o
} else {
o[[1]] <- f
o
}
}
#-------
.split.formula.for.select <- function(x) {
x <- .split.formula(x)[[1]]
.n <- x[[1]]
.x <- .split.formula(x,.n)
if (length(.x) > 1 && length(.x[[1]]) > 1) {
o <-.x[-1]
n <- rep(as.character(.n),length(.x)-1)
} else {
o <- .x
n <- rep(as.character(.n),length(.x))
}
while (length(.x) > 1) {
if (length(.x[[1]]) > 1) {
.n <- .x[[1]][[1]]
.x <- .split.formula(.x[[1]],.n)
if (length(.x) > 1 && length(.x[[1]]) > 1) {
o <- c(.x[-1],o)
n <- c(rep(as.character(.n),length(.x)-1),n)
} else {
if (length(.x) > 1) {
o <- c(.x,o)
n <- c(rep(as.character(.n),length(.x)),n)
} else {
o <- c(.x,o)
n <- c(as.character(.n),n)
}
}
} else {
break
}
}
if (any(n == '-')) {
.k <- as.character(o[which(n != '-')])
if (length(.k) == 0) .k <- as.character(o[1])
return(list(select=.k,keep = as.character(o[which(n[-1] == '-')+1])))
} else {
return(list(select=as.character(o)))
}
}
#----
.fixFormula <- function(formula) {
if (length(formula) == 3) {
nsp <- trim(unlist(strsplit(as.character(formula[2]),'[+|]')))
nsp <- nsp[nsp != '']
if ('.' %in% nsp) {
nsp <- nsp[nsp != '.']
if (length(nsp) == 0) formula <- as.formula(paste(formula[1],formula[3]),env = parent.frame())
else formula <- as.formula(paste(paste(nsp,collapse='+'),formula[1],formula[3]),env = parent.frame())
}
}
formula
}
#------- excludes items in y from x
.excludeVector <- function(x,y) {
w <- unlist(lapply(y,function(z){which(x == z)}))
if (length(w) > 0) x <- x[-w]
if (length(x) == 0) x <- NULL
x
}
#-------
.getRhsFromFormula <- function(f,env=parent.frame()) {
if (length(f) == 3) as.formula(paste('~',deparse(f[[3]])),env=env)
else if (length(f) == 2) f
else as.formula(paste('~',deparse(f)),env=env)
}
#------
# remove coords term from formula!
.rmCoordsInFormula <- function(f) {
sf <- .split.formula(f)
lhs <- rhs <- NULL
if (length(sf) > 2) stop('in the right hand side of the formula, the `~` can only be in m(...)')
if (length(sf) == 1) rhs <- sf[[1]]
else {
lhs <- sf[[1]]
rhs <- sf[[2]]
}
if (length(rhs) == 2) rhsi <- list(rhs)
else rhsi <- .split.formula(rhs,'+')
#-----
temp <- unlist(lapply(rhsi,function(x) as.character(x)[[1]] %in% c('coords','coord','coordinates','coordinate','xy','geom','coods','crds','crd','cords','cord')))
if (any(temp)) {
#.nxy <- as.character(.split.formula(rhsi[[which(temp)]][[2]],'+'))
if (is.null(lhs)) as.formula(paste('~',paste(rhsi[-which(temp)],collapse = '+')))
else {
if (length(lhs) > 1 && lhs[[1]] == '+') {
as.formula(paste(paste(.split.formula(lhs,'+'),collapse = '+'),'~',paste(rhsi[-which(temp)],collapse = '+')),env = parent.frame())
} else {
as.formula(paste(as.character(lhs),'~',paste(rhsi[-which(temp)],collapse = '+')),env = parent.frame())
}
}
} else f
}
#-----------
.getDataParams <- function(data,nf=NULL,nFact=NULL,id=NULL) {
if (!is.null(id)) data <- data[id,,drop=FALSE]
if (all(c(is.null(nf),is.null(nFact)))) {
nf <- colnames(data)
nFact <- nf[.where(is.factor,data)]
nFact <- c(nFact,nf[.where(is.character,data)])
if (length(nFact) == 0) nFact <- NULL
nf <- .excludeVector(nf,nFact)
nt <- nf[.where(.is.Date,data[,nf])]
if (length(nt) > 0 && all(is.na(nt))) nt <- NULL
nf <- .excludeVector(nf,nt)
}
if (!is.null(nf)) {
df<- data[,nf,drop=FALSE]
df <- data.frame(names=nf,min=round(apply(df,2,min,na.rm=TRUE),5),
max=round(apply(df,2,max,na.rm=TRUE),5),
mean=round(apply(df,2,mean,na.rm=TRUE),5),
sd=round(apply(df,2,sd,na.rm=TRUE),5),
type=apply(df,2,function(x) {
x <- x[!is.na(x)]
if (all((x - round(x,0)) == 0)) "integer"
else "numeric"
}),
unique_count=apply(df,2,function(x) length(unique(x))))
}
if (!is.null(nFact)) {
dFact <- list()
for (n in nFact) {
.tab <- table(data[,n])
dFact[[n]] <- data.frame(levels=names(.tab),count=as.vector(.tab))
}
}
if (any(c(is.null(nf),is.null(nFact)))) {
if (is.null(nf)) dFact
else df
} else {
list(continuous = df, categorical = dFact)
}
}
#------
#################---- detect the terms in the nested formula (model) inside the main formula:
# .nested_terms <- function(x) {
# .nm <- new('.nestedModel',term=x)
# #--------
# a <- c('formula','method','setting','output')
# s <- list()
# n <- names(x[-1])
# if (length(n) > 0) {
# for (i in seq_along(n)) {
# if (n[i] != '') {
# .w <- .pmatch(tolower(n[i]),a)
# if (!is.na(.w)) n[i] <- .w
# }
# }
# } else n <- rep('',length(x[-1]))
#
# if (length(n[n != '']) > 0 && !all(n[n != ''] %in% a)) stop('some arguments in the formula:model (m) function is unknown!')
# if (length(x) > 5) stop('the arguments in the formula:model (m) function are not match!')
# for (i in 1:length(n)) {
# if (n[i] != '') s[[n[i]]] <- x[[i+1]]
# else s[[a[i]]] <- x[[i+1]]
# }
# x <- s[['formula']]
#
# if (length(x) > 1) {
# if (x[[1]] == '~') {
# if (length(x) == 3) {
# x <- .fixFormula(x)
# l <- .split.formula(x[[3]],'+')
# if (length(.split.formula(x[[2]],'+')) > 1) stop('nested formula in the rhs, cannot be multi-response!')
# .nm@response <- as.character(x[[2]])
# } else l <- .split.formula(x[[2]],'+')
# } else l <- .split.formula(x,'+')
# } else l <- list(x)
# #----------
#
# .nm@terms <- lapply(l,.term)
# x <- s[['method']]
# if (!is.null(x)) {
# w <- unlist(.sdmMethods$getMethodNames(alt = TRUE))
# names(w) <- NULL
#
# if (length(x) > 1) {
# if (x[[1]] == 'c') {
# x <- tolower(as.character(x[-1]))
# if (!all(x %in% w)) {
# if (!any(x %in% w)) .nm@method <- NULL
# else .nm@method <- x[x %in% w]
# } else .nm@method <- x
# }
# } else {
# x <- tolower(as.character(x))
# if (!x %in% w) .nm@method <- NULL
# else .nm@method <- x
# }
# }
#
# #----
# x <- s[['setting']]
# if (!is.null(x)) {
# if (length(x) > 1) {
# if (x[[1]] == 'c') x[1] <- call('list')
#
# .nm@setting <- eval(x)
# }
# }
# #-------
#
# x <- s[['output']]
# if (!is.null(x)) {
# if (length(x) == 1) {
#
# x <- tolower(as.character(x))
# x <- .pmatch(x,c('prediction','residual'))
# if (!is.na(x)) .nm@output <- x
# } else .nm@output <- 'prediction'
# } else .nm@output <- 'prediction'
# #-------
# .nm
# }
#----
.nested_terms <- function(x) {
.nm <- new('.nestedModel',term=x)
#--------
a <- c('formula','method','setting','output')
s <- list()
n <- names(x[-1])
if (length(n) > 0) {
for (i in seq_along(n)) {
if (n[i] != '') {
.w <- .pmatch(tolower(n[i]),a)
if (!is.na(.w)) n[i] <- .w
}
}
} else n <- rep('',length(x[-1]))
if (length(n[n != '']) > 0 && !all(n[n != ''] %in% a)) stop('some arguments in the formula:model (m) function is unknown!')
if (length(x) > 5) stop('the arguments in the formula:model (m) function are not match!')
for (i in 1:length(n)) {
if (n[i] != '') s[[n[i]]] <- x[[i+1]]
else s[[a[i]]] <- x[[i+1]]
}
x <- s[['formula']]
if (length(x) > 1) {
if (x[[1]] == '~') {
if (length(x) == 3) {
x <- .fixFormula(x)
l <- all.vars(x[[3]])
#l <- .split.formula(x[[3]],'+')
if (length(.split.formula(x[[2]],'+')) > 1) stop('nested formula in the rhs, cannot be multi-response!')
.nm@response <- as.character(x[[2]])
} else l <- all.vars(x[[2]])
} else l <- all.vars(x)
} else l <- list(x)
#----------
.nm@predictors <- l
x <- s[['method']]
if (!is.null(x)) {
w <- unlist(.sdmMethods$getMethodNames(alt = TRUE))
names(w) <- NULL
if (length(x) > 1) {
if (x[[1]] == 'c') {
x <- tolower(as.character(x[-1]))
if (!all(x %in% w)) {
if (!any(x %in% w)) .nm@method <- NULL
else .nm@method <- x[x %in% w]
} else .nm@method <- x
}
} else {
x <- tolower(as.character(x))
if (!x %in% w) .nm@method <- NULL
else .nm@method <- x
}
}
#----
x <- s[['setting']]
if (!is.null(x)) {
if (length(x) > 1) {
if (x[[1]] == 'c') x[1] <- call('list')
.nm@setting <- eval(x)
}
}
#-------
x <- s[['output']]
if (!is.null(x)) {
if (length(x) == 1) {
x <- tolower(as.character(x))
x <- .pmatch(x,c('prediction','residual'))
if (!is.na(x)) .nm@output <- x
} else .nm@output <- 'prediction'
} else .nm@output <- 'prediction'
#-------
.nm
}
#----------
#----------
.exPCA <- function(x) {
a <- c('formula','n')
#-----
s <- list()
if (length(x) == 1) {
.pc <- new('.pcaSetting',vars='.',n=3,term=x)
} else {
.n <- names(x)
if (length(.n) > 0) {
for (i in seq_along(.n)) {
if (.n[i] != '') {
.w <- .pmatch(tolower(.n[i]),a)
if (!is.na(.w)) .n[i] <- .w
}
}
} else .n <- rep('',length(x))
if (length(.n[.n != '']) > 0 && !all(.n[.n != ''] %in% a)) stop('some arguments in pca function is unknown!')
if (length(x) > 3) stop('the arguments in the pca function are not match!')
for (i in 2:length(.n)) {
if (.n[i] != '') s[[.n[i]]] <- x[[i]]
else s[[a[i-1]]] <- x[[i]]
}
if (length(s[['formula']]) > 1) {
if (s[['formula']][[1]] != '+') stop('something in `pca` is wrong; pca(var1+var2+var3,n=3); pca(.,n="90%"); pca(.,n="auto"); pca(.,n=3)')
else {
l <- .split.formula(s[['formula']],'+')
if (any(unlist(lapply(l,function(x) {length(x) > 1})))) stop('something wrong with pca; example: pca(var1+var2+var3,n=3); pca(.,n="90%"); pca(.,n="auto"); pca(.,n=3)')
}
} else l <- list(s[['formula']])
.pc <- new('.pcaSetting',term=x)
if (!is.null(s[['n']])) .pc@n <- s[['n']]
else .pc@n <- 3
if (any(as.character(l) %in% c("NULL","."))) .pc@vars <- '.'
else .pc@vars <- as.character(l)
}
.pc
}
#--------
.exScale <- function(x) {
a <- c('formula','method')
s <- list()
if (length(x) == 1) {
n <- new('.scaleSetting',vars='.',method="minmax")
} else {
n <- names(x)
if (length(n) > 0) {
for (i in seq_along(n)) {
if (n[i] != '') {
.w <- .pmatch(tolower(n[i]),a)
if (!is.na(.w)) n[i] <- .w
}
}
} else n <- rep('',length(x))
if (length(n[n != '']) > 0 && !all(n[n != ''] %in% a)) stop('some arguments in the scale function is unknown!')
if (length(x) > 3) stop('the arguments in the scale function are not correct!')
for (i in 2:length(n)) {
if (n[i] != '') s[[n[i]]] <- x[[i]]
else s[[a[i-1]]] <- x[[i]]
}
if (length(s[['formula']]) > 1) {
if (s[['formula']][[1]] != '+') stop('something in `scale` is wrong; example: scale(var1+var2+var3,method="minmax")...')
else {
l <- .split.formula(s[['formula']],'+')
if (any(unlist(lapply(l,function(x) {length(x) > 1})))) stop('something is wrong in the scale function in formula; example: scale(var1+var2+var3,method="minmax")')
}
} else l <- list(s[['formula']])
n <- new('.scaleSetting',term=x)
if (!is.null(s[['method']])) n@method <- s[['method']]
else n@method <- 'minmax'
if (any(as.character(l) %in% c("NULL","."))) n@vars <- '.'
else n@vars <- as.character(l)
}
n
}
#----
.exInteraction <- function(x) {
a <- .sdmFormulaFuncs$getFuncs('int')$int@args
s <- list()
n <- names(x)
if (length(n) > 0) {
for (i in seq_along(n)) {
if (n[i] != '') {
.w <- .pmatch(tolower(n[i]),a)
if (!is.na(.w)) n[i] <- .w
}
}
} else n <- rep('',length(x))
if (length(n[n != '']) > 0 && !all(n[n != ''] %in% a)) stop('Some arguments in the interaction function in the formula is unknown!')
if (length(x) > 3) stop('Arguments in the interaction function in the formula are not correct!')
for (i in 2:length(n)) {
if (n[i] != '') s[[n[i]]] <- x[[i]]
else s[[a[i-1]]] <- x[[i]]
}
if (length(s[['x']]) > 1) {
if (s[['x']][[1]] != '+') stop('something in `interaction` is wrong: Examples: int(., depth=2); int(x1 + x2 + x3, depth=3) !')
else {
l <- .split.formula(s[['x']],'+')
if (any(unlist(lapply(l,function(x) {length(x) > 1})))) stop('something wrong with scale; example: scale(var1+var2+var3,method="minmax")')
}
} else l <- list(s[['x']])
n <- new('.interaction',term=x)
if (!is.null(s[['depth']])) {
if (is.numeric(s[['depth']]) && s[['depth']] > 0) n@depth <- ceiling(s[['depth']])
} else n@depth <- 1
if (any(as.character(l) %in% c("NULL","."))) n@x <- '.'
else n@x <- as.character(l)
n
}
#--------- detect the class of the term in the formula
.term <- function(x) {
if (length(x) == 1) {
if (x == '.') return(new('.all.vars',names=as.character(x)))
else return(new('.var',name=as.character(x)))
} else if (length(x) > 1) {
if (as.character(x[[1]]) %in% c('m','M','mo','model','mod','MODEL','Model')) {
.nested_terms(x)
} else if (as.character(x[[1]]) %in% c('select','se','sel','SEL','SELECT','SE')) {
.select.terms(x)
} else if (as.character(x[[1]]) %in% c('coords','coord','coordinates','coordinate','xy','geom','coods','crds','crd','cords','cord') || any(!is.na(pmatch(c("co"),tolower(as.character(x[[1]])))))) {
.exCoords(x)
} else if (as.character(x[[1]]) %in% c('g','G','gr','group','Group','GROUP','GR','gro','grop','grp')) {
.exGroup(x)
} else if (as.character(x[[1]]) %in% c('time','Time','tim','TIME','Tim')) {
.exTime(x)
} else if (as.character(x[[1]]) %in% c('info','Info','inf','INFO')) {
.exInfo(x)
} else if (as.character(x[[1]]) %in% c('*',':','product','p','P','Product','prod','Prod','pro','Pro')) {
.exProduct(x)
} else if (as.character(x[[1]]) %in% c('scale','SCALE','sc')) {
.exScale(x)
} else if (as.character(x[[1]]) %in% c('int','INT','interaction','Int','in','In')) {
.exInteraction(x)
} else if (as.character(x[[1]]) %in% c('pca','PCA','prcomp','princomp')) {
.exPCA(x)
} else .exFunc(x)
}
}
#-------
.exGroup <- function(x) {
new('.grouping',group.var=as.character(x[[2]]),term=x)
}
#------
.exTime <- function(x) {
xx <- as.character(x[[1]])
s <- list()
n <- names(x)
if (!is.null(n)) {
for (i in 2:length(n)) {
if (n[i] != '') s[[n[i]]] <- x[[i]]
else s[[(i-1)]] <- x[[i]]
}
} else {
for (i in 2:length(x)) s[[(i-1)]] <- x[[i]]
}
new('.time',name=xx,terms=s,term=x)
}
#--------
.exInfo <- function(x) {
n <- NULL
if (length(x[[2]]) > 1 && as.character(x[[2]][[1]]) %in% c('|','+')) {
if (as.character(x[[2]][[1]]) == '+') n <- as.character(.split.formula(x[[2]],'+'))
else n <- as.character(.split.formula(x[[2]],'|'))
} else {
n <- as.character(x[[2]])
}
if (!is.null(n)) new('.Info',names=n)
}
#---------
.exFunc <- function(x) {
xx <- as.character(x[[1]])
mn <- .sdmFormulaFuncs$funcNames
names(mn) <- mn
if (xx %in% mn) xx <- names(mn)[mn == xx]
else {
mnlist <- lapply(mn,function(x) .sdmFormulaFuncs$funcs[[x]]@name)
u <- unlist(lapply(mnlist,function(x) xx %in% x))
if (any(u)) xx <- names(u)[which(u)]
else xx <- NULL
}
if (!is.null(xx)) {
ss <- .sdmFormulaFuncs$getFuncs(xx)
a <- ss[[xx]]@args
cls <- new(ss[[xx]]@cls[[2]])
n <- names(x)
n <- n[2:length(n)]
if (!is.null(n)) {
if (length(n[n != ''] > 0) && !all(n[n != ''] %in% a)) stop(paste0('some arguments in function ',xx, ' is unknown!'))
for (i in 1:length(n)) {
if (n[i] != '') {
if (inherits(x[[i+1]],'name')) {
slot(cls,n[i]) <- as.character(x[[i+1]])
} else slot(cls,n[i]) <- x[[i+1]]
} else {
if (inherits(x[[i+1]],'name')) slot(cls,a[i]) <- as.character(x[[i+1]])
else slot(cls,a[i]) <- x[[i+1]]
}
}
} else {
for (i in 2:length(x)) {
if (inherits(x[[i]],'name')) slot(cls,a[i-1]) <- as.character(x[[i]])
else slot(cls,a[i-1]) <- x[[i]]
}
}
} else {
if (exists(as.character(x[[1]]),mode='function')) {
cls <- new('.simple.func')
cls@x <- x[[2]]
cls@varName <- all.vars(x)
} else stop(paste(as.character(x[[1]]),'is not a known function!'))
}
cls@term <- x
cls
}
#--------
.exProduct <- function(x) {
cls <- new('.product')
if (as.character(x[[1]]) %in% c('*',':')) {
cls@x <- unique(as.character(.split.formula(x,as.character(x[[1]]))))
} else {
if (length(x) == 2) {
xx <- x[[2]]
cls@x <- unique(as.character(.split.formula(xx,as.character(xx[[1]]))))
} else {
xx <- c()
for (i in 2:length(x)) xx <- c(xx,as.character(x[[i]]))
cls@x <- unique(xx)
}
}
cls@term <- x
cls
}
#--------
.exCoords <- function(x) {
if (length(x[[2]]) > 1 && as.character(x[[2]][[1]]) %in% c('|','+')) {
xy <- as.character(x[[2]])[2:3]
} else if (length(x) == 3) {
xy <- c(as.character(x[[2]]),as.character(x[[3]]))
} else stop('in formula, coordinates are not properly defined; Example: ~...+coords(x+y)+...')
new('.coord.vars',xy=xy)
}
#-------------
.select.terms <- function(x) {
a <- c('formula','method','th')
s <- list()
n <- names(x)
if (length(n) > 0) {
for (i in seq_along(n)) {
if (n[i] != '') {
.w <- .pmatch(tolower(n[i]),a)
if (!is.na(.w)) n[i] <- .w
}
}
} else n <- rep('',length(x))
if (length(n[n != '']) > 0 && !all(n[n != ''] %in% a)) stop('some arguments in select function is unknown!')
if (length(x) > 5) stop('the arguments in select function are not match!')
for (i in 2:length(n)) {
if (n[i] != '') s[[n[i]]] <- x[[i]]
else s[[a[i-1]]] <- x[[i]]
}
if (length(s[['formula']]) > 1) {
l <- .split.formula.for.select(s[['formula']])
} else l <- list(select=as.character(s[['formula']]))
n <- new('.selectFrame',term=x)
if (!is.null(s[['th']])) n@th <- s[['th']]
if (!is.null(s[['method']])) n@method <- s[['method']]
n@vars <- l$select
n@keep <- l$keep
n
}
#----
########
# .exFormula extract terms in formula and detect what each term is. it may be a model.term (including a
# variable, a function, a nested model, etc.) or a data.term (including coordinates, select function, group, etc.)
.exFormula <- function(f,data,detect=TRUE) {
f <- .fixFormula(f)
v <- colnames(data)
nFact <- nf <- ng <- ni <- nt <- nxy <- nsp <- NULL
nall <- n <- all.vars(f)
if ('.' %in% n) {
n <- n[-which(n == '.')]
nall <- unique(c(v,n))
}
nFact <- v[.where(is.factor,data)]
nFact <- c(nFact,v[.where(is.character,data)])
if (length(nFact) == 0) nFact <- NULL
else {
if (any(nFact %in% nall)) nFact <- nFact[nFact %in% nall]
else nFact <- NULL
}
sf <- .split.formula(f)
lhs <- rhs <- NULL
if (length(sf) > 2) stop('in the right hand side of the formula, the `~` can only be in m(...)')
f <- new('sdmFormula',formula=f)
if (length(sf) == 1) rhs <- sf[[1]]
else {
lhs <- sf[[1]]
rhs <- sf[[2]]
}
if (!is.null(lhs)) {
lhs <- .split.formula(lhs,'+')
nsp <- as.character(lhs)
nall <- .excludeVector(nall,nsp)
n <- .excludeVector(n,nsp)
nFact <- .excludeVector(nFact,nsp)
} else {
if (detect) {
w <- which(unlist(lapply(data,.isBinomial)))
if (length(w) > 0) {
nsp <- v[w]
nsp <- nsp[!nsp %in% n]
nall <- .excludeVector(nall,nsp)
nFact <- .excludeVector(nFact,nsp)
lhs <- as.list(nsp)
} else nsp <- NULL
} else nsp <- NULL
}
#f@vars <- nall
#f@species <- as.character(lhs)
if (length(rhs) == 2) rhsi <- list(rhs)
else rhsi <- .split.formula(rhs,'+')
temp <- unlist(lapply(rhsi,function(x) as.character(x)[[1]] %in% c('coords','coord','coordinates','coordinate','xy','geom','coods','crds','crd','cords','cord')))
if (any(temp)) nxy <- as.character(.split.formula(rhsi[[which(temp)]][[2]],'+'))
vars <- .excludeVector(nall,c(n,nxy,nFact))
w <- unlist(lapply(rhsi,function(x) x == '.'))
if (any(w)) {
if (!is.null(vars)) rhsi <- c(rhsi[!w],.split.formula(as.formula(paste('~',paste(vars,collapse='+')))[[2]],'+'))
else rhsi <- rhsi[!w]
}
if (!is.null(nFact)) {
for (i in seq_along(rhsi)) {
if (length(as.character(rhsi[[i]])) == 1) {
if (any(nFact == as.character(rhsi[[i]]))) {
rhsi[[i]] <- as.formula(paste('~f(',nFact[nFact == as.character(rhsi[[i]])],')'))[[2]]
}
}
}
}
nf <- .excludeVector(nall,c(nxy,nFact))
func.cls <- unlist(lapply(.sdmFormulaFuncs$funcNames,function(x) .sdmFormulaFuncs$funcs[[x]]@cls[[2]]))
temp <- lapply(rhsi,.term)
.fc <- unlist(lapply(temp,class)) # classes of the items in formula
#---
if ('.selectFrame' %in% .fc) {
if (!is.null(temp[[which(.fc == '.selectFrame')]]@keep)) {
w <- FALSE
for (.k in temp[[which(.fc == '.selectFrame')]]@keep) {
wt <- sapply(rhsi,function(x) x == as.name(.k))
if (!any(wt)) {
rhsi <- c(rhsi,as.name(.k))
w <- TRUE
}
}
if (w) {
temp <- lapply(rhsi,.term)
.fc <- unlist(lapply(temp,class)) # classes of the items in formula
}
}
}
#----
wt <- which(.fc %in% c('.var','.nestedModel',func.cls))
if (length(wt) > 0) f@model.terms <- temp[wt]
wt <- which(.fc %in% c('.coord.vars','.grouping','.Info','.time','.scaleSetting','.selectFrame','.pcaSetting'))
if (length(wt) > 0) {
f@data.terms <- c(f@data.terms,temp[wt])
w <- unlist(lapply(f@data.terms,class))
if (".grouping" %in% w) {
wt <- f@data.terms[which(w == ".grouping")]
ng <- sapply(wt,function(x) x@group.var)
nf <- .excludeVector(nf,ng)
nFact <- .excludeVector(nFact,ng)
}
#---
if ('.Info' %in% w) {
wt <- f@data.terms[which(w == ".Info")]
ni <- sapply(wt,function(x) as.character(x@names))
nf <- .excludeVector(nf,ni)
nFact <- .excludeVector(nFact,ni)
}
#----
if ('.time' %in% w) {
wt <- f@data.terms[which(w == ".time")]
nt <- sapply(wt,function(x) as.character(x@terms[1]))
nf <- .excludeVector(nf,nt)
nFact <- .excludeVector(nFact,nt)
} else {
if (!is.null(nf)) nt <- nf[.where(.is.Date,data[,nf])]
if (length(nt) > 0) {
nf <- .excludeVector(nf,nt)
nt <- nt[1]
for (i in 1:length(f@model.terms)) {
if (inherits(f@model.terms[[i]], '.var') && f@model.terms[[i]]@name == nt ) {
f@model.terms <- f@model.terms[-i]
f@data.terms <- c(f@data.terms,.exTime(.split.formula(as.formula(paste('~time(',nt,')')))[[1]]))
break
}
}
} else nt <- NULL
}
#----
} else {
if (!is.null(nf)) nt <- nf[.where(.is.Date,data[,nf])]
if (length(nt) > 0) {
nf <- .excludeVector(nf,nt)
nt <- nt[1]
for (i in 1:length(f@model.terms)) {
if (inherits(f@model.terms[[i]], '.var') && f@model.terms[[i]]@name == nt ) {
f@model.terms <- f@model.terms[-i]
f@data.terms <- c(f@data.terms,.exTime(.split.formula(as.formula(paste('~time(',nt,')')))[[1]]))
break
}
}
} else nt <- NULL
}
#-----
if (!is.null(f@model.terms)) {
w <- unlist(lapply(f@model.terms,class))
if ('.factor' %in% w) {
wi <- which(w == '.factor')
for (i in wi) {
w <- as.character(f@model.terms[[i]]@x)
w <- .excludeVector(w,'+')
nFact <- unique(c(nFact,w))
if (is.factor(data[,w])) f@model.terms[[i]]@levels <- levels(data[,w])
else f@model.terms[[i]]@levels <- sort(unique(as.character(data[,w])))
}
}
}
nf <- .excludeVector(nf,nFact)
if (!is.null(nf)) w1 <- .getDataParams(data,nf=nf)
else w1 <- NULL
if (!is.null(nFact)) w2 <- .getDataParams(data,nFact=nFact)
else w2 <- NULL
if (any(!is.null(c(nxy,ng,ni,nt)))) {
#w3 <- data.frame(name='xxx',type='xxx',details='xxx')[0,]
w3 <- data.frame(name='xxx',type='xxx')[0,]
if (!is.null(nxy)) {
#w3 <- rbind(w3,data.frame(name=nxy,type=c('x_coordinate','y_coordinate'),details=c(paste('mean:',round(mean(data[,nxy[1]],na.rm=T),2)),paste('mean:',round(mean(data[,nxy[2]],na.rm=T),2)))))
w3 <- rbind(w3,data.frame(name=nxy,type=c('x_coordinate','y_coordinate')))
}
if (!is.null(nt)) {
#w3 <- rbind(w3,data.frame(name=nt,type='Date/Time',details=paste0('range: ',paste(range(data[,nt]),collapse=':'))))
w3 <- rbind(w3,data.frame(name=nt,type='Date/Time'))
}
if (!is.null(ng)) {
w3 <- rbind(w3,data.frame(name=ng,type=rep('group',length(ng))))
}
if (!is.null(ni)) {
w3 <- rbind(w3,data.frame(name=ni,type=rep('Info',length(ni))))
}
} else w3 <- NULL
f@vars <- new('.variables',names=c(nsp,nf,nFact,nxy,nt,ng,ni),
species=nsp,numeric=w1,categorical=w2,others=w3)
if (!is.null(w2)) {
nFact <- names(w2)
w <- which(sapply(f@model.terms,class) == '.factor')
if (length(w) > 0) {
w <- which(!nFact %in% sapply(f@model.terms[w],function(x) x@x))
if (length(w) > 0) {
for (i in w) {
f@model.terms <- c(f@model.terms,
new('.factor',x=nFact[i],levels=w2[[nFact[i]]]$levels))
}
}
} else {
for (i in 1:length(nFact)) {
n <- nFact[i]
f@model.terms <- c(f@model.terms,
new('.factor',x=n,levels=w2[[n]]$levels,term=.eval(paste0("call('f',substitute(",n,'))'),environment())))
}
}
}
f
}
#-----------
###################
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