https://github.com/cran/RandomFields
Revision 34a453721b3918d1a8ce82b414ac3e6435072559 authored by Martin Schlather on 12 September 2016, 08:11:22 UTC, committed by cran-robot on 12 September 2016, 08:11:22 UTC
1 parent 6332d8d
Tip revision: 34a453721b3918d1a8ce82b414ac3e6435072559 authored by Martin Schlather on 12 September 2016, 08:11:22 UTC
version 3.1.24
version 3.1.24
Tip revision: 34a4537
convert_new.R
## Authors
## Martin Schlather, schlather@math.uni-mannheim.de
##
##
## Copyright (C) 2015 Alexander Malinowski, Martin Schlather
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License
## as published by the Free Software Foundation; either version 3
## of the License, or (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program; if not, write to the Free Software
## Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
### Diese Datei wandelt RMmodel in eine Liste um
### Kleinigkeiten geaendert: Jan 2015, M. Schlather
reps <- function(n, sign=",") paste(rep(sign, n), collapse="")
## @FUNCTION-STARP***********************************************************************************
# @NAME parseModel
# @PARAM $model - list, formula
# @RETURN list
# @REQUIRE $model is a linear mixed model in list or formula syntax
# @ENSURE $listModel is a linear mixed model in list syntax
# @SEE RMmodel, RFsimulate, devel-doc
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
parseModel <- function(model, ..., x=NULL) {
#Print(model)
## check whether $model is already in list syntax
if (is.list(model)) return(model)
## check whether $model is already in list syntax
if (isModel(model)) return(buildCovList(model, x=x))
## check whether $model has correct formula syntax
if (!isFormulaModel(model)) stop(syntaxError)
## extract tokens
summands <- extractSummands(model)
# Print(summands)
listModel <- list()
if (length(summands) == 1) {
listModel <- buildFactorList(summands[[1]], ..., x=x)#, last=TRUE)
} else {
listModel <- list(ZF_SYMBOLS_PLUS)
##last <- getLastCovIndex(summands)
for (i in 1:length(summands)) {
listModel <- c(listModel, list(buildFactorList(summands[[i]], ..., x=x)))
}
}
# Print(listModel); kkk
return(listModel)
}
# @FUNCTION-STARP***********************************************************************************
# @NAME isListModel
# @PARAM $model - any r-object
# @RETURN TRUE, FALSE
# @REQUIRE none
# @ENSURE it is confirmed that either $model has a correct model syntax or not
# @SEE devel-doc
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
isModel <- function(model)
{
return(is(model, ZF_MODEL))
}
# @FUNCTION-STARP***********************************************************************************
# @NAME isFormulaModel
# @PARAM $model - any r-object
# @RETURN TRUE, FALSE
# @REQUIRE none
# @ENSURE it is confirmed that either $model has a correct model syntax or not
# @SEE devel-doc
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
isFormulaModel <- function(model)
{
if (missing(model) || is.null(model)) return(FALSE)
if (!is(model, "formula")) return(FALSE)
# ensure the @ operator is just bivariate
if (regexpr("[[:alnum:]_]+@[[:alnum:]_]*@",
tail(as.character(model), 1)) != -1)
return(FALSE)
return(TRUE)
}
# @FUNCTION-STARP***********************************************************************************
# @NAME buildCovList
# @PARAM $model - RMmodel
# @RETURN list
# @REQUIRE none
# @ENSURE isListModel(output) == TRUE
# @SEE RMmodel, devel-doc
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# modified 2015 by Martin Schlather
## @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
buildCovList <- function(model, x=NULL) {
if (is.atomic(model) || is.list(model) ||
is.language(model) || is.environment(model))
return(model) ## for recursive calling
if (!is(model, ZF_MODEL))
stop('model must be of class ZF_MODEL')
if (model@name==ZF_COORD) model@name <- ZF_MIXED[1]
li <- c(list(model@name),
lapply(model@par.model[model@par.model != ZF_DEFAULT_STRING],
FUN=buildCovList, x=x),
lapply(model@submodels,
FUN=buildCovList, x=x)
)
if (li[[1]] == ZF_PLUS[1]) li[[1]] <- ZF_SYMBOLS_PLUS
if (li[[1]] == ZF_MULT[1]) li[[1]] <- ZF_SYMBOLS_MULT
if (li[[1]] == ZF_COVARIATE && length(x) > 0 &&
all(names(li) != "x")) {
li$x <- x
}
## par.general.is.default <-
## unlist(lapply(model@par.general, FUN=function(x) x==ZF_DEFAULT_STRING))
if (length(model@par.general)>0 &
!all(model@par.general==ZF_DEFAULT_STRING)) {
li <- c(DOLLAR[1],
lapply(model@par.general[model@par.general != ZF_DEFAULT_STRING],
FUN=buildCovList, x=x),
list(li))
if (length(pos <- which(names(li)=="Aniso")) > 0)
## in c-level, parameter is called 'A'
names(li)[pos] <- "A"
}
return(li)
}
# @FUNCTION-STARP***********************************************************************************
# @NAME syntaxError
# @PARAM none
# @RETURN string
# @REQUIRE none
# @ENSURE none
# @SEE none
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
syntaxError <- "Malformed model expression -- maybe you have used a wrong or obsolete definition, or just used an incorrect option name. See ?RMmodel for the model definition. Check manual for further information (RMmodel, RFsimulate)"
# @FUNCTION-STARP***********************************************************************************
# @NAME extractSummands
# @PARAM $model - formula
# @RETURN list[string]
# @REQUIRE isFormulaModel(model) == TRUE
# @ENSURE the output is a complete list of all summands
# @SEE RMModel, devel-doc
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
extractSummands <- function(model) {
tmpList <- list()
## ignore rest of the formula
rightSide <- tail(as.character(model), 1)
chars <- strsplit(rightSide, "")[[1]]
## toggles parenthesis, eg. whether we confront a toplevel plus or not
parToggle <- 0
token <- ""
for (char in chars) {
if (char == ZF_SYMBOLS_PLUS && parToggle == 0) {
tmpList <- c(tmpList, token)
token <- ""
} else {
if (char != " ") token <- paste(token, char, sep="")
if (char == ZF_SYMBOLS_L_PAR) parToggle <- parToggle+ 1
if (char == ZF_SYMBOLS_R_PAR) parToggle <- parToggle- 1
}
}
tmpList <- c(tmpList, token)
tokenList <- list()
for (token in tmpList) {
tokenList <- c(tokenList, removeParenthesis(token))
}
if (length(tokenList)==1)
return(tokenList) ## sonst steht unten paste(NULL), was "" gibt
iscov <- unlist(lapply(tokenList, FUN=isGenuineCovModel))
# Print(iscov)
tokenList <- c(tokenList[!iscov],
list(paste(unlist(tokenList[iscov]),
collapse=ZF_SYMBOLS_PLUS)))
return(tokenList)
}
# @FUNCTION-STARP***********************************************************************************
# @NAME removeParenthesis
# @PARAM $string - string
# @RETURN string
# @REQUIRE none
# @ENSURE The returned string is one not enclosed by parenthesis
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
removeParenthesis <- function(string)
{
# split the string
chars <- strsplit(string, "")[[1]]
while (head(chars, 1) == ZF_SYMBOLS_L_PAR &&
tail(chars, 1) == ZF_SYMBOLS_R_PAR)
{
chars <- chars[-1]
chars <- chars[-length(chars)]
}
# rejoin the string
string <- ""
for (char in chars)
{
string <- paste(string, char, sep="")
}
#print(string)
return (string)
}
# @FUNCTION-STARP***********************************************************************************
# @NAME buildFactorList
# @PARAM $summand - string
# @RETURN list
# @REQUIRE $summand is one of the form: string"@"string
# $last - an indicator telling the function if the covariance function is the last of
# its kind, for the rule exists to encapsulate all covariance functions in RMmixed
# except the last
# @ENSURE the output is a correct list
# @SEE RMModel, devel-doc
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
## @DATE 29.08.2011
## changed by Martin Schlather 2015
# @FUNCTION-END*************************************************************************************
buildFactorList <- function(summand, ..., x=x) { #, last)
factorList <- strsplit(summand, ZF_SYMBOLS_AT)[[1]]
factorsNr <- length(factorList)
## remove parenthesis
factorA <- removeParenthesis(factorList[[1]])
if (factorsNr == 2) {
factorB <- removeParenthesis(factorList[[2]])
if (isFormalCovModel(factorA))
stop(paste(factorA, "must NOT be a covariance model"))
}
## Print(summand, factorsNr, isFormalCovModel(factorA), factorA)
## do we have a mixed model
X <- catch(factorA, ...)
if (!(factorsNr == 1 && isFormalCovModel(factorA))) {# && last))
if (factorsNr == 1) {
#str(X)
# Print(X, is.factor(X))
if (is.factor(X)) {
lev <- levels(X)
m <- matrix(nrow=length(X), ncol=length(lev) - 1)
for (i in 2:length(lev)) m[, i - 1] <- as.numeric(X == lev[i])
tmpList <- list(ZF_COVARIATE)
tmpList[[COVARIATE_C_NAME]] <- m
tmpList[[COVARIATE_X_NAME]] <- x
tmpList[[COVARIATE_ADDNA_NAME]] <- TRUE
} else if (is.vector(X)) {
if (length(X) == 1) {
tmpList <- list(ZF_SYMBOLS_CONST)
tmpList[[CONST_A_NAME]] <-
if (is.finite(X) && X == 1) NA else as.numeric(X)
} else {
tmpList <- list(ZF_COVARIATE)
tmpList[[COVARIATE_C_NAME]] <- as.numeric(X)
tmpList[[COVARIATE_X_NAME]] <- x
tmpList[[COVARIATE_ADDNA_NAME]] <- TRUE
}
} else {
tmpList <- list(ZF_MIXED[1])
tmpList[[MIXED_X_NAME]] <- X
tmpList[[MIXED_BETA_NAME]] <- NA
}
} else {
tmpList <- list(ZF_MIXED[1])
tmpList[[MIXED_X_NAME]] <- X
if (isGenuineCovModel(factorB)) {
model <- catch(factorB, ...)
if (model@name==ZF_COORD) {
tmpList[["coord"]] <- model@par.model$coord
tmpList[["dist"]] <- model@par.model$dist
tmpList[["cov"]] <-
(buildCovList(model@submodels[[1]], x=x))
} else {
tmpList[["cov"]] <-
(buildCovList(model, x=x))
}
} else {
tmpList[["b"]] <- extractFixed(factorB, ...)
}
}
# Print(tmpList)
return(tmpList)
} else {
tmpList <- buildCovList(X, x=x)
return(tmpList)
}
}
# @FUNCTION-STARP***********************************************************************************
# @NAME isCovModel: isFormalCovModel, isGenuineCovModel
# @PARAM $name - string
# @RETURN TRUE, FALSE
# @REQUIRE none
# @ENSURE The $name argument is a function that returns an RMmodel object
# @SEE RFModel, devel-doc
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 29.08.2011
# @FUNCTION-END*************************************************************************************
isFormalCovModel <- function(name)
{
## Martin: habe hier RFtrend hinzugefuegt!
if (is(try(tmp <- eval(parse(text=name)), silent=TRUE),ZF_MODEL))
return(TRUE)
## has signature, eg. funName"("funPar")"
if (regexpr("^[[:alnum:]_]+\\([[:print:]]*\\)$", name) != 1)
return(FALSE)
fun <- strsplit(name, "\\(")[[1]][1]
return(exists(fun) && is(get(fun), ZF_MODEL_FACTORY))
}
isGenuineCovModel <- function(name)
{
## Martin: habe hier RFtrend hinzugefuegt!
if (substr(name, 1, length(ZF_TRENDFCT)) == ZF_TRENDFCT) return(FALSE)
if (is(try(tmp <- eval(parse(text=name)), silent=TRUE), ZF_MODEL))
return(TRUE)
## has signature, eg. funName"("funPar")"
if (regexpr("^[[:alnum:]_]+\\([[:print:]]*\\)$", name) != 1)
return(FALSE)
fun <- strsplit(name, "\\(")[[1]][1]
return(exists(fun) && is(get(fun), ZF_MODEL_FACTORY))
}
# @FUNCTION-STARP***********************************************************************************
# @NAME extractFixed
# @PARAM $factor - string
# @RETURN vector
# @REQUIRE $factor has format RMfixed(<b=>r-vector)
# @ENSURE none
# @SEE RMmodel
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
extractFixed <- function(factor, ...)
{
# has signature, eg. funName"("funPar")"
if (regexpr(paste("^",ZF_FIXED,"\\([[:print:]]*\\)$",sep=""),
factor) != 1) {
stop(paste("Second factor is not a cov model AND does not start with",
ZF_FIXED, "\n", syntaxError))
}
# extract the argument of RMfixed
first_par <- regexpr("{1}\\(", factor)
last_par <- regexpr("\\)$", factor)
if (first_par == -1 || last_par == -1)
arg <- factor
else
arg <- substr(factor, first_par+1, last_par-1)
#arg <- strsplit(factor,"\\)")[[1]]
#arg <- strsplit(arg, "\\(")[[1]][2]
beta <- catch(arg, ...)
return(beta)
}
# @FUNCTION-STARP***********************************************************************************
# @NAME catch
# @PARAM $expr - expression
# $handler - the error handler function
# @RETURN r-object
# @REQUIRE none
# @ENSURE stops if the expression fails
# @SEE
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
catch <- function(expr, handler=function(res){stop(res)}, ...)
{
# Print("catch", expr)
tmpENV <- new.env(parent=.GlobalEnv)
dots <- list(...)
assign("dots", dots, envir=tmpENV)
if (length(dots)>0) {
text <- paste(names(dots), "<- dots[[", 1:length(dots), "]]", collapse=";")
eval(envir=tmpENV, parse(text=text))
}
res <-try(eval(envir=tmpENV, parse(text=expr)), silent=TRUE)
if (class(res) == "try-error")
handler(res)
return(res)
}
# @FUNCTION-STARP***********************************************************************************
# @NAME prepareData
# @REQUIRE $model is of type formula
# $simObj is an RFsp object
# @ENSURE
# @SEE
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
selectDataAccordingFormula <- function(simObj, model) {
varNames <- extractVarNames(model)
#Print(varNames)
## are there any variablenames given
if (is.null(varNames)) {
##warning("'model' is not given as a formula or model formula contains an empty left side --> all colums of the data matrix in 'data' are selected")
coord <- RFoptions()$coord
if (is.na(coord$varnames[1])) return (simObj)
varnames <- coord$varnames
}
cleanNames <- (if (simObj@.RFparams$n == 1) colnames(simObj@data) else
sapply(colnames(simObj@data), FUN=cleanse))
mymatch <- match(cleanNames, varNames)#, dup=TRUE)
if (!all(varNames %in% cleanNames))
stop("response variable names could not be found in colnames of data object")
#Print(simObj, mymatch)
simObj <- simObj[!is.na(mymatch)]
simObj@.RFparams$vdim <- length(varNames)
return(simObj)
}
selectAccordingFormula <- function(data, model)
{
varNames <- extractVarNames(model)
#Print(varNames)
if (is.null(varNames)) {
coord <- RFoptions()$coord
if (is.na(coord$varnames[1])) return(NULL)
varNames <- coord$varnames
}
## are there any variablenames given
if (is.matrix(data) || is.data.frame(data)) {
cleanNames <- colnames(data)
if (!all(varNames %in% cleanNames))
stop("response variable names could not be found in colnames of data object")
mymatch <- !is.na(match(cleanNames, varNames))#, dup=TRUE)
return(mymatch)
}
}
# @FUNCTION-STARP***********************************************************************************
# @NAME extractVarNames
# @REQUIRE $model is a formula or a RMmodel
# @ENSURE the return value is a vector with the names of the response variables of the formula
# or NULL if no left side given
# @SEE
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011; 2014 Martin Schlather modified
# @FUNCTION-END*************************************************************************************
extractVarNames <- function(model)
{
if (missing(model) ||
length(model) <= 2 || !is(model, "formula")) return (NULL)
tmp <- as.character(model)[2]
tmp <- strsplit(tmp, "c\\(")[[1]]
tmp <- paste(tmp, sep="", collapse="")
tmp <- strsplit(tmp, "\\)")[[1]]
tmp <- paste(tmp, sep="", collapse="")
varNames <- strsplit(tmp, ", ")[[1]]
## ignore numeric formated varNames
i<- 1
while (i <= length(varNames))
{
if (regexpr("^[[:digit:]]", varNames[i]) > 0)
varNames<- varNames[-i]
else
i<- i+ 1
}
if (length(varNames) == 0)
return (NULL)
return (varNames)
}
# @FUNCTION-STARP***********************************************************************************
# @NAME cleanse
# @REQUIRE $x a character string
# @ENSURE if $x ends with '.n[:digit:]+' this part is cut off
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 26.08.2011
# @FUNCTION-END*************************************************************************************
cleanse <- function(x)
{
return (strsplit(x, "\\.n[[:digit:]]+$")[[1]][1])
}
# @FUNCTION-STARP***********************************************************************************
# @NAME cutoffArray
# @REQUIRE $data is a numeric array
# $grid is a sequence matrix and each $data point has a corresponding $grid point
# in particular the expanded $grid has the same size as $data
# $len is a numeric vector sorted in ascending order
# all three parameters start with 0
# @ENSURE $data is returned and the original array with each point lying on an coordinate axis
# having a maximum distance less or equal the last entry of $len
# @AUTHOR Sebastian Gross <sebastian.gross@stud.uni-goettingen.de>
# @DATE 14.09.2011
# @FUNCTION-END*************************************************************************************
cutoffArray <- function(data, grid, len)
## Was macht diese Funktion? (Frage von Martin)
## arrays abschneiden, sodass es in keiner orthogonalen raumrichtung punkte gibt
## die einen abstand groesser len haben
{
len <- tail(len, 1)
## cut off in each direction
for (dir in c(1:dim(grid)[2]))
{
## retrieve the number of points within bin length
nrPts <- ceiling(len/grid[2,dir])+ 1
text <- paste("data[", reps(dir-1), "1:", nrPts,
reps(dim(grid)[2]-dir), ",drop=FALSE]")
data <- eval(parse(text=text))
}
return (data)
}
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