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Formula <- function(object) {
if(inherits(object, "Formula")) return(object)
stopifnot(inherits(object, "formula"))
object_split <- split_formula(object)
structure(object, lhs = object_split$lhs, rhs = object_split$rhs,
class = c("Formula", "formula"))
}
as.Formula <- function(x, ...) UseMethod("as.Formula")
as.Formula.default <- function(x, ..., env = parent.frame()) Formula(as.formula(x, env = env))
as.Formula.Formula <- function(x, ...) x
as.Formula.formula <- function(x, ..., env) {
## preserve original environment
if(missing(env)) env <- environment(x)
## combine all arguments to formula list
x <- c(list(x), list(...))
x <- lapply(x, as.formula)
## split all
x_split <- lapply(x, split_formula)
x_lhs <- do.call("c", lapply(x_split, "[[", "lhs"))
x_rhs <- do.call("c", lapply(x_split, "[[", "rhs"))
## recombine
x_all <- paste_formula(x_lhs, x_rhs)
## create formula
## (we have everything to do this by hand, but for encapsulating code
## call Formula() again...which splits again)
rval <- Formula(x_all)
## re-attach original environment
environment(rval) <- env
return(rval)
}
is.Formula <- function(object) inherits(object, "Formula")
formula.Formula <- function(x, lhs = NULL, rhs = NULL, collapse = FALSE,
update = FALSE, drop = TRUE, ...)
{
## available parts
lpart <- 1L:length(attr(x, "lhs"))
rpart <- 1L:length(attr(x, "rhs"))
## default: keep all parts
lhs <- if(is.null(lhs)) lpart else lpart[lhs]
rhs <- if(is.null(rhs)) rpart else rpart[rhs]
if(any(is.na(lhs))) {
lhs <- as.vector(na.omit(lhs))
if(length(lhs) < 1L) lhs <- 0L
warning("subscript out of bounds, not all 'lhs' available")
}
if(any(is.na(rhs))) {
rhs <- as.vector(na.omit(rhs))
if(length(rhs) < 1L) rhs <- 0L
warning("subscript out of bounds, not all 'rhs' available")
}
## collapse: keep parts separated by "|" or collapse with "+"
collapse <- rep(as.logical(collapse), length.out = 2)
rval <- paste_formula(attr(x, "lhs")[lhs], attr(x, "rhs")[rhs],
lsep = ifelse(collapse[1L], "+", "|"),
rsep = ifelse(collapse[2L], "+", "|"))
## omit potentially redundant terms
if(all(collapse) & update) rval <- update(rval, if(length(rval) > 2) . ~ . else ~ .)
## reconvert to Formula if desired
if(!drop) rval <- Formula(rval)
## re-attach original environment
environment(rval) <- environment(x)
return(rval)
}
terms.Formula <- function(x, ..., lhs = NULL, rhs = NULL, dot = "separate")
{
## simplify to standard formula
form <- simplify_to_formula(x, lhs = lhs, rhs = rhs)
## if necessary try to expand/update/simplify formula parts with dot
if(has_dot(form)) {
x_orig <- x
dot <- match.arg(dot, c("separate", "sequential", "previous"))
## lhs and rhs calls
ll <- formula(x, rhs = 0L, collapse = TRUE)[[2L]]
rr <- attr(x, "rhs")
## update and simplify again
for(i in seq_along(rr)) {
if(dot == "sequential" && i > 1L) ll <- c_formula(ll, rr[[i - 1L]], sep = "+")
fi <- paste_formula(ll, rr[[i]]) #probably better than:# paste_formula(NULL, c_formula(rr[[i]], ll, sep = "-"))
rr[[i]] <- if(dot == "previous" && i > 1L) {
update(paste_formula(ll, rr[[i - 1]]), fi)[[3L]]
} else {
update(formula(terms(fi, ...)), . ~ .)[[3L]]
}
}
attr(x, "rhs") <- rr
form <- simplify_to_formula(x, lhs = lhs, rhs = rhs)
## call traditional terms()
mt <- terms(form, ...)
## store updating for future reference (e.g., in model.part)
attr(mt, "Formula_with_dot") <- x_orig
attr(mt, "Formula_without_dot") <- x
attr(mt, "dot") <- dot
} else {
## call traditional terms()
mt <- terms(form, ...)
}
return(mt)
}
model.frame.Formula <- function(formula, data = NULL, ..., lhs = NULL, rhs = NULL, dot = "separate")
{
model.frame(terms(formula, lhs = lhs, rhs = rhs, data = data, dot = dot), data = data, ...)
}
model.matrix.Formula <- function(object, data = environment(object), ..., lhs = NULL, rhs = 1, dot = "separate")
{
if(dot == "separate") {
form <- formula(object, lhs = lhs, rhs = rhs, collapse = c(FALSE, TRUE))
mt <- delete.response(terms(form, data = data))
} else {
mt <- delete.response(terms(object, lhs = lhs, rhs = rhs, dot = dot))
}
model.matrix(mt, data = data, ...)
}
## as model.response() is not generic, we do this:
model.part <- function(object, ...)
UseMethod("model.part")
model.part.formula <- function(formula, data, ..., drop = FALSE) {
formula <- Formula(formula)
NextMethod()
}
model.part.Formula <- function(object, data, lhs = 0, rhs = 0, drop = FALSE, terms = FALSE, dot = NULL, ...) {
## *hs = NULL: keep all parts
if(is.null(lhs)) lhs <- 1L:length(attr(object, "lhs"))
if(is.null(rhs)) rhs <- 1L:length(attr(object, "rhs"))
if(isTRUE(all.equal(as.numeric(lhs), rep(0, length(lhs)))) &
isTRUE(all.equal(as.numeric(rhs), rep(0, length(rhs)))))
stop("Either some 'lhs' or 'rhs' has to be selected.")
if(is.null(dot)) {
if(is.null(attr(attr(data, "terms"), "dot"))) {
dot <- "separate"
} else {
dot <- attr(attr(data, "terms"), "dot")
}
} else {
dot <- match.arg(dot, c("separate", "sequential", "previous"))
}
##
if(has_dot(object) &&
!is.null(attr(data, "terms")) &&
all(c("Formula_with_dot", "Formula_without_dot", "dot") %in% names(attributes(attr(data, "terms")))) &&
dot == attr(attr(data, "terms"), "dot") &&
simplify_to_formula(object, lhs = lhs, rhs = rhs) == simplify_to_formula(attr(attr(data, "terms"), "Formula_with_dot"), lhs = lhs, rhs = rhs)
) {
object <- attr(attr(data, "terms"), "Formula_without_dot")
}
## construct auxiliary terms object
mt <- terms(object, lhs = lhs, rhs = rhs, dot = dot, data = data)
## subset model frame
ix <- attr(mt, "variables")[-1L]
if(is.null(ix)) {
ix <- 0
} else {
ix <- sapply(ix, deparse, width.cutoff = 500L) ## for width beyond 500: paste(..., collapse = "") ?
if(!all(ix %in% names(data))) stop(
paste("'data' does not seem to be an appropriate 'model.frame':",
paste(paste("'", ix[!(ix %in% names(data))], "'", sep = ""), collapse = ", "),
"not found")
)
}
rval <- data[, ix, drop = drop]
if(!is.data.frame(rval)) names(rval) <- rownames(data)
if(terms) attr(rval, "terms") <- mt
return(rval)
}
update.Formula <- function(object, new,...) {
new <- Formula(new)
## extract all building blocks
o_lhs <- attr(object, "lhs")
o_rhs <- attr(object, "rhs")
n_lhs <- attr(new, "lhs")
n_rhs <- attr(new, "rhs")
lhs <- rep(list(NULL), length.out = max(length(o_lhs), length(n_lhs)))
rhs <- rep(list(NULL), length.out = max(length(o_rhs), length(n_rhs)))
## convenience function for updating components
update_components <- function(x, y) {
xf <- yf <- ~ .
xf[[2L]] <- x
yf[[2L]] <- y
update(xf, yf)[[2L]]
}
if(length(lhs) > 0L) for(i in 1L:length(lhs)) {
lhs[[i]] <- if(length(o_lhs) < i) n_lhs[[i]]
else if(length(n_lhs) < i) o_lhs[[i]]
else update_components(o_lhs[[i]], n_lhs[[i]])
}
if(length(rhs) > 0L) for(i in 1L:length(rhs)) {
rhs[[i]] <- if(length(o_rhs) < i) n_rhs[[i]]
else if(length(n_rhs) < i) o_rhs[[i]]
else update_components(o_rhs[[i]], n_rhs[[i]])
}
## recombine
rval <- paste_formula(lhs, rhs)
## create formula
## (we have everything to do this by hand, but for encapsulating code
## call Formula() again...which splits again)
rval <- Formula(rval)
## preserve original environment
environment(rval) <- environment(object)
return(rval)
}
length.Formula <- function(x) {
## NOTE: return length of both sides, not only rhs
c(length(attr(x, "lhs")), length(attr(x, "rhs")))
}
print.Formula <- function(x, ...) {
## we could avoid calling formula() by computing on the internal
## structure attr(x, "rhs") <- attr(x, "lhs") <- NULL
## but this is probably cleaner...
print(formula(x))
invisible(x)
}
all.equal.Formula <- function(target, current, ...) {
rval <- NULL
if(length(target)[1L] != length(current)[1L]) {
rval <- c(rval, paste("Length mismatch: target, current differ in number of LHS parts: ",
length(target)[1L], ", ", length(current)[1L], sep = ""))
} else if(!isTRUE(all.equal(attr(target, "lhs"), attr(current, "lhs")))) {
rval <- c(rval, "Formula mismatch: LHS formulas differ in contents")
}
if(length(target)[2L] != length(current)[2L]) {
rval <- c(rval, paste("Length mismatch: target, current differ in number of RHS parts: ",
length(target)[2L], ", ", length(current)[2L], sep = ""))
} else if(!isTRUE(all.equal(attr(target, "rhs"), attr(current, "rhs")))) {
rval <- c(rval, "Formula mismatch: RHS formulas differ in contents")
}
if(is.null(rval)) TRUE else rval
}
str.Formula <- function(object, ...) {
le <- length(object)
ls <- if(sum(le) > 2L | any(le > 1L)) "s" else ""
writeLines(c(
sprintf("'Formula' with %s left-hand and %s right-hand side%s: %s",
le[1L], le[2L], ls, format(object)),
sprintf(" ..- attr(*, \".Environment\")=%s", format(attr(object, ".Environment")))))
invisible()
}
## convenience tools #################################################
## split formulas
split_formula <- function(f) {
stopifnot(inherits(f, "formula"))
rhs <- if(length(f) > 2) f[[3L]] else f[[2L]]
lhs <- if(length(f) > 2) f[[2L]] else NULL
extract_parts <- function(x, sep = "|") {
if(is.null(x)) return(NULL)
rval <- list()
if(length(x) > 1L && x[[1L]] == sep) {
while(length(x) > 1L && x[[1L]] == sep) {
rval <- c(x[[3L]], rval)
x <- x[[2L]]
}
}
return(c(x, rval))
}
list(lhs = extract_parts(lhs), rhs = extract_parts(rhs))
}
## combine (parts of) formulas
c_formula <- function(f1, f2, sep = "~") {
stopifnot(length(sep) == 1L, nchar(sep) == 1L,
sep %in% c("~", "+", "-", "|", "&"))
if(sep == "~") {
rval <- . ~ .
rval[[3L]] <- f2
rval[[2L]] <- f1
} else {
rval <- as.formula(paste(". ~ .", sep, "."))
rval[[3L]][[3L]] <- f2
rval[[3L]][[2L]] <- f1
rval <- rval[[3L]]
}
return(rval)
}
## reassemble formulas
paste_formula <- function(lhs, rhs, lsep = "|", rsep = "|") {
stopifnot(all(nchar(lsep) == 1L), all(lsep %in% c("+", "|", "&")))
stopifnot(all(nchar(rsep) == 1L), all(rsep %in% c("+", "|", "&")))
if(length(lhs) > 1L) lsep <- rep(lsep, length.out = length(lhs) - 1L)
if(length(rhs) > 1L) rsep <- rep(rsep, length.out = length(rhs) - 1L)
if(is.null(lhs)) lhs <- list()
if(is.null(rhs)) rhs <- list()
if(!is.list(lhs)) lhs <- list(lhs)
if(!is.list(rhs)) rhs <- list(rhs)
lval <- if(length(lhs) > 0L) lhs[[1L]] else NULL
if(length(lhs) > 1L) {
for(i in 2L:length(lhs)) lval <- c_formula(lval, lhs[[i]], sep = lsep[[i - 1L]])
}
rval <- if(length(rhs) > 0L) rhs[[1L]] else 0 ## FIXME: Is there something better?
if(length(rhs) > 1L) {
for(i in 2L:length(rhs)) rval <- c_formula(rval, rhs[[i]], sep = rsep[[i - 1L]])
}
c_formula(lval, rval, sep = "~")
}
## simplify a Formula to a formula that can be processed with
## terms/model.frame etc.
simplify_to_formula <- function(Formula, lhs = NULL, rhs = NULL) {
## get desired subset as formula and Formula
form <- formula(Formula, lhs = lhs, rhs = rhs)
Form <- Formula(form)
## convenience functions for checking extended features
is_lhs_extended <- function(Formula) {
## check for multiple parts
if(length(attr(Formula, "lhs")) > 1L) {
return(TRUE)
} else {
## and multiple responses
if(length(attr(Formula, "lhs")) < 1L) return(FALSE)
return(length(attr(terms(paste_formula(NULL,
attr(Formula, "lhs"), rsep = "+")), "term.labels")) > 1L)
}
}
is_rhs_extended <- function(Formula) {
## check for muliple parts
length(attr(Formula, "rhs")) > 1L
}
## simplify (if necessary)
ext_lhs <- is_lhs_extended(Form)
if(ext_lhs | is_rhs_extended(Form)) {
form <- if(ext_lhs) {
if(length(attr(Form, "rhs")) == 1L & identical(attr(Form, "rhs")[[1L]], 0)) {
paste_formula(NULL, attr(Form, "lhs"), rsep = "+")
} else {
paste_formula(NULL, c(attr(Form, "lhs"), attr(Form, "rhs")), rsep = "+")
}
} else {
paste_formula(attr(Form, "lhs"), attr(Form, "rhs"), rsep = "+")
}
}
## re-attach original environment and return
environment(form) <- environment(Formula)
return(form)
}
## check whether formula has a dot (FIXME: can other problems than just '.' occur?)
has_dot <- function(formula) inherits(try(terms(formula), silent = TRUE), "try-error")
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