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`%:::%` <- function(pkg, fun) {
get(fun, envir = asNamespace(pkg), inherits = FALSE)
}
## taken from gam4
#' @noRd
#' @importFrom methods as cbind2 is
gamm4.setup <- function(formula, pterms, data = NULL, knots = NULL) {
## first simply call `gam.setup'....
if (is.null(formula$response)) {
formula$response <- 1
pterms$response <- 1
}
gam.setup <- `%:::%`("mgcv", "gam.setup")
G <- gam.setup(formula, pterms,
data = data, knots = knots, sp = NULL, min.sp = NULL,
H = NULL, absorb.cons = TRUE, sparse.cons = 0,
gamm.call = TRUE
)
if (!is.null(G$L)) {
stop(
"gamm can not handle linked smoothing parameters",
"(probably from use of `id' or adaptive smooths)"
)
}
first.f.para <- G$nsdf + 1
random <- list()
if (G$nsdf > 0) ind <- 1:G$nsdf else ind <- rep(0, 0)
X <- G$X[, ind, drop = FALSE] # accumulate fixed effects into here
xlab <- rep("", 0)
## sparse version of full matrix, treating smooths as fixed
G$Xf <- as(X, "dgCMatrix")
first.para <- G$nsdf + 1
used.names <- names(data) ## keep track of all variable names already used
if (G$m) {
for (i in 1:G$m) { ## work through the smooths
sm <- G$smooth[[i]]
sm$X <- G$X[, sm$first.para:sm$last.para, drop = FALSE]
## convert smooth to random effect and fixed effects
rasm <- mgcv::smooth2random(sm, used.names, type = 2)
used.names <- c(used.names, names(rasm$rand))
sm$fixed <- rasm$fixed
## deal with creation of sparse full model matrix
if (!is.null(sm$fac)) {
flev <- levels(sm$fac) ## grouping factor for smooth
n.lev <- length(flev)
for (k in 1:n.lev) {
G$Xf <- cbind2(G$Xf, as(
sm$X * as.numeric(sm$fac == flev[k]),
"dgCMatrix"
))
}
} else {
n.lev <- 1
G$Xf <- cbind2(G$Xf, as(sm$X, "dgCMatrix"))
}
## now append random effects to main list
n.para <- 0 ## count random coefficients
if (!sm$fixed) {
for (k in 1:length(rasm$rand)) n.para <- n.para + ncol(rasm$rand[[k]])
sm$lmer.name <- names(rasm$rand)
random <- c(random, rasm$rand)
sm$trans.D <- rasm$trans.D
sm$trans.U <- rasm$trans.U ## matrix mapping fit coefs back to original
}
## ensure stored first and last para relate to G$Xf in expanded version
sm$last.para <- first.para + ncol(rasm$Xf) + n.para - 1
sm$first.para <- first.para
first.para <- sm$last.para + 1
if (ncol(rasm$Xf)) {
Xfnames <- rep("", ncol(rasm$Xf))
k <- length(xlab) + 1
for (j in 1:ncol(rasm$Xf)) {
xlab[k] <- Xfnames[j] <-
mgcv::new.name(paste(sm$label, "Fx", j, sep = ""), xlab)
k <- k + 1
}
colnames(rasm$Xf) <- Xfnames
}
X <- cbind(X, rasm$Xf) # add fixed model matrix to overall fixed X
sm$first.f.para <- first.f.para
first.f.para <- first.f.para + ncol(rasm$Xf)
## note less than sm$first.f.para => no fixed
sm$last.f.para <- first.f.para - 1
## store indices of random parameters in smooth specific array
sm$rind <- rasm$rind
sm$rinc <- rasm$rinc
## pen.ind==i TRUE for coef penalized by ith penalty
sm$pen.ind <- rasm$pen.ind
sm$n.para <- n.para
sm$X <- NULL ## delete model matrix
G$smooth[[i]] <- sm ## replace smooth object with extended version
}
}
G$random <- random ## named list of random effect matrices
G$X <- X ## fixed effects model matrix
G
}
## refactored from gamm4 to return the model matrix for generating predictions
## with fit$mer and newdata
#' @noRd
model.matrix.gamm4 <- function(formula, random = NULL, data = NULL,
family = gaussian()) {
if (!is.null(random)) {
if (!inherits(random, "formula")) {
stop("gamm4 requires `random' to be a formula")
}
random.vars <- all.vars(random)
} else {
random.vars <- NULL
}
# create model frame.....
gp <- mgcv::interpret.gam(formula) # interpret the formula
mf <- match.call(expand.dots = FALSE)
mf$formula <- gp$fake.formula
mf$REML <- mf$verbose <- mf$control <- mf$start <- mf$family <- mf$scale <-
mf$knots <- mf$random <- mf$... <- NULL ## mf$weights?
mf[[1]] <- as.name("model.frame")
pmf <- mf
gmf <- eval(mf, parent.frame())
gam.terms <- attr(gmf, "terms")
if (length(random.vars)) {
mf$formula <- as.formula(paste(paste(deparse(gp$fake.formula,
backtick = TRUE
), collapse = ""), "+", paste(random.vars,
collapse = "+"
)))
mf <- eval(mf, parent.frame())
} else {
mf <- gmf
}
rm(gmf)
if (nrow(mf) < 2) {
stop("Not enough (non-NA) data to do anything meaningful")
}
## summarize the *raw* input variables
## note can't use get_all_vars here -- buggy with matrices
vars <- all.vars(gp$fake.formula[-2]) ## drop response here
inp <- parse(text = paste("list(", paste(vars, collapse = ","), ")"))
dl <- eval(inp, data, parent.frame())
names(dl) <- vars ## list of all variables needed
## summarize the input data
variable.summary <- `%:::%`("mgcv", "variable.summary")
var.summary <- variable.summary(gp$pf, dl, nrow(mf))
## lmer offset handling work around...
## variables not in mf raw -- can cause lmer problem
mvars <- vars[!vars %in% names(mf)]
if (length(mvars) > 0) {
for (i in 1:length(mvars)) {
mf[[mvars[i]]] <- dl[[mvars[i]]]
}
} ## append raw versions to mf
pmf$formula <- gp$pf
pmf <- eval(pmf, parent.frame()) # pmf contains all data for non-smooth part
pTerms <- attr(pmf, "terms")
G <- gamm4.setup(gp, pterms = pTerms, data = mf)
G$var.summary <- var.summary
## number of random smooths (i.e. s(...,fx=FALSE,...) terms)
n.sr <- length(G$random)
if (is.null(random) && n.sr == 0) {
return(mf)
}
yname <- mgcv::new.name("y", names(mf))
eval(parse(text = paste("mf$", yname, "<-G$y", sep = "")))
Xname <- mgcv::new.name("X", names(mf))
eval(parse(text = paste("mf$", Xname, "<-G$X", sep = "")))
offset.name <- attr(mf, "names")[attr(attr(mf, "terms"), "offset")]
lme4.formula <- paste(yname, "~", Xname, "-1")
if (length(offset.name)) {
lme4.formula <- paste(lme4.formula, "+", offset.name)
}
## Add the random effect dummy variables for the smooth
r.name <- names(G$random)
if (n.sr) {
## adding the constructed variables to the model frame avoiding name
## duplication
for (i in 1:n.sr) {
mf[[r.name[i]]] <- factor(rep(1:ncol(G$random[[i]]),
length = nrow(G$random[[i]])
))
lme4.formula <- paste(lme4.formula, "+ (1|", r.name[i], ")")
}
}
if (!is.null(random)) { ## append the regular random effects
lme4.formula <- paste(
lme4.formula, "+",
substring(paste(deparse(random, backtick = TRUE), collapse = ""),
first = 2
)
)
}
lme4.formula <- as.formula(lme4.formula)
if (family$family == "gaussian" && family$link == "identity") {
linear <- TRUE
} else {
linear <- FALSE
}
control <- if (linear) {
lme4::lmerControl()
} else {
lme4::glmerControl()
}
## NOTE: further arguments should be passed here...
b <- if (linear) {
lme4::lFormula(lme4.formula,
data = mf, weights = G$w, REML = TRUE,
control = control,
)
} else {
lme4::glFormula(lme4.formula,
data = mf, family = family, weights = G$w,
control = control,
)
}
if (n.sr) {
tn <- names(b$reTrms$cnms)
ind <- 1:length(tn)
sn <- names(G$random) ## names of smooth random components
for (i in 1:n.sr) { ## loop through random effect smooths
k <- ind[sn[i] == tn] ## which term should contain G$random[[i]]
ii <- (b$reTrms$Gp[k] + 1):b$reTrms$Gp[k + 1]
b$reTrms$Zt[ii, ] <- as(t(G$random[[i]]), "dgCMatrix")
b$reTrms$cnms[[k]] <- attr(G$random[[i]], "s.label")
}
}
return(nlist(mf, b))
}
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