#' gamMRSea model function
#'
#' See \code{\link{glm}} for details. A \code{splineParams} object may be specified as part of the model object.
#'
#' @author LAS Scott-Hayward, University of St Andrews
#'
#' @export
#'
gamMRSea<-function (formula, family = gaussian, data, weights, subset,
na.action, start = NULL, etastart, mustart, offset, control = list(...),
model = TRUE, method = "glm.fit", x = FALSE, y = TRUE, contrasts = NULL, splineParams=NULL, ...)
{
if(!is.null(splineParams)){
dists<-splineParams[[1]]$dist
aR<-splineParams[[1]]$knotPos
radii<-splineParams[[1]]$radii
radiusIndices<-splineParams[[1]]$radiusIndices
# create new dataframe:
}
call <- match.call()
if (is.character(family))
family <- get(family, mode = "function", envir = parent.frame())
if (is.function(family))
family <- family()
if (is.null(family$family)) {
print(family)
stop("'family' not recognized")
}
if (missing(data))
data <- environment(formula)
mf <- match.call(expand.dots = FALSE)
m <- match(c("formula", "data", "subset", "weights", "na.action",
"etastart", "mustart", "offset", "splineParams"), names(mf), 0L)
mf <- mf[c(1L, m)]
mf$drop.unused.levels <- TRUE
mf[[1L]] <- quote(MRSea::model.frame.gamMRSea)
mf <- eval(mf, envir=parent.frame())
if (identical(method, "model.frame.gamMRSea"))
return(mf)
if (!is.character(method) && !is.function(method))
stop("invalid 'method' argument")
if (identical(method, "glm.fit"))
control <- do.call("glm.control", control)
mt <- attr(mf, "terms")
Y <- model.response(mf, "any")
if (length(dim(Y)) == 1L) {
nm <- rownames(Y)
dim(Y) <- NULL
if (!is.null(nm))
names(Y) <- nm
}
X <- if (!is.empty.model(mt))
model.matrix(mt, mf, contrasts)
else matrix(, NROW(Y), 0L)
weights <- as.vector(model.weights(mf))
if (!is.null(weights) && !is.numeric(weights))
stop("'weights' must be a numeric vector")
if (!is.null(weights) && any(weights < 0))
stop("negative weights not allowed")
offset <- as.vector(model.offset(mf))
if (!is.null(offset)) {
if (length(offset) != NROW(Y))
stop(gettextf("number of offsets is %d should equal %d (number of observations)",
length(offset), NROW(Y)), domain = NA)
}
mustart <- model.extract(mf, "mustart")
etastart <- model.extract(mf, "etastart")
fit <- eval(call(if (is.function(method)) "method" else method,
x = X, y = Y, weights = weights, start = start, etastart = etastart,
mustart = mustart, offset = offset, family = family,
control = control, intercept = attr(mt, "intercept") >
0L))
if (length(offset) && attr(mt, "intercept") > 0L) {
fit2 <- eval(call(if (is.function(method)) "method" else method,
x = X[, "(Intercept)", drop = FALSE], y = Y, weights = weights,
offset = offset, family = family, control = control,
intercept = TRUE))
if (!fit2$converged)
warning("fitting to calculate the null deviance did not converge -- increase 'maxit'?")
fit$null.deviance <- fit2$deviance
}
if (model)
fit$model <- mf
fit$na.action <- attr(mf, "na.action")
if (x)
fit$x <- X
if (!y)
fit$y <- NULL
varshortnames<-unlist(sapply(splineParams,"[[","covar"))
fit <- c(fit, list(call = call, formula = formula, terms = mt,
data = data, offset = offset, control = control, method = method, contrasts = attr(X, "contrasts"), xlevels = .getXlevels(mt, mf), splineParams=splineParams, varshortnames=varshortnames))
class(fit) <- c(fit$class, c("gamMRSea", "glm", "lm"))
fit
}
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