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#' Models used in the geoBayes package
#'
#' This hidden variable contains a choice of models that can be fit
#' with this package. The model can be chosen in the \code{family}
#' input of the relevant function. This variable cannot be
#' overwritten.
#' @name geoBayes_models
#' @export
.geoBayes_models <-
data.frame(
family = c("gaussian", # 1
"binomial.robit", # 2
"binomial.logit", # 3
"binomial.probit", # 4
"binomial.Wallace", # 5
"poisson.modifiedbc", # 6
"poisson.boxcox", # 7
"Gamma.modifiedbc", # 8
"Gamma.boxcox", # 9
"binomial.modifiedGEV",# 10
"binomial.modifiedGEVns",# 11
"binomial.GEV" # 12
),
needlinkp = c(TRUE, # 1 "gaussian",
TRUE, # 2 "binomial.robit",
FALSE, # 3 "binomial.logit",
FALSE, # 4 "binomial.probit",
TRUE, # 5 "binomial.Wallace",
TRUE, # 6 "poisson.modifiedbc",
TRUE, # 7 "poisson.boxcox",
TRUE, # 8 "Gamma.modifiedbc",
TRUE, # 9 "Gamma.boxcox"
TRUE, # 10 "binomial.modifiedGEV"
TRUE, # 11 "binomial.modifiedGEVns"
TRUE # 12 "binomial.GEV"
),
linkplb = c(-Inf, # 1 "gaussian",
0, # 2 "binomial.robit",
NA, # 3 "binomial.logit",
NA, # 4 "binomial.probit",
0, # 5 "binomial.Wallace",
0, # 6 "poisson.modifiedbc",
-Inf, # 7 "poisson.boxcox",
0, # 8 "Gamma.modifiedbc",
-Inf, # 9 "Gamma.boxcox"
0, # 10 "binomial.modifiedGEV"
0, # 11 "binomial.modifiedGEVns"
-Inf # 12 "binomial.GEV"
),
incllb = c(NA, # 1 "gaussian",
FALSE, # 2 "binomial.robit",
NA, # 3 "binomial.logit",
NA, # 4 "binomial.probit",
FALSE, # 5 "binomial.Wallace",
TRUE, # 6 "poisson.modifiedbc",
NA, # 7 "poisson.boxcox",
TRUE, # 8 "Gamma.modifiedbc",
NA, # 9 "Gamma.boxcox"
TRUE, # 10 "binomial.modifiedGEV"
TRUE, # 11 "binomial.modifiedGEVns"
NA # 12 "binomial.GEV"
),
linkpub = c(Inf, # 1 "gaussian",
Inf, # 2 "binomial.robit",
NA, # 3 "binomial.logit",
NA, # 4 "binomial.probit",
Inf, # 5 "binomial.Wallace",
Inf, # 6 "poisson.modifiedbc",
Inf, # 7 "poisson.boxcox",
Inf, # 8 "Gamma.modifiedbc",
Inf, # 9 "Gamma.boxcox"
Inf, # 10 "binomial.modifiedGEV"
Inf, # 11 "binomial.modifiedGEVns"
Inf # 12 "binomial.GEV"
),
inclub = c(NA, # 1 "gaussian",
NA, # 2 "binomial.robit",
NA, # 3 "binomial.logit",
NA, # 4 "binomial.probit",
NA, # 5 "binomial.Wallace",
NA, # 6 "poisson.modifiedbc",
NA, # 7 "poisson.boxcox",
NA, # 8 "Gamma.modifiedbc",
NA, # 9 "Gamma.boxcox"
NA, # 10 "binomial.modifiedGEV"
NA, # 11 "binomial.modifiedGEVns"
NA # 12 "binomial.GEV"
),
haswo = c(FALSE, # 1 "gaussian",
TRUE, # 2 "binomial.robit",
FALSE, # 3 "binomial.logit",
FALSE, # 4 "binomial.probit",
FALSE, # 5 "binomial.Wallace",
FALSE, # 6 "poisson.modifiedbc",
TRUE, # 7 "poisson.boxcox",
FALSE, # 8 "Gamma.modifiedbc",
FALSE, # 9 "Gamma.boxcox"
FALSE, # 10 "binomial.modifiedGEV"
FALSE, # 11 "binomial.modifiedGEVns"
TRUE # 12 "binomial.GEV"
),
stringsAsFactors = FALSE)
lockBinding(".geoBayes_models", environment())
.geoBayes_family <- function (family) {
## family is a character, partially matching .geoBayes_models before
## and after the dot.
nfamily <- length(family)
if (nfamily > 1) {
stop ("You cannot use more than one family.")
} else if (nfamily == 0) {
as.integer(1L)
} else if (pmatch(family, "transformed.gaussian", 0)) {
as.integer(0L)
} else if (is.numeric(family) && family >= 0 &&
family <= length(.geoBayes_models$family)) {
as.integer(family)
} else if (is.character(family)) {
fl <- strsplit(family, split = "[[:punct:][:space:]]+")[[1]]
pattern <- if(length(fl) > 1)
paste0("\\.", fl[-1], "[[:alnum:]]*", collapse = "")
pattern <- paste0("^", fl[1], "[[:alnum:]]*", pattern)
out <- grep(pattern, .geoBayes_models$family, value = FALSE)
if (length(out) == 0) stop ("Cannot deduce family from input.")
as.integer(out[1])
} else {
stop ("Cannot deduce family.")
}
}
## Checks whether the link parameter is consistent with the family and
## returns a real representation of the link parameter.
.geoBayes_getlinkp <- function (linkp, ifam) {
lbt <- `>`; ubt <- `<`
if (ifam == 0 || pmatch(ifam, "transformed.gaussian", 0)) {
family <- "transformed.gaussian"
lb <- 0; ub <- Inf; needlinkp <- TRUE
} else {
if (!is.numeric(ifam)) ifam <- .geoBayes_family(ifam)
family <- .geoBayes_models$family[ifam]
lb <- .geoBayes_models$linkplb[ifam]
ub <- .geoBayes_models$linkpub[ifam]
needlinkp <- .geoBayes_models$needlinkp[ifam]
if (needlinkp && is.finite(lb) && .geoBayes_models$incllb[ifam])
lbt <- `>=`
if (needlinkp && is.finite(ub) && .geoBayes_models$inclub[ifam])
ubt <- `<=`
}
if (!needlinkp) return(0.)
if (is.finite(lb) && !all(lbt(linkp, lb))) {
stop (paste("Link parameter must be", gsub("[^><=]","",deparse(lbt)), lb,
"for the", family, "family"))
}
if (is.finite(ub) && !all(ubt(linkp, ub))) {
stop (paste("Link parameter must be", gsub("[^><=]","",deparse(ubt)), ub,
"for the", family, "family"))
}
as.double(linkp)
}
### valid <- .geoBayes_models_opts$linkp[[family]]
### for (i in seq_along(valid)) {
### test <- valid[[i]]
### nmtest <- names(valid[i])
### if (length(nmtest) && nmtest != "") { # Character value
### if (all(as.character(linkp) == nmtest))
### return (rep(as.double(test), k))
### } else if (length(test) == 2) { # Interval value
### if (all(linkp > test[1]) && all(linkp < test[2]))
### return (as.double(linkp))
### } else if (length(test) == 1) { # Scalar value
### return (rep(as.double(test), k))
### }
### }
### stop ("Cannot deduce link parameter from family.")
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