#' @title Get link-inverse function from model object
#' @name link_inverse
#'
#' @description Returns the link-inverse function from a model object.
#'
#' @param what For `gamlss` models, indicates for which distribution
#' parameter the link (inverse) function should be returned; for
#' `betareg` or `DirichletRegModel`, can be `"mean"` or
#' `"precision"`.
#' @inheritParams find_predictors
#' @inheritParams find_formula
#'
#' @return A function, describing the inverse-link function from a model-object.
#' For multivariate-response models, a list of functions is returned.
#'
#' @examples
#' # example from ?stats::glm
#' counts <- c(18, 17, 15, 20, 10, 20, 25, 13, 12)
#' outcome <- gl(3, 1, 9)
#' treatment <- gl(3, 3)
#' m <- glm(counts ~ outcome + treatment, family = poisson())
#'
#' link_inverse(m)(0.3)
#' # same as
#' exp(0.3)
#' @export
link_inverse <- function(x, ...) {
UseMethod("link_inverse")
}
# Default method ---------------------------------------
#' @export
link_inverse.default <- function(x, ...) {
if (inherits(x, "list") && object_has_names(x, "gam")) {
x <- x$gam
class(x) <- c(class(x), c("glm", "lm"))
}
if (inherits(x, "Zelig-relogit")) {
stats::make.link(link = "logit")$linkinv
} else {
.extract_generic_linkinv(x)
}
}
.extract_generic_linkinv <- function(x, default_link = NULL) {
# general approach
out <- .safe(stats::family(x)$linkinv)
# if it fails, try to retrieve from model information
if (is.null(out)) {
# get model family, consider special gam-case
ff <- .gam_family(x)
if ("linkfun" %in% names(ff)) {
# return link function, if exists
out <- ff$linkinv
} else if ("link" %in% names(ff) && is.character(ff$link)) {
# else, create link function from link-string
out <- .safe(stats::make.link(link = ff$link)$linkinv)
# or match the function - for "exp()", make.link() won't work
if (is.null(out)) {
out <- .safe(match.fun(ff$link))
}
}
}
# if all fails, force default link
if (is.null(out) && !is.null(default_link)) {
out <- switch(default_link,
identity = .safe(stats::gaussian(link = "identity")$linkinv),
.safe(stats::make.link(link = default_link)$linkinv)
)
}
out
}
# GLM families ---------------------------------------------------
#' @export
link_inverse.glm <- function(x, ...) {
.extract_generic_linkinv(x, "logit")
}
#' @export
link_inverse.speedglm <- link_inverse.glm
#' @export
link_inverse.bigglm <- link_inverse.glm
#' @export
link_inverse.nestedLogit <- function(x, ...) {
stats::make.link(link = "logit")$linkinv
}
# Tobit Family ---------------------------------
#' @export
link_inverse.tobit <- function(x, ...) {
.make_tobit_family(x)$linkinv
}
#' @export
link_inverse.crch <- link_inverse.tobit
#' @export
link_inverse.survreg <- link_inverse.tobit
#' @export
link_inverse.psm <- link_inverse.tobit
#' @export
link_inverse.flexsurvreg <- function(x, ...) {
distribution <- parse(text = safe_deparse(x$call))[[1]]$dist
.make_tobit_family(x, distribution)$linkinv
}
# Gaussian identity links ---------------------------------
#' @export
link_inverse.lm <- function(x, ...) {
.extract_generic_linkinv(x, "identity")
}
#' @export
link_inverse.phylolm <- link_inverse.lm
#' @export
link_inverse.bayesx <- link_inverse.lm
#' @export
link_inverse.mmrm <- link_inverse.lm
#' @export
link_inverse.mmrm_fit <- link_inverse.lm
#' @export
link_inverse.mmrm_tmb <- link_inverse.lm
#' @export
link_inverse.systemfit <- link_inverse.lm
#' @export
link_inverse.lqmm <- link_inverse.lm
#' @export
link_inverse.lqm <- link_inverse.lm
#' @export
link_inverse.biglm <- link_inverse.lm
#' @export
link_inverse.aovlist <- link_inverse.lm
#' @export
link_inverse.ivreg <- link_inverse.lm
#' @export
link_inverse.ivFixed <- link_inverse.lm
#' @export
link_inverse.iv_robust <- link_inverse.lm
#' @export
link_inverse.mixed <- link_inverse.lm
#' @export
link_inverse.lme <- link_inverse.lm
#' @export
link_inverse.rq <- link_inverse.lm
#' @export
link_inverse.rqs <- link_inverse.lm
#' @export
link_inverse.rqss <- link_inverse.lm
#' @export
link_inverse.crq <- link_inverse.lm
#' @export
link_inverse.crqs <- link_inverse.lm
#' @export
link_inverse.censReg <- link_inverse.lm
#' @export
link_inverse.plm <- link_inverse.lm
#' @export
link_inverse.lm_robust <- link_inverse.lm
#' @export
link_inverse.truncreg <- link_inverse.lm
#' @export
link_inverse.felm <- link_inverse.lm
#' @export
link_inverse.feis <- link_inverse.lm
#' @export
link_inverse.gls <- link_inverse.lm
#' @export
link_inverse.lmRob <- link_inverse.lm
#' @export
link_inverse.MANOVA <- link_inverse.lm
#' @export
link_inverse.RM <- link_inverse.lm
#' @export
link_inverse.lmrob <- link_inverse.lm
#' @export
link_inverse.complmrob <- link_inverse.lm
#' @export
link_inverse.speedlm <- link_inverse.lm
#' @export
link_inverse.afex_aov <- link_inverse.lm
#' @export
link_inverse.svy2lme <- link_inverse.lm
#' @rdname link_inverse
#' @export
link_inverse.betareg <- function(x, what = c("mean", "precision"), ...) {
what <- match.arg(what)
switch(what,
mean = x$link$mean$linkinv,
precision = x$link$precision$linkinv
)
}
#' @rdname link_inverse
#' @export
link_inverse.DirichletRegModel <- function(x, what = c("mean", "precision"), ...) {
what <- match.arg(what)
if (x$parametrization == "common") {
stats::make.link("logit")$linkinv
} else {
switch(what,
mean = stats::make.link("logit")$linkinv,
precision = stats::make.link("log")$linkinv
)
}
}
# Logit links -----------------------------------
#' @export
link_inverse.gmnl <- function(x, ...) {
.extract_generic_linkinv(x, "logit")
}
#' @export
link_inverse.mlogit <- link_inverse.gmnl
#' @export
link_inverse.mclogit <- link_inverse.gmnl
#' @export
link_inverse.mmclogit <- link_inverse.gmnl
#' @export
link_inverse.mblogit <- link_inverse.gmnl
#' @export
link_inverse.logitr <- link_inverse.gmnl
#' @export
link_inverse.BBreg <- link_inverse.gmnl
#' @export
link_inverse.BBmm <- link_inverse.gmnl
#' @export
link_inverse.coxph <- link_inverse.gmnl
#' @export
link_inverse.riskRegression <- link_inverse.gmnl
#' @export
link_inverse.comprisk <- link_inverse.gmnl
#' @export
link_inverse.coxr <- link_inverse.gmnl
#' @export
link_inverse.survfit <- link_inverse.gmnl
#' @export
link_inverse.coxme <- link_inverse.gmnl
#' @export
link_inverse.lrm <- link_inverse.gmnl
#' @export
link_inverse.orm <- link_inverse.gmnl
#' @export
link_inverse.cph <- link_inverse.gmnl
#' @export
link_inverse.logistf <- link_inverse.gmnl
#' @export
link_inverse.flac <- link_inverse.gmnl
#' @export
link_inverse.flic <- link_inverse.gmnl
#' @export
link_inverse.multinom <- link_inverse.gmnl
#' @export
link_inverse.multinom_weightit <- function(x, ...) {
stats::make.link(link = x$family$link)$linkinv
}
#' @export
link_inverse.ordinal_weightit <- link_inverse.multinom_weightit
# Probit link ------------------------
#' @export
link_inverse.ivprobit <- function(x, ...) {
stats::make.link(link = "probit")$linkinv
}
#' @export
link_inverse.mvord <- function(x, ...) {
link_name <- x$rho$link$name
l <- stats::make.link(link = ifelse(link_name == "mvprobit", "probit", "logit"))
l$linkinv
}
# Log-links ---------------------------------------
#' @export
link_inverse.zeroinfl <- function(x, ...) {
stats::make.link("log")$linkinv
}
#' @export
link_inverse.hurdle <- link_inverse.zeroinfl
#' @export
link_inverse.zerotrunc <- link_inverse.zeroinfl
# Ordinal models -----------------------------------
#' @export
link_inverse.clm <- function(x, ...) {
stats::make.link(.get_ordinal_link(x))$linkinv
}
#' @export
link_inverse.clmm <- link_inverse.clm
#' @export
link_inverse.clm2 <- link_inverse.clm
#' @export
link_inverse.serp <- link_inverse.clm
#' @export
link_inverse.mixor <- link_inverse.clm
# mfx models ------------------------------------------------------
#' @rdname link_inverse
#' @export
link_inverse.betamfx <- function(x, what = c("mean", "precision"), ...) {
what <- match.arg(what)
link_inverse.betareg(x$fit, what = what, ...)
}
#' @export
link_inverse.betaor <- link_inverse.betamfx
#' @export
link_inverse.logitmfx <- function(x, ...) {
link_inverse(x$fit, ...)
}
#' @export
link_inverse.poissonmfx <- link_inverse.logitmfx
#' @export
link_inverse.probitmfx <- link_inverse.logitmfx
#' @export
link_inverse.negbinmfx <- link_inverse.logitmfx
#' @export
link_inverse.logitor <- link_inverse.logitmfx
#' @export
link_inverse.probitirr <- link_inverse.logitmfx
#' @export
link_inverse.negbinirr <- link_inverse.logitmfx
# Other models ----------------------------
#' @export
link_inverse.Rchoice <- function(x, ...) {
stats::make.link(link = x$link)$linkinv
}
#' @export
link_inverse.merModList <- function(x, ...) {
link_inverse.default(x[[1]], ...)
}
#' @export
link_inverse.robmixglm <- function(x, ...) {
switch(tolower(x$family),
gaussian = stats::make.link(link = "identity")$linkinv,
binomial = stats::make.link(link = "logit")$linkinv,
gamma = stats::make.link(link = "inverse")$linkinv,
poisson = ,
truncpoisson = stats::make.link(link = "log")$linkinv,
stats::make.link(link = "identity")$linkinv
)
}
#' @export
link_inverse.cglm <- function(x, ...) {
link <- parse(text = safe_deparse(x$call))[[1]]$link
method <- parse(text = safe_deparse(x$call))[[1]]$method
if (!is.null(method) && method == "clm") {
link <- "identity"
}
stats::make.link(link = link)$linkinv
}
#' @export
link_inverse.cpglmm <- function(x, ...) {
f <- .get_cplm_family(x)
f$linkinv
}
#' @export
link_inverse.cpglm <- link_inverse.cpglmm
#' @export
link_inverse.zcpglm <- link_inverse.cpglmm
#' @export
link_inverse.bcplm <- link_inverse.cpglmm
#' @export
link_inverse.fixest <- function(x, ...) {
if (is.null(x$family)) {
if (!is.null(x$method) && x$method == "feols") {
stats::gaussian(link = "identity")$linkinv
}
} else if (inherits(x$family, "family")) {
x$family$linkinv
} else {
link <- switch(x$family,
poisson = ,
negbin = "log",
logit = "logit",
gaussian = "identity"
)
stats::make.link(link)$linkinv
}
}
#' @export
link_inverse.feglm <- link_inverse.fixest
#' @export
link_inverse.glmx <- function(x, ...) {
x$family$glm$linkinv
}
#' @export
link_inverse.bife <- function(x, ...) {
x$family$linkinv
}
#' @export
link_inverse.glmgee <- link_inverse.bife
#' @export
link_inverse.glmmadmb <- function(x, ...) {
x$ilinkfun
}
#' @export
link_inverse.polr <- function(x, ...) {
link <- x$method
if (link == "logistic") link <- "logit"
stats::make.link(link)$linkinv
}
#' @export
link_inverse.svyolr <- function(x, ...) {
link <- x$method
if (link == "logistic") link <- "logit"
stats::make.link(link)$linkinv
}
#' @export
link_inverse.averaging <- function(x, ...) {
ml <- attributes(x)$modelList
if (is.null(ml)) {
format_warning("Can't retrieve data. Please use `fit = TRUE` in `model.avg()`.")
return(NULL)
}
link_inverse(ml[[1]])
}
#' @export
link_inverse.LORgee <- function(x, ...) {
if (grepl(pattern = "logit", x = x$link, fixed = TRUE)) {
link <- "logit"
} else if (grepl(pattern = "probit", x = x$link, fixed = TRUE)) {
link <- "probit"
} else if (grepl(pattern = "cauchit", x = x$link, fixed = TRUE)) {
link <- "cauchit"
} else if (grepl(pattern = "cloglog", x = x$link, fixed = TRUE)) {
link <- "cloglog"
} else {
link <- "logit"
}
stats::make.link(link)$linkinv
}
#' @export
link_inverse.glimML <- function(x, ...) {
stats::make.link(x@link)$linkinv
}
#' @export
link_inverse.glmmTMB <- function(x, ...) {
ff <- stats::family(x)
if ("linkinv" %in% names(ff)) {
ff$linkinv
} else if ("link" %in% names(ff) && is.character(ff$link)) {
stats::make.link(ff$link)$linkinv
} else {
match.fun("exp")
}
}
#' @export
link_inverse.MCMCglmm <- function(x, ...) {
switch(x$Residual$original.family,
cengaussian = ,
gaussian = stats::gaussian(link = "identity")$linkinv,
categorical = ,
multinomial = ,
zibinomial = ,
ordinal = stats::make.link("logit")$linkinv,
poisson = ,
cenpoisson = ,
zipoisson = ,
zapoisson = ,
ztpoisson = ,
hupoisson = stats::make.link("log")$linkinv
)
}
#' @export
link_inverse.glmm <- function(x, ...) {
switch(tolower(x$family.glmm$family.glmm),
bernoulli.glmm = ,
binomial.glmm = stats::make.link("logit")$linkinv,
poisson.glmm = stats::make.link("log")$linkinv,
stats::gaussian(link = "identity")$linkinv
)
}
#' @export
link_inverse.gamm <- function(x, ...) {
x <- x$gam
class(x) <- c(class(x), c("glm", "lm"))
NextMethod()
}
#' @export
link_inverse.stanmvreg <- function(x, ...) {
fam <- stats::family(x)
lapply(fam, function(.x) .x$linkinv)
}
#' @export
link_inverse.gbm <- function(x, ...) {
switch(x$distribution$name,
laplace = ,
tdist = ,
gaussian = stats::gaussian(link = "identity")$linkinv,
poisson = stats::poisson(link = "log")$linkinv,
huberized = ,
adaboost = ,
coxph = ,
bernoulli = stats::make.link("logit")$linkinv
)
}
#' @export
link_inverse.phyloglm <- function(x, ...) {
if (startsWith(x$method, "logistic")) {
stats::make.link("logit")$linkinv
} else {
stats::poisson(link = "log")$linkinv
}
}
#' @export
link_inverse.brmsfit <- function(x, ...) {
fam <- stats::family(x)
if (is_multivariate(x)) {
lapply(fam, .brms_link_inverse)
} else {
.brms_link_inverse(fam)
}
}
#' @rdname link_inverse
#' @export
link_inverse.gamlss <- function(x, what = c("mu", "sigma", "nu", "tau"), ...) {
what <- match.arg(what)
faminfo <- get(x$family[1], asNamespace("gamlss"))()
# exceptions
if (faminfo$family[1] == "LOGNO") {
function(eta) pmax(exp(eta), .Machine$double.eps)
} else {
switch(what,
mu = faminfo$mu.linkinv,
sigma = faminfo$sigma.linkinv,
nu = faminfo$nu.linkinv,
tau = faminfo$tau.linkinv,
faminfo$mu.linkinv
)
}
}
#' @export
link_inverse.bamlss <- function(x, ...) {
flink <- stats::family(x)$links[1]
tryCatch(
stats::make.link(flink)$linkinv,
error = function(e) {
print_colour("\nCould not find appropriate link-inverse-function.\n", "red")
}
)
}
#' @export
link_inverse.glmmPQL <- function(x, ...) {
x$family$linkinv
}
#' @export
link_inverse.MixMod <- link_inverse.glmmPQL
#' @export
link_inverse.cgam <- link_inverse.glmmPQL
#' @export
link_inverse.vgam <- function(x, ...) {
x@family@linkinv
}
#' @export
link_inverse.vglm <- link_inverse.vgam
#' @export
link_inverse.svy_vglm <- function(x, ...) {
link_inverse(x$fit)
}
#' @export
link_inverse.model_fit <- link_inverse.svy_vglm
#' @export
link_inverse.gam <- function(x, ...) {
li <- .safe(.gam_family(x)$linkinv)
if (is.null(li)) {
mi <- .gam_family(x)
if (object_has_names(mi, "linfo")) {
if (object_has_names(mi$linfo, "linkinv")) {
li <- mi$linfo$linkinv
} else {
li <- mi$linfo[[1]]$linkinv
}
}
}
li
}
#' @export
link_inverse.mipo <- function(x, ...) {
models <- eval(x$call$object)
link_inverse(models$analyses[[1]])
}
#' @export
link_inverse.mira <- function(x, ...) {
check_if_installed("mice")
link_inverse(mice::pool(x), ...)
}
# helper --------------
.brms_link_inverse <- function(fam) {
# do we have custom families?
if (!is.null(fam$family) && (is.character(fam$family) && fam$family == "custom")) {
il <- stats::make.link(fam$link)$linkinv
} else if ("linkinv" %in% names(fam)) {
il <- fam$linkinv
} else if ("link" %in% names(fam) && is.character(fam$link)) {
il <- stats::make.link(fam$link)$linkinv
} else {
ff <- get(fam$family, asNamespace("stats"))
il <- ff(fam$link)$linkinv
}
il
}
.get_cplm_family <- function(x) {
link <- parse(text = safe_deparse(x@call))[[1]]$link
if (is.null(link)) link <- "log"
if (is.numeric(link)) {
check_if_installed("statmod")
statmod::tweedie(link.power = link)
} else {
stats::poisson(link = link)
}
}
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