From 48b417a314308d41a8c11ebc7676b34456f4cd05 Mon Sep 17 00:00:00 2001
From: jsocolar <jacob.socolar@gmail.com>
Date: Sat, 28 Oct 2023 14:06:04 -0400
Subject: [PATCH] roxygenize

---
 R/log_lik.R               |  6 +++-
 R/pp_mixture.R            | 61 +--------------------------------------
 man/hu_families.Rd        | 13 +++++++++
 man/pp_mixture.brmsfit.Rd |  9 ++++++
 man/zi_families.Rd        | 13 +++++++++
 5 files changed, 41 insertions(+), 61 deletions(-)
 create mode 100644 man/hu_families.Rd
 create mode 100644 man/zi_families.Rd

diff --git a/R/log_lik.R b/R/log_lik.R
index 950d3b614..849c7adeb 100644
--- a/R/log_lik.R
+++ b/R/log_lik.R
@@ -963,7 +963,11 @@ log_lik_mixture <- function(i, prep, mix = TRUE, zihu = FALSE) {
   
   families <- family_names(prep$family)
   
-  n_zi <- sum(is.zihufamily(families)) + sum(families == "zero_one_inflated_beta")
+  if (zihu) {
+    n_zi <- sum(is.zihufamily(families)) + sum(families == "zero_one_inflated_beta")
+  } else {
+    n_zi <- 0
+  }
   
   if (!mix & zihu) {
     out <- array(NA, dim = c(prep$ndraws, 1 + n_zi))
diff --git a/R/pp_mixture.R b/R/pp_mixture.R
index b5c940b7b..75626eb77 100644
--- a/R/pp_mixture.R
+++ b/R/pp_mixture.R
@@ -95,6 +95,7 @@ pp_mixture.brmsfit <- function(x, newdata = NULL, re_formula = NULL,
   if (z_mix & !any_zihu) {
     stop2("Method 'pp_mixture(..., z_mix = TRUE)' can only be applied to zero-inflated and hurdle models.")
   }
+  
   if (!is.mixfamily(family) & !z_mix) {
     stop2("Method 'pp_mixture' can only be applied to mixture models.")
   }
@@ -141,66 +142,6 @@ pp_mixture <- function(x, ...) {
   UseMethod("pp_mixture")
 }
 
-# 
-# latent_zi_state_prob <- function (brmsfit, ...) {
-#   fam <- brmsfit$family$family
-#   if(!is.zifamily(fam)) {
-#     stop2(paste0(
-#       "latent zi probs available only for discrete zero-inflated families (",
-#       paste(zi_families(), collapse = ", "),
-#       "). Supplied brmsfit has family: ",
-#       fam
-#     ))
-#   }
-#   lik <- exp(log_lik(brmsfit, ...))
-#   zi_lik_given_obs_zero <- posterior_linpred(
-#     brmsfit, 
-#     dpar = "zi",
-#     transform = TRUE,
-#     ...
-#   )
-#   resp_name <- brmsfit$formula$resp
-#   resp_data <- brmsfit$data[[resp_name]]
-#   resp_is_zero <- as.integer(resp_data == 0)
-#   zi_lik <- sweep(zi_lik_given_obs_zero, MARGIN=2, resp_is_zero, `*`)
-#   zi_lik / lik
-# }
-# 
-# 
-# latent_hu_state_prob <- function (brmsfit) {
-#   fam <- brmsfit$family$family
-#   if(!is.hufamily(fam)) {
-#     stop2(paste0(
-#       "latent hu probs available only for hurdle and zero-inflated continuous families (",
-#       paste(hu_families(), collapse = ", "),
-#       "). Supplied brmsfit has family: ",
-#       fam
-#     ))
-#   }
-#   
-#   resp_name <- brmsfit$formula$resp 
-#   
-#   if (is.null(newdata)) {
-#     the_data <- brmsfit$data
-#   } else {
-#     the_data <- newdata
-#   }
-#   
-#   if (fam == "zero_one_inflated_beta") {
-#     out <- data.frame(
-#       ni = as.integer(!(the_data[[resp]] %in% c(0, 1))),
-#       zi = as.integer(the_data[[resp]] == 0),
-#       oi = as.integer(the_data[[resp]] == 1)
-#   } else {
-#     out <- data.frame(
-#       ni = as.integer(the_data != 0),
-#       zi = as.integer(the_data == 0)
-#     )
-#   }
-#   out
-# }
-# 
-
 #' List of all hurdle families, where "hurdle" means anything where observed 
 #' zeros are guaranteed to be due to the zero-inflation component.
 hu_families <- function() {
diff --git a/man/hu_families.Rd b/man/hu_families.Rd
new file mode 100644
index 000000000..41c3d0481
--- /dev/null
+++ b/man/hu_families.Rd
@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pp_mixture.R
+\name{hu_families}
+\alias{hu_families}
+\title{List of all hurdle families, where "hurdle" means anything where observed 
+zeros are guaranteed to be due to the zero-inflation component.}
+\usage{
+hu_families()
+}
+\description{
+List of all hurdle families, where "hurdle" means anything where observed 
+zeros are guaranteed to be due to the zero-inflation component.
+}
diff --git a/man/pp_mixture.brmsfit.Rd b/man/pp_mixture.brmsfit.Rd
index 14225530c..96ac59f8e 100644
--- a/man/pp_mixture.brmsfit.Rd
+++ b/man/pp_mixture.brmsfit.Rd
@@ -16,6 +16,7 @@
   summary = TRUE,
   robust = FALSE,
   probs = c(0.025, 0.975),
+  z_mix = FALSE,
   ...
 )
 
@@ -59,6 +60,14 @@ Only used if \code{summary} is \code{TRUE}.}
 \item{probs}{The percentiles to be computed by the \code{quantile}
 function. Only used if \code{summary} is \code{TRUE}.}
 
+\item{z_mix}{Logical. If TRUE, returns the mixture component
+memberships for the hurdle/zero-inflation state in hurdle
+and zero-inflated models. For an explicit mixture model 
+including a zero-inflated model in the mixture, probabilities
+are returned for each mixture component, treating the 
+zero-inflation state and the non-zero-inflation state as
+separate mixture components.}
+
 \item{...}{Further arguments passed to \code{\link{prepare_predictions}}
 that control several aspects of data validation and prediction.}
 }
diff --git a/man/zi_families.Rd b/man/zi_families.Rd
new file mode 100644
index 000000000..c556c0705
--- /dev/null
+++ b/man/zi_families.Rd
@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pp_mixture.R
+\name{zi_families}
+\alias{zi_families}
+\title{List of all true zero-inflated families, where observed zeros may arise
+either from the zero-inflation component or from the other component.}
+\usage{
+zi_families()
+}
+\description{
+List of all true zero-inflated families, where observed zeros may arise
+either from the zero-inflation component or from the other component.
+}