From f64580a252935caccbe6a2aa566c81e9f69054c1 Mon Sep 17 00:00:00 2001
From: mtwesley <mlen.too.wesley@gmail.com>
Date: Sun, 24 Nov 2024 21:05:19 -0500
Subject: [PATCH] updating, running roxygen2 and adding censored files

---
 DESCRIPTION                    |  2 +-
 R/censored.R                   | 54 ++++++++++++++++++++++++++++++++++
 man/greta.template.Rd          | 13 ++++++++
 tests/testthat/test-censored.R | 13 ++++++++
 4 files changed, 81 insertions(+), 1 deletion(-)
 create mode 100644 R/censored.R
 create mode 100644 tests/testthat/test-censored.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 986376a..259bb6a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -34,7 +34,7 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.2
 SystemRequirements: Python (>= 2.7.0) with header files and shared
     library; TensorFlow (v1.14; https://www.tensorflow.org/); TensorFlow
     Probability (v0.7.0; https://www.tensorflow.org/probability/)
diff --git a/R/censored.R b/R/censored.R
new file mode 100644
index 0000000..1e2a5fb
--- /dev/null
+++ b/R/censored.R
@@ -0,0 +1,54 @@
+exponential_censored_distribution <- R6::R6Class(
+  "exponential_censored_distribution",
+  inherit = distribution_node,
+  public = list(
+    initialize = function(rate, is_censored, censoring_type, lower, upper, dim) {
+      rate <- as.greta_array(rate)
+      is_censored <- check_param_greta_array(is_censored)
+      check_numeric_length_1(lower)
+      check_numeric_length_1(upper)
+      check_finite(lower)
+      check_finite(upper)
+      check_x_gte_y(lower, upper)
+
+      dim <- check_dims(rate, is_censored, target_dim = dim)
+
+      super$initialize("exponential_censored", dim)
+      self$add_parameter(rate, "rate")
+      self$add_parameter(is_censored, "is_censored")
+      self$censoring_type <- censoring_type
+      self$lower <- lower
+      self$upper <- upper
+    },
+    tf_distrib = function(parameters, dag) {
+      rate <- parameters$rate
+      is_censored <- parameters$is_censored
+      exp_dist <- tfp$distributions$Exponential(rate = rate)
+      censored_log_prob <- switch(
+        self$censoring_type,
+        "right" = function(y) exp_dist$log_survival_function(y),
+        "left" = function(y) exp_dist$log_cdf(y),
+        "interval" = function(y) {
+          log_cdf_upper <- exp_dist$log_cdf(self$upper)
+          log_cdf_lower <- exp_dist$log_cdf(self$lower)
+          tf$log(tf$exp(log_cdf_upper) - tf$exp(log_cdf_lower))
+        },
+        function(y) exp_dist$log_prob(y)
+      )
+      uncensored_log_prob <- function(y) exp_dist$log_prob(y)
+      list(
+        log_prob = function(y) {
+          tf$where(
+            tf$equal(is_censored, 1),
+            censored_log_prob(y),
+            uncensored_log_prob(y)
+          )
+        }
+      )
+    }
+  )
+)
+
+exponential_censored <- function(rate, is_censored, censoring_type, lower, upper, dim) {
+  distrib("exponential_censored", rate, is_censored, censoring_type = censoring_type, lower = lower, upper = upper, dim = dim)
+}
\ No newline at end of file
diff --git a/man/greta.template.Rd b/man/greta.template.Rd
index 955a6bc..d4231ec 100644
--- a/man/greta.template.Rd
+++ b/man/greta.template.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/package.R
 \docType{package}
 \name{greta.template}
+\alias{greta.template-package}
 \alias{greta.template}
 \title{What the Package Does (One Line, Title Case)}
 \description{
@@ -12,3 +13,15 @@ describe your package here, you can re-use the text from DESCRIPTION
 # add a simple example here to introduce the package!
 
 }
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/your_username/your_repository}
+  \item Report bugs at \url{https://github.com/your_username/your_repository/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: First Last \email{first.last@example.com} (\href{https://orcid.org/YOUR-ORCID-ID}{ORCID})
+
+}
diff --git a/tests/testthat/test-censored.R b/tests/testthat/test-censored.R
new file mode 100644
index 0000000..c27e3d8
--- /dev/null
+++ b/tests/testthat/test-censored.R
@@ -0,0 +1,13 @@
+test_that("exponential_censored_distribution initializes correctly", {
+  rate <- as.greta_array(1)
+  is_censored <- as.greta_array(0)
+  dist <- exponential_censored_distribution$new(rate, is_censored, "right", 0, 1, dim = c(1, 1))
+  expect_s3_class(dist, "exponential_censored_distribution")
+})
+
+test_that("exponential_censored function works", {
+  rate <- as.greta_array(1)
+  is_censored <- as.greta_array(0)
+  dist <- exponential_censored(rate, is_censored, "right", 0, 1, dim = c(1, 1))
+  expect_s3_class(dist, "distribution_node")
+})
\ No newline at end of file