Merge branch 'main' into 402-individual-loo

DESCRIPTION

@@ -24,6 +24,8 @@ Description: Implements joint models combining a non-linear mixed effects model
 License: Apache License (>= 2)
 Encoding: UTF-8
 Language: en-GB
+URL: https://genentech.github.io/jmpost/
+BugReports: https://github.com/Genentech/jmpost/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Depends:
@@ -58,8 +60,9 @@ Suggests:
     purrr,
     vdiffr,
     prodlim,
-    loo,
-    brms
+    brms,
+    tidyr,
+    loo
 Additional_repositories: https://stan-dev.r-universe.dev
 Config/testthat/edition: 3
 Config/testthat/parallel: true
@@ -111,6 +114,7 @@ Collate:
     'SimLongitudinalSteinFojo.R'
     'SimSurvival.R'
     'SurvivalExponential.R'
+    'SurvivalGamma.R'
     'SurvivalLoglogistic.R'
     'SurvivalWeibullPH.R'
     'brier_score.R'

NAMESPACE

@@ -208,12 +208,14 @@ export(SimLongitudinalRandomSlope)
 export(SimLongitudinalSteinFojo)
 export(SimSurvival)
 export(SimSurvivalExponential)
+export(SimSurvivalGamma)
 export(SimSurvivalLogLogistic)
 export(SimSurvivalWeibullPH)
 export(StanModel)
 export(StanModule)
 export(Surv)
 export(SurvivalExponential)
+export(SurvivalGamma)
 export(SurvivalLogLogistic)
 export(SurvivalModel)
 export(SurvivalQuantities)
@@ -287,6 +289,7 @@ exportClasses(SimSurvival)
 exportClasses(StanModel)
 exportClasses(StanModule)
 exportClasses(SurvivalExponential)
+exportClasses(SurvivalGamma)
 exportClasses(SurvivalLogLogistic)
 exportClasses(SurvivalModel)
 exportClasses(SurvivalWeibullPH)
@@ -304,9 +307,11 @@ importFrom(stats,.checkMFClasses)
 importFrom(stats,acf)
 importFrom(stats,as.formula)
 importFrom(stats,delete.response)
+importFrom(stats,dgamma)
 importFrom(stats,median)
 importFrom(stats,model.frame)
 importFrom(stats,model.matrix)
+importFrom(stats,pgamma)
 importFrom(stats,qlogis)
 importFrom(stats,rbeta)
 importFrom(stats,rcauchy)

R/SimSurvival.R

@@ -176,7 +176,7 @@ sampleObservations.SimSurvival <- function(object, times_df) {
         dplyr::mutate(event = 0)
 
     if (!(nrow(os_had_censor) == 0)) {
-        message(sprintf("INFO: %i subjects did not die before max(times)", nrow(os_had_censor)))
+        message(sprintf("INFO: %i subject(s) did not die before max(times)", nrow(os_had_censor)))
     }
 
     os_dat_complete <- os_had_event |>
@@ -289,3 +289,40 @@ SimSurvivalExponential <- function(
         name = "SimSurvivalExponential"
     )
 }
+
+
+#' Simulate Survival Data from a Gamma Proportional Hazard Model
+#'
+#' @param k (`number`)\cr the shape parameter.
+#' @param theta (`number`)\cr the scale parameter.
+#'
+#' @inheritParams SimSurvival-Shared
+#' @inheritSection SimSurvival-Shared Hazard Evaluation
+#'
+#' @family SimSurvival
+#'
+#' @importFrom stats dgamma pgamma
+#'
+#' @export
+SimSurvivalGamma <- function(
+    k,
+    theta,
+    time_max = 2000,
+    time_step = 1,
+    lambda_censor = 1 / 3000,
+    beta_cont = 0.2,
+    beta_cat = c("A" = 0, "B" = -0.4, "C" = 0.2)
+) {
+    SimSurvival(
+        time_max = time_max,
+        time_step = time_step,
+        lambda_censor = lambda_censor,
+        beta_cont = beta_cont,
+        beta_cat = beta_cat,
+        loghazard = function(time) {
+            dgamma(time, k, scale = theta, log = TRUE) -
+                pgamma(time, k, scale = theta, lower.tail = FALSE, log.p = TRUE)
+        },
+        name = "SimSurvivalGamma"
+    )
+}

R/SurvivalGamma.R

@@ -0,0 +1,45 @@
+#' @include SurvivalModel.R
+NULL
+
+
+#' `SurvivalGamma`
+#'
+#' This class extends the general [`SurvivalModel`] class for using the
+#' Gamma survival model.
+#'
+#' @exportClass SurvivalGamma
+.SurvivalGamma <- setClass(
+    Class = "SurvivalGamma",
+    contains = "SurvivalModel"
+)
+
+# SurvivalGamma-constructors ----
+
+#' @rdname SurvivalGamma-class
+#'
+#' @param k (`Prior`)\cr for the shape `k`.
+#' @param theta (`Prior`)\cr for the scale `theta`.
+#' @param beta (`Prior`)\cr for covariates coefficients `beta`.
+#'
+#' @export
+SurvivalGamma <- function(
+    k = prior_gamma(2, 0.5),
+    theta = prior_gamma(2, 0.5),
+    beta = prior_normal(0, 2)
+) {
+
+    k <- set_limits(k, lower = 0)
+    theta <- set_limits(theta, lower = 0)
+
+    .SurvivalGamma(
+        SurvivalModel(
+            name = "Gamma",
+            stan = StanModule(x = "sm-gamma/model.stan"),
+            parameters = ParameterList(
+                Parameter(name = "sm_gamma_k", prior = k, size = 1),
+                Parameter(name = "sm_gamma_theta", prior = theta, size = 1),
+                Parameter(name = "beta_os_cov", prior = beta, size = "p_os_cov_design")
+            )
+        )
+    )
+}

R/SurvivalWeibullPH.R

@@ -28,6 +28,10 @@ SurvivalWeibullPH <- function(
     gamma = prior_gamma(2, 0.5),
     beta = prior_normal(0, 2)
 ) {
+
+    lambda <- set_limits(lambda, lower = 0)
+    gamma <- set_limits(gamma, lower = 0)
+
     .SurvivalWeibullPH(
         SurvivalModel(
             name = "Weibull-PH",

README.md

@@ -94,7 +94,7 @@ sim_data <- SimJointData(
         gamma = 0.97
     )
 )
-#> INFO: 1 subjects did not die before max(times)
+#> INFO: 1 subject(s) did not die before max(times)
 
 joint_data <- DataJoint(
     subject = DataSubject(

_pkgdown.yml

@@ -48,6 +48,7 @@ reference:
       - SimSurvivalLogLogistic
       - SimSurvivalExponential
       - SimSurvivalWeibullPH
+      - SimSurvivalGamma
       - SimGroup
   - title: Prior Distributions
     contents:
@@ -79,6 +80,7 @@ reference:
       - SurvivalLogLogistic
       - SurvivalModel
       - SurvivalWeibullPH
+      - SurvivalGamma
 
 
   - title: Link Specification

inst/stan/sm-gamma/model.stan

@@ -0,0 +1,33 @@
+
+
+functions {
+    //
+    // Source - sm-gamma/model.stan
+    //
+    matrix log_h0(matrix time, vector pars_os) {
+        real k = pars_os[1];
+        real theta = pars_os[2];
+        matrix[rows(time), cols(time)] result;
+        result = (k - 1) .* log(time) - (time ./ theta) -
+            (k * log(theta)) - log(tgamma(k) * (1 - gamma_p(k, time ./ theta)));
+        return result;
+    }
+}
+
+
+parameters {
+    //
+    // Source - sm-gamma/model.stan
+    //
+    real<lower={{ machine_double_eps }}> sm_gamma_k;
+    real<lower={{ machine_double_eps }}> sm_gamma_theta;
+}
+
+
+transformed parameters {
+    //
+    // Source - sm-gamma/model.stan
+    //
+    vector[2] pars_os = [sm_gamma_k, sm_gamma_theta]';
+}
+

tests/testthat/_snaps/SurvivalGamma.md

@@ -0,0 +1,26 @@
+# Print method for SurvivalGamma works as expected
+
+    Code
+      x <- SurvivalGamma()
+      print(x)
+    Output
+      
+      Gamma Survival Model with parameters:
+          sm_gamma_k ~ gamma(alpha = 2, beta = 0.5)
+          sm_gamma_theta ~ gamma(alpha = 2, beta = 0.5)
+          beta_os_cov ~ normal(mu = 0, sigma = 2)
+      
+
+---
+
+    Code
+      x <- SurvivalGamma(k = prior_gamma(3, 4), theta = prior_cauchy(0, 1))
+      print(x)
+    Output
+      
+      Gamma Survival Model with parameters:
+          sm_gamma_k ~ gamma(alpha = 3, beta = 4)
+          sm_gamma_theta ~ cauchy(mu = 0, sigma = 1)
+          beta_os_cov ~ normal(mu = 0, sigma = 2)
+      
+