Add Stein-Fojo Model

DESCRIPTION

@@ -80,6 +80,7 @@ Collate:
     'LongitudinalGSF.R'
     'LongitudinalQuantities.R'
     'LongitudinalRandomSlope.R'
+    'LongitudinalSteinFojo.R'
     'SurvivalExponential.R'
     'SurvivalLoglogistic.R'
     'SurvivalWeibullPH.R'
@@ -92,5 +93,6 @@ Collate:
     'simulations_gsf.R'
     'simulations_os.R'
     'simulations_rs.R'
+    'simulations_sf.R'
     'zzz.R'
 VignetteBuilder: knitr

NAMESPACE

@@ -54,11 +54,14 @@ S3method(compileStanModel,JointModel)
 S3method(dim,Quantities)
 S3method(enableLink,LongitudinalGSF)
 S3method(enableLink,LongitudinalRandomSlope)
+S3method(enableLink,LongitudinalSteinFojo)
 S3method(extractVariableNames,DataSubject)
 S3method(extractVariableNames,DataSurvival)
 S3method(generateQuantities,JointModelSamples)
 S3method(getParameters,Link)
 S3method(getParameters,LinkComponent)
+S3method(getParameters,StanModel)
+S3method(getParameters,default)
 S3method(initialValues,JointModel)
 S3method(initialValues,Link)
 S3method(initialValues,LinkComponent)
@@ -70,11 +73,14 @@ S3method(length,Link)
 S3method(linkDSLD,LongitudinalGSF)
 S3method(linkDSLD,LongitudinalModel)
 S3method(linkDSLD,LongitudinalRandomSlope)
+S3method(linkDSLD,LongitudinalSteinFojo)
 S3method(linkIdentity,LongitudinalGSF)
 S3method(linkIdentity,LongitudinalModel)
 S3method(linkIdentity,LongitudinalRandomSlope)
+S3method(linkIdentity,LongitudinalSteinFojo)
 S3method(linkTTG,LongitudinalGSF)
 S3method(linkTTG,LongitudinalModel)
+S3method(linkTTG,LongitudinalSteinFojo)
 S3method(names,Parameter)
 S3method(names,ParameterList)
 S3method(sampleStanModel,JointModel)
@@ -97,6 +103,7 @@ export(LongitudinalGSF)
 export(LongitudinalModel)
 export(LongitudinalQuantities)
 export(LongitudinalRandomSlope)
+export(LongitudinalSteinFojo)
 export(Parameter)
 export(ParameterList)
 export(Prior)
@@ -142,6 +149,7 @@ export(sampleStanModel)
 export(show)
 export(sim_lm_gsf)
 export(sim_lm_random_slope)
+export(sim_lm_sf)
 export(sim_os_exponential)
 export(sim_os_loglogistic)
 export(sim_os_weibull)
@@ -157,6 +165,7 @@ exportClasses(Link)
 exportClasses(LongitudinalGSF)
 exportClasses(LongitudinalModel)
 exportClasses(LongitudinalRandomSlope)
+exportClasses(LongitudinalSteinFojo)
 exportClasses(Parameter)
 exportClasses(ParameterList)
 exportClasses(Prior)

R/LongitudinalSteinFojo.R

@@ -0,0 +1,136 @@
+#' @include LongitudinalModel.R
+#' @include StanModule.R
+#' @include generics.R
+#' @include ParameterList.R
+#' @include Parameter.R
+#' @include Link.R
+NULL
+
+
+#' `LongitudinalSteinFojo`
+#'
+#' This class extends the general [`LongitudinalModel`] class for using the
+#' Stein-Fojo model for the longitudinal outcome.
+#'
+#' @exportClass LongitudinalSteinFojo
+.LongitudinalSteinFojo <- setClass(
+    Class = "LongitudinalSteinFojo",
+    contains = "LongitudinalModel"
+)
+
+
+#' @rdname LongitudinalSteinFojo-class
+#'
+#' @param mu_bsld (`Prior`)\cr for the mean baseline value `mu_bsld`.
+#' @param mu_ks (`Prior`)\cr for the mean shrinkage rate `mu_ks`.
+#' @param mu_kg (`Prior`)\cr for the mean growth rate `mu_kg`.
+#'
+#' @param omega_bsld (`Prior`)\cr for the baseline value standard deviation `omega_bsld`.
+#' @param omega_ks (`Prior`)\cr for the shrinkage rate standard deviation `omega_ks`.
+#' @param omega_kg (`Prior`)\cr for the growth rate standard deviation `omega_kg`.
+#'
+#' @param sigma (`Prior`)\cr for the variance of the longitudinal values `sigma`.
+#'
+#' @param centred (`logical`)\cr whether to use the centred parameterization.
+#'
+#' @export
+LongitudinalSteinFojo <- function(
+
+    mu_bsld = prior_normal(log(60), 1),
+    mu_ks = prior_normal(log(0.5), 1),
+    mu_kg = prior_normal(log(0.3), 1),
+
+    omega_bsld = prior_lognormal(log(0.2), 1),
+    omega_ks = prior_lognormal(log(0.2), 1),
+    omega_kg = prior_lognormal(log(0.2), 1),
+
+    sigma = prior_lognormal(log(0.1), 1),
+
+    centred = FALSE
+) {
+
+    sf_model <- StanModule(decorated_render(
+        .x = paste0(read_stan("lm-stein-fojo/model.stan"), collapse = "\n"),
+        centred = centred
+    ))
+
+    parameters <- list(
+        Parameter(name = "lm_sf_mu_bsld", prior = mu_bsld, size = "n_studies"),
+        Parameter(name = "lm_sf_mu_ks", prior = mu_ks, size = "n_arms"),
+        Parameter(name = "lm_sf_mu_kg", prior = mu_kg, size = "n_arms"),
+
+        Parameter(name = "lm_sf_omega_bsld", prior = omega_bsld, size = 1),
+        Parameter(name = "lm_sf_omega_ks", prior = omega_ks, size = 1),
+        Parameter(name = "lm_sf_omega_kg", prior = omega_kg, size = 1),
+
+        Parameter(name = "lm_sf_sigma", prior = sigma, size = 1)
+    )
+
+    assert_flag(centred)
+    parameters_extra <- if (centred) {
+        list(
+            Parameter(
+                name = "lm_sf_psi_bsld",
+                prior = prior_init_only(prior_lognormal(mu_bsld@init, omega_bsld@init)),
+                size = "Nind"
+            ),
+            Parameter(
+                name = "lm_sf_psi_ks",
+                prior = prior_init_only(prior_lognormal(mu_ks@init, omega_ks@init)),
+                size = "Nind"
+            ),
+            Parameter(
+                name = "lm_sf_psi_kg",
+                prior = prior_init_only(prior_lognormal(mu_kg@init, omega_kg@init)),
+                size = "Nind"
+            )
+        )
+    } else {
+        list(
+            Parameter(name = "lm_sf_eta_tilde_bsld", prior = prior_std_normal(), size = "Nind"),
+            Parameter(name = "lm_sf_eta_tilde_ks", prior = prior_std_normal(), size = "Nind"),
+            Parameter(name = "lm_sf_eta_tilde_kg", prior = prior_std_normal(), size = "Nind")
+        )
+    }
+    parameters <- append(parameters, parameters_extra)
+
+    x <- LongitudinalModel(
+        name = "Stein-Fojo",
+        stan = merge(
+            sf_model,
+            StanModule("lm-stein-fojo/functions.stan")
+        ),
+        parameters = do.call(ParameterList, parameters)
+    )
+    .LongitudinalSteinFojo(x)
+}
+
+
+
+#' @rdname standard-link-methods
+#' @export
+enableLink.LongitudinalSteinFojo <- function(object, ...) {
+    object@stan <- merge(
+        object@stan,
+        StanModule("lm-stein-fojo/link.stan")
+    )
+    object
+}
+
+#' @rdname standard-link-methods
+#' @export
+linkDSLD.LongitudinalSteinFojo <- function(object, ...) {
+    StanModule("lm-stein-fojo/link_dsld.stan")
+}
+
+#' @rdname standard-link-methods
+#' @export
+linkTTG.LongitudinalSteinFojo <- function(object, ...) {
+    StanModule("lm-stein-fojo/link_ttg.stan")
+}
+
+#' @rdname standard-link-methods
+#' @export
+linkIdentity.LongitudinalSteinFojo <- function(object, ...) {
+    StanModule("lm-stein-fojo/link_identity.stan")
+}

R/StanModel.R

@@ -68,6 +68,7 @@ as.list.StanModel <- function(x, ...) {
 # getParameters-StanModel ----
 
 #' @rdname getParameters
+#' @export
 getParameters.StanModel <- function(object) object@parameters
 
 

R/defaults.R

@@ -10,6 +10,7 @@ NULL
 
 
 #' @rdname getParameters
+#' @export
 getParameters.default <- function(object) {
     if (missing(object) || is.null(object)) {
         return(NULL)

R/simulations.R

@@ -93,12 +93,18 @@ simulate_joint_data <- function(
         msg = "The longitudinal dataset must be sorted by pt, time"
     )
 
+
     os_dat_chaz <- time_dat_baseline |>
         dplyr::mutate(log_haz_link = lm_dat$log_haz_link) |> # only works if lm_dat is sorted pt, time
         dplyr::mutate(log_bl_haz = os_fun(.data$evalp)) |>
         # Fix to avoid issue with log(0) = NaN values
         dplyr::mutate(log_bl_haz = dplyr::if_else(.data$evalp == 0, -999, .data$log_bl_haz)) |>
         dplyr::mutate(hazard_instant = exp(.data$log_bl_haz + .data$log_haz_cov + .data$log_haz_link)) |>
+        # Reset Inf values to large number to avoid NaN issues downstream
+        # This is suitable as Hazard limits tend to be in the range of -10 to 10 so large numbers
+        # are essentially equivalent to infinity for simulation purposes
+        dplyr::mutate(hazard_instant = dplyr::if_else(.data$hazard_instant == Inf, 999, .data$hazard_instant)) |>
+        dplyr::mutate(hazard_instant = dplyr::if_else(.data$hazard_instant == -Inf, -999, .data$hazard_instant)) |>
         dplyr::mutate(hazard_interval = .data$hazard_instant * .data$width) |>
         dplyr::group_by(.data$pt) |>
         dplyr::mutate(chazard = cumsum(.data$hazard_interval)) |>

R/simulations_sf.R

@@ -0,0 +1,106 @@
+
+
+
+#' Stein-Fojo Functionals
+#'
+#' @param time (`numeric`)\cr time grid.
+#' @param b (`number`)\cr baseline.
+#' @param s (`number`)\cr shrinkage.
+#' @param g (`number`)\cr growth.
+#'
+#' @returns The function results.
+#' @keywords internal
+#'
+#' @examples
+#' sf_sld(1:10, 20, 0.3, 0.6)
+sf_sld <- function(time, b, s, g) {
+    b * (exp(-s * time) + exp(g * time) - 1)
+}
+
+
+#' @rdname sf_sld
+#' @examples
+#' sf_ttg(1:10, 20, 0.3, 0.6)
+sf_ttg <- function(time, b, s, g) {
+    t1 <- (log(s) - log(g)) / (g + s)
+    t1[t1 <= 0] <- 0
+    return(t1)
+}
+
+
+#' @rdname sf_sld
+#' @examples
+#' sf_dsld(1:10, 20, 0.3, 0.6)
+sf_dsld <- function(time, b, s, g) {
+    t1 <- g * exp(g * time)
+    t2 <- s * exp(-s * time)
+    return(b * (t1 - t2))
+}
+
+
+
+#' Construct a Simulation Function for Longitudinal Data from Stein-Fojo Model
+#'
+#' @param sigma (`number`)\cr the variance of the longitudinal values.
+#' @param mu_s (`numeric`)\cr the mean shrinkage rates for the two treatment arms.
+#' @param mu_g (`numeric`)\cr the mean growth rates for the two treatment arms.
+#' @param mu_b (`numeric`)\cr the mean baseline values for the two treatment arms.
+#' @param omega_b (`number`)\cr the baseline value standard deviation.
+#' @param omega_s (`number`)\cr the shrinkage rate standard deviation.
+#' @param omega_g (`number`)\cr the growth rate standard deviation.
+#' @param link_dsld (`number`)\cr the link coefficient for the derivative contribution.
+#' @param link_ttg (`number`)\cr the link coefficient for the time-to-growth contribution.
+#' @param link_identity (`number`)\cr the link coefficient for the SLD Identity contribution.
+#'
+#' @returns A function with argument `lm_base` that can be used to simulate
+#'   longitudinal data from the corresponding Stein-Fojo model.
+#'
+#' @export
+sim_lm_sf <- function(
+    sigma = 0.01,
+    mu_s = c(0.6, 0.4),
+    mu_g = c(0.25, 0.35),
+    mu_b = 60,
+    omega_b = 0.2,
+    omega_s = 0.2,
+    omega_g = 0.2,
+    link_dsld = 0,
+    link_ttg = 0,
+    link_identity = 0
+) {
+    function(lm_base) {
+
+        assert_that(
+            length(unique(lm_base$study)) == length(mu_b),
+            length(mu_b) == 1,
+            length(sigma) == 1,
+            length(mu_s) == length(unique(lm_base$arm)),
+            length(mu_s) == length(mu_g),
+            length(c(omega_b, omega_s, omega_g)) == 3
+        )
+
+        baseline_covs <- lm_base |>
+            dplyr::distinct(.data$pt, .data$arm, .data$study) |>
+            dplyr::mutate(study_idx = as.numeric(factor(as.character(.data$study)))) |>
+            dplyr::mutate(arm_idx = as.numeric(factor(as.character(.data$arm)))) |>
+            dplyr::mutate(psi_b = stats::rlnorm(dplyr::n(), log(mu_b[.data$study_idx]), omega_b)) |>
+            dplyr::mutate(psi_s = stats::rlnorm(dplyr::n(), log(mu_s[.data$arm_idx]), omega_s)) |>
+            dplyr::mutate(psi_g = stats::rlnorm(dplyr::n(), log(mu_g[.data$arm_idx]), omega_g))
+
+
+        lm_dat <- lm_base |>
+            dplyr::select(!dplyr::all_of(c("study", "arm"))) |>
+            dplyr::left_join(baseline_covs, by = "pt") |>
+            dplyr::mutate(mu_sld = sf_sld(.data$time, .data$psi_b, .data$psi_s, .data$psi_g)) |>
+            dplyr::mutate(dsld = sf_dsld(.data$time, .data$psi_b, .data$psi_s, .data$psi_g)) |>
+            dplyr::mutate(ttg = sf_ttg(.data$time, .data$psi_b, .data$psi_s, .data$psi_g)) |>
+            dplyr::mutate(sld = stats::rnorm(dplyr::n(), .data$mu_sld, .data$mu_sld * sigma)) |>
+            dplyr::mutate(
+                log_haz_link =
+                    (link_dsld * .data$dsld) +
+                    (link_ttg * .data$ttg) +
+                    (link_identity * .data$mu_sld)
+            )
+        return(lm_dat)
+    }
+}