v0.2.8

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bmstate
 Type: Package
 Title: Bayesian multistate modeling
-Version: 0.2.7
+Version: 0.2.8
 Authors@R:
     c(person(given = "Juho",
            family = "Timonen",

R/DosingData.R

@@ -1,5 +1,8 @@
 #' Dosing data class (R6 class)
 #'
+#' @description
+#' Contains information about taken doses and dose times.
+#'
 #' @export
 #' @field subject_ids Subject ids.
 DosingData <- R6::R6Class(
@@ -31,6 +34,9 @@ DosingData <- R6::R6Class(
 #' Partially steady-state dosing data class (R6 class)
 #'
 #' @export
+#' @description
+#' Contains information about taken doses and dose times.
+#'
 #' @field doses Dose amounts (list with length equal to number of subjects).
 #' Corresponds to doses after the steady state.
 #' @field times Dose times (list with length equal to number of subjects).

R/JointData.R

@@ -10,6 +10,9 @@ pd_to_jointdata <- function(data) {
 #' Joint data class (R6 class)
 #'
 #' @export
+#' @description
+#' Contains data about both the state paths and dosing.
+#'
 #' @field paths The events data, an object of class \code{\link{PathData}}.
 #' @field dosing The dosing data, an object of class \code{\link{DosingData}}.
 JointData <- R6::R6Class(

R/MultistateModel.R

@@ -30,6 +30,8 @@ create_msm <- function(tm, hazard_covs = NULL, pk_covs = NULL,
 
 #' Main model class
 #'
+#' @description Class that represents a multistate model.
+#'
 #' @export
 #' @field system A \code{\link{MultistateSystem}}
 #' @field pk_model A \code{\link{PKModel}} or NULL.

R/MultistateModelFit.R

@@ -1,5 +1,7 @@
 #' Minimal fit class
 #'
+#' @description Class that represents a multistate model with certain parameters
+#' or parameter draws.
 #' @export
 #' @field model The \code{\link{MultistateModel}}
 #' @field data A  \code{\link{JointData}} object

R/MultistateSystem.R

@@ -1,5 +1,6 @@
 #' A multistate system with proportional spline hazards
 #'
+#' @description Class that represents a multistate system.
 #' @export
 MultistateSystem <- R6::R6Class("MultistateSystem",
 

R/PKModel.R

@@ -1,5 +1,7 @@
 #' One-compartment PK Model
 #'
+#' @description Class that represents a one-compartment PK model with linear
+#' oral absorption.
 #' @export
 PKModel <- R6::R6Class("PKModel",
 
@@ -131,14 +133,15 @@ PKModel <- R6::R6Class("PKModel",
       dd <- simulate_dosing(df_subjects, tau = tau)
       THETA <- matrix(0, N, 3)
       xu <- unique(c(self$ka_covs(), self$CL_covs(), self$V2_covs()))
+      check_columns(df_subjects, xu)
       x <- data.frame(normalize_columns(as.matrix(df_subjects[, xu])))
 
       # Simulate observation times and parameters
       t_obs <- list()
       SUB_ID <- rep("s", N)
       for (n in seq_len(N)) {
         theta_n <- list(
-          ka = exp(-2 + sum(x[n, self$ka_covs()] * beta_pk$ka) + 0.1 * stats::rnorm(1)),
+          ka = exp(-3 + sum(x[n, self$ka_covs()] * beta_pk$ka) + 0.1 * stats::rnorm(1)),
           CL = exp(-2 + sum(x[n, self$CL_covs()] * beta_pk$CL) + 0.1 * stats::rnorm(1)),
           V2 = exp(-2 + sum(x[n, self$V2_covs()] * beta_pk$V2) + 0.1 * stats::rnorm(1))
         )
@@ -162,7 +165,11 @@ PKModel <- R6::R6Class("PKModel",
         df_out <- rbind(df_out, out)
       }
       df_out <- data.frame(df_out)
-      colnames(df_out) <- c("t_pre", "t_post", "conc_pre", "conc_post", "ss_auc")
+      df_out <- cbind(df_out, THETA)
+      colnames(df_out) <- c(
+        "t_pre", "t_post", "conc_pre", "conc_post", "ss_auc",
+        "ka", "CL", "V2"
+      )
       rownames(df_out) <- NULL
       df_out$pk_lloq <- 0
       df_out$subject_id <- df_subjects$subject_id

R/PathData.R

@@ -1,7 +1,8 @@
 #' Path data class (R6 class)
 #'
 #' @export
-#' @description It is not recommended for users to try to create data using
+#' @description Class containing information about state paths and subjects.
+#' @details It is not recommended for users to try to create data using
 #' the constructor of this class. Rather use \code{\link{df_to_pathdata}}.
 #' @field subject_df Data frame with one row per subject. Must have one
 #' row for each subject, and

R/TransitionMatrix.R

@@ -1,6 +1,7 @@
 #' Defines states and possible transitions
 #'
 #' @export
+#' @description Class that represents a transition matrix.
 #' @field matrix a binary \code{N} x \code{N} matrix where
 #' \code{matrix[i,j]} is 1 if transition
 #' from state \code{i} to \code{j} is possible