Merge pull request #804 from metrumresearchgroup/release/0.10.9

Release/0.10.9

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 0.10.8
+Version: 0.10.9
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),

NAMESPACE

@@ -34,7 +34,6 @@ S3method(handle_spec_block,specPARAM)
 S3method(handle_spec_block,specPKMODEL)
 S3method(handle_spec_block,specPLUGIN)
 S3method(handle_spec_block,specPRED)
-S3method(handle_spec_block,specSET)
 S3method(handle_spec_block,specSIGMA)
 S3method(handle_spec_block,specTABLE)
 S3method(handle_spec_block,specTHETA)
@@ -246,6 +245,7 @@ importFrom(rlang,as_label)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,eval_tidy)
+importFrom(rlang,is_named)
 importFrom(rlang,quo_name)
 importFrom(rlang,quos)
 importFrom(rlang,syms)

NEWS.md

@@ -1,3 +1,22 @@
+# mrgsolve 0.10.9
+
+- Dosing into a compartment that is off at the time of the dose turns the 
+  compartment back on regardless of whether bioavailability is zero or non-zero 
+  (this is a bug fix where the compartment was not turned on when 
+  bioavailability was zero). (#800)
+- `simeta()` and `simeps()` now accept an (optional) integer argument to limit
+  re-simulation to single ETA or EPS values (#789)
+- `as.list(mod)` output now includes a data frame of `C++` variables and 
+  pre-processor definitions in the `cpp_variables` slot. (#780)
+- `$PARAM`, `$THETA`, `$CMT`, `$INIT`, `$OMEGA` and `$SIGMA` blocks all include 
+  the directives `@object` and `@as_object` so that block contents can be 
+  specified programmatically. `@object` names an object that was coded into
+  `$ENV` and `@as_object` indicates that the block contains code to realize
+  the object.  See `?BLOCK_PARSE` help topic for more information on how this
+  all works. (#783)
+- `$NMEXT` now lets the user select between multiple tables for scraping 
+  parameter estimates. (#782)
+
 # mrgsolve 0.10.8
 - Allow simulation from compartmental models with negative times #778
 - Enable dynamic capture of pre-processor directives at compile time #776

R/Aaaa.R

@@ -29,6 +29,7 @@
 #' @importFrom magrittr %>%
 #' @importFrom tibble tibble as_tibble
 #' @importFrom rlang quos enquo enquos quo_name syms !!! !! eval_tidy as_label
+#' @importFrom rlang is_named
 #' @importFrom lifecycle deprecate_soft
 #' @importFrom glue glue
 #' @importFrom Rcpp evalCpp

R/annot.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2019  Metrum Research Group
+# Copyright (C) 2013 - 2021  Metrum Research Group
 #
 # This file is part of mrgsolve.
 #
@@ -110,12 +110,9 @@ parse_annot_line <- function(x, novalue=FALSE, noname=FALSE,context="not given")
 ##' 
 ##' mrgsolve:::details(mod)
 ##' 
-details <- function(x,complete=FALSE,values=TRUE,...) {
-
+details <- function(x, complete = FALSE, values = TRUE,...) {
   stopifnot(is.mrgmod(x))
-
   ans <- x@annot[["data"]]
-
   if(nrow(ans)==0) {
     ans <- cobble_details(x)
   } else {
@@ -134,9 +131,7 @@ store_annot <- function(x,what,loc=soloc(x),...) {
 }
 
 cobble_details <- function(x) {
-
   ans <- list()
-
   par <- as.numeric(param(x))
   if(length(par) > 0) {
     ans[[1]] <- tibble(block="PARAM",name=names(par))  
@@ -159,23 +154,18 @@ cobble_details <- function(x) {
                            value = unname(this_mat))
     }
   }
-
-
   ans <- dplyr::bind_rows(ans)
   ans <- dplyr::mutate(ans,descr='.', units='.', options='.')
   ans <- ans[,c("block","name","descr","units","options"),drop=FALSE]
   as.data.frame(ans)
-
 }
 
 complete_details <- function(annot,x) {
-
   par <- as.numeric(param(x))
   cmt <- as.numeric(init(x))
   fx <- as.numeric(x@fixed)
   name <- unique(annot[annot$block %in% c("PARAM", "CMT", "FIXED"),"name"])
   dum <- annot[0,]
-
   if(length(par) > 0) {
     miss <- setdiff(names(par),name)
     if(length(miss) > 0) {
@@ -185,7 +175,6 @@ complete_details <- function(annot,x) {
     }
     annot <- dplyr::bind_rows(annot,par)
   }
-
   if(length(cmt) > 0) {
     miss <- setdiff(names(cmt),name)
     if(length(miss) > 0) {
@@ -195,7 +184,6 @@ complete_details <- function(annot,x) {
     }
     annot <- dplyr::bind_rows(annot,cmt)
   }
-
   if(length(fx) > 0) {
     miss <- setdiff(names(fx),name)
     if(length(miss) > 0) {
@@ -216,7 +204,6 @@ add_detail_values <- function(annot,x) {
   x <- tibble(name=names(x),value=x)
   annot <- dplyr::left_join(annot,x,by="name")
   return(annot)
-
 }
 
 #nocov end

R/class_matlist.R

@@ -87,11 +87,14 @@ dim_matlist <- function(x) {
 
 create_matlist <- function(x=list(),class,labels=list(),signature=NULL,...) {
   x <- x[!sapply(x,nrow)==0]
+  # names ---
   if(is.null(names(x))) names(x) <- rep("...", length(x))
   names(x)[nchar(names(x))==0] <- "..."
+  # end names ---
   if(is.null(unlist(labels))) {
     labels <- lapply(x, function(y) rep('.',nrow(y)))
   } 
+  # check for duplicates ----
   all <- unlist(labels, use.names=FALSE)
   all <- all[all != "."]
   if(any(duplicated(all))) {
@@ -100,6 +103,7 @@ create_matlist <- function(x=list(),class,labels=list(),signature=NULL,...) {
       stop("duplicate labels found when creating matlist object: ", dup,
            call.=FALSE)  
   }
+  # done check for duplicates ---
   x <- new(class, data=x, labels=labels)
   x@n <- dim_matlist(x)
   return(x)

R/class_mrgmod.R

@@ -467,6 +467,8 @@ setMethod("names", "mrgmod", function(x) {
 #' - `random`: names and labels of `$OMEGA` and `$SIGMA`
 #' - `code`: model source code from `cfile`
 #' - `details`: model details data frame
+#' - `cpp_variables`: a data frame listing variables internal to the model 
+#'   cpp file
 #' - `atol`: see [solversettings]
 #' - `rtol`: see [solversettings]
 #' - `ss_atol`: absolute tolerance to use when advancing to PK steady state
@@ -477,7 +479,6 @@ setMethod("names", "mrgmod", function(x) {
 #' - `envir`: the model environment
 #' - `plugins`: plugins invoked in the model
 #' - `digits`: number of digits to request in simulated data
-
 #' - `tscale`: multiplicative scalar for time in results only
 #' - `mindt`: simulation output time below which there model will assume to 
 #'   have not advanced
@@ -512,6 +513,7 @@ setMethod("as.list", "mrgmod", function(x, deep = FALSE, ...) {
       advan <- x@advan
       functions <- funset(x)
     }
+    cpp_variables <- x@shlib[["cpp_variables"]]
     details <- x@annot
     code <- x@code
     random <- names(x)[c("omega", "sigma", "omega_labels", "sigma_labels")]

R/class_numericlist.R

@@ -21,6 +21,7 @@ null_list <- setNames(list(), character(0))
 valid.numericlist <- function(object) {
   x1 <- all(sapply(object@data,single.number))
   x2 <- all(names(object@data) !="")
+  x2 <- rlang::is_named(object@data)
   x3 <- !any(grepl("=|\\.",names(object),perl=TRUE))
 
   x <- x1 & x2 & x3