From 8e53a2fd6ad0d19e0c20f0440407d02548dd7f9b Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 11 May 2021 06:54:56 -0500
Subject: [PATCH 01/31] re-start development versioning

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a40a74ed..3a7908d5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 0.11.1
+Version: 0.11.1.9000
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 2546d1df..4b5d41ca 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+# mrgsolve (development version)
+
 # mrgsolve 0.11.1
 
 - `mrgsim()` will now periodically check for user interrupt signal so that 

From 8fb00187dc26a49701058651659a893964845e0e Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 19 May 2021 08:13:52 -0500
Subject: [PATCH 02/31] scale cent by v1 not v2

---
 inst/maintenance/unit/test-modlib.R | 5 +++++
 inst/models/pk2iv.cpp               | 3 +--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/inst/maintenance/unit/test-modlib.R b/inst/maintenance/unit/test-modlib.R
index 4cfea92d..2369a349 100644
--- a/inst/maintenance/unit/test-modlib.R
+++ b/inst/maintenance/unit/test-modlib.R
@@ -100,3 +100,8 @@ test_that("all modlib models", {
   expect_is(x[[1]],"mrgmod")
   expect_is(x[[2]],"mrgsims")
 })
+
+test_that("pk2iv uses V1 to scale CENT", {
+  x <- readLines(file.path(modlib(), "pk2iv.cpp"))
+  expect_match(x, "#define CP (CENT/V1)", fixed = TRUE, all = FALSE)
+})
diff --git a/inst/models/pk2iv.cpp b/inst/models/pk2iv.cpp
index c5291b3d..e8d0a20b 100644
--- a/inst/models/pk2iv.cpp
+++ b/inst/models/pk2iv.cpp
@@ -9,10 +9,9 @@ CENT   : Central compartment (mass)
 PERIPH : Peripheral compartment (mass) 
 
 $GLOBAL
-#define CP (CENT/V2)
+#define CP (CENT/V1)
 
 $PKMODEL ncmt = 2, depot = FALSE
 
 $CAPTURE @annotated
 CP : Plasma concentration (mass/time)
-  

From f88767aad2c2bc9ef283ca62a830284beb23dc7b Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 19 May 2021 08:54:32 -0500
Subject: [PATCH 03/31] update NEWS

---
 NEWS.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 4b5d41ca..0cf226b4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,8 @@
 # mrgsolve (development version)
 
+- In `pk2iv`, change scaling volume for `CENT` from `V2` (incorrect) to 
+  `V1` (#831, #832, #833)
+
 # mrgsolve 0.11.1
 
 - `mrgsim()` will now periodically check for user interrupt signal so that 

From 218ff22e68deb220b48f798e666b81f586373eed Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Mon, 28 Jun 2021 09:12:33 -0500
Subject: [PATCH 04/31] typo; soloc

---
 R/funset.R                         | 6 +++---
 inst/maintenance/unit/test-mread.R | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/funset.R b/R/funset.R
index ac5d979b..d7bcddd1 100644
--- a/R/funset.R
+++ b/R/funset.R
@@ -19,10 +19,10 @@
 FUNSET_ERROR__ <- 
   '
 There was a problem accessing the model shared object.
-  Either the model object is corrupted or the model was 
+  Either the model object was corrupted or the model was 
   not properly compiled and/or loaded. If the model is 
-  not loaded, use loadso(mod) to do so. This is usually 
-  required for parallel simuilation on a worker node that
+  not loaded, use `loadso(mod)` to do so. This is usually 
+  required for parallel simulation on a worker node that
   was not forked (e.g. when using future::multisession).
   Also check mrgsolve:::funset(mod) for more information.
 '
diff --git a/inst/maintenance/unit/test-mread.R b/inst/maintenance/unit/test-mread.R
index 15415547..3e064503 100644
--- a/inst/maintenance/unit/test-mread.R
+++ b/inst/maintenance/unit/test-mread.R
@@ -70,7 +70,7 @@ $SIGMA @block
 
 '
 
-mod <- suppressWarnings(mcode("test2",code, warn=TRUE, soloc = '.'))
+mod <- suppressWarnings(mcode("test2",code, warn=TRUE))
 
 test_that("Parameters are parsed properly with mread", {
   expect_equal(param(mod)$CL,1)

From 5bfa121c9d05f31d7236ab2e8946caa66cd52997 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Mon, 28 Jun 2021 09:13:31 -0500
Subject: [PATCH 05/31] linting test file

---
 inst/maintenance/unit/test-mread.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/inst/maintenance/unit/test-mread.R b/inst/maintenance/unit/test-mread.R
index 3e064503..2657e092 100644
--- a/inst/maintenance/unit/test-mread.R
+++ b/inst/maintenance/unit/test-mread.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2019  Metrum Research Group, LLC
+# Copyright (C) 2013 - 2021  Metrum Research Group
 #
 # This file is part of mrgsolve.
 #
@@ -116,14 +116,12 @@ test_that("Sigma matrices are properly parsed", {
   expect_equivalent(mat[3,2],0.002)
 })
 
-
 test_that("EPS values have proper variance", {
   set.seed(8282)
   out <- mrgsim(mod,end=100000, delta=1, init = list(GUT = 0, CENT = 0))
   expect_equal(round(var(out$EPS1),2),0.55)
 })
 
-
 test_that("Error when code is passed as project", {
   expect_error(suppressWarnings(mread("hey",code)))
 })
@@ -136,4 +134,3 @@ test_that("Error with duplicate blocks", {
   expect_error(mcode("a", "$MAIN \n $MAIN",compile = FALSE))
   expect_error(mcode("a", "$SET \n $SET",compile = FALSE))
 })
-

From 0d0facae5a8b47bf79f19891fd5c9e0667614a85 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 30 Jun 2021 17:28:39 -0500
Subject: [PATCH 06/31] bump the version after some typo fixes

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3a7908d5..ac00ec18 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 0.11.1.9000
+Version: 0.11.1.9001
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),

From 2a3f711d1bb94e81fb039e26506cec15d332646c Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 22 Jul 2021 21:26:50 -0500
Subject: [PATCH 07/31] re-factor some recover information

---
 R/class_build.R                    | 48 +++++++++++++++---------------
 R/mread.R                          |  2 +-
 R/utils.R                          |  6 ++++
 inst/maintenance/unit/test-mread.R | 18 ++++++++++-
 4 files changed, 48 insertions(+), 26 deletions(-)

diff --git a/R/class_build.R b/R/class_build.R
index 0c13dd9c..fcf5aeb3 100644
--- a/R/class_build.R
+++ b/R/class_build.R
@@ -209,20 +209,26 @@ build_output_cleanup <- function(x,build) {
   patt <- "^ *In function .*void _model.*:$"
   errr <- msub(pattern = patt, replacement = "", x = errr)
   x[["stderr"]] <- errr
-  x <- structure(x, class = "mrgsolve-build-error")
+  x <- structure(x, class = c("mrgsolve-build-error", "list"))
   x
 }
 
-
-build_failed <- function(out,build,mod,ignore.stdout) {
-  outt <- list(out)
-  names(outt) <- paste0("mrgsolve.build.", build[["model"]])
-  options(outt)
+build_failed <- function(out,build,mod,spec,ignore.stdout) {
   out <- build_output_cleanup(out,build)
-  if(build[["recover"]]) {
+  if(isTRUE(build[["recover"]])) {
     warning("returning object for debugging purposes only.")
-    ans <- list(build = build, mod = as.list(mod), shlib=list(compiled=FALSE), out=out)
-    return(structure(ans,class = "mrgsolve-build-recover"))
+    build <- as.list(build)
+    mod <- as.list(mod)
+    mod[["envir"]] <- as.list(mod[["envir"]])
+    mod[["shlib"]][["version"]] <- unlist(mod[["shlib"]][["version"]])
+    mod[["shlib"]][["compiled"]] <- FALSE
+    ans <- list(
+      out = out,
+      build = build, 
+      mod = mod, 
+      spec = spec
+    )
+    return(structure(ans, class = c("mrgsolve-build-recover", "list")))
   }
   if(!ignore.stdout) {
     msg <- divider_msg("stdout")
@@ -241,22 +247,16 @@ build_failed <- function(out,build,mod,ignore.stdout) {
   stop("the model build step failed.",call.=FALSE)
 }
 
-
-build_save_output <- function(out) {
-  out[["date"]] <- date()
-  path <- file.path(tempdir(), "mrgsolve-build-result.RDS")
-  saveRDS(out, file=path)
-  return(invisible(path))
-}
-
-build_get_output <- function() {
-  file <- file.path(tempdir(),"mrgsolve-build-result.RDS")
-  file <- normalizePath(file,mustWork=FALSE)
-  if(!file.exists(file)) {
-    message("No build output was found.")
-    return(invisible(list()))
+build_format_recover <- function(data, path = NULL) {
+  if(!requireNamespace("yaml")) {
+    stop("please install the yaml package to format recovery data", call.=FALSE)  
+  }
+  ans <- yaml::as.yaml(data)
+  if(is.character(path)) {
+    writeLines(text = ans, con = path)
+    return(invisible(ans))
   }
-  return(readRDS(file))
+  ans
 }
 
 build_handle_127 <- function(out) {
diff --git a/R/mread.R b/R/mread.R
index ce6fab32..5cd9cb11 100644
--- a/R/mread.R
+++ b/R/mread.R
@@ -539,7 +539,7 @@ mread <- function(model, project = getOption("mrgsolve.project", getwd()),
   
   if(!comp_success) {
     if(ignore.stdout) message("error.\n", appendLF=FALSE)
-    return(build_failed(out,build,x,ignore.stdout))
+    return(build_failed(out,build,x,spec,ignore.stdout))
   } 
   
   if(ignore.stdout) {
diff --git a/R/utils.R b/R/utils.R
index 80bdacb8..aff79b96 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -570,7 +570,13 @@ system4 <- function(cmd, args=character(0), pattern, path) {
   files <- file.path(path, paste0("system4__",c("stdout","stderr"),"__", pattern))
   x <- list(status=system2(cmd, args, stdout = files[1], stderr = files[2]))
   x[["stdout"]] <- readLines(files[1])
+  if(length(x[["stdout"]])==0) {
+    x[["stdout"]] <- "stdout could not be recovered after system4 call"  
+  }
   x[["stderr"]] <- readLines(files[2])
+  if(length(x[["stderr"]])==0) {
+    x[["stderr"]] <- "stderr could not be recovered after system4 call"  
+  }
   x
 }
 
diff --git a/inst/maintenance/unit/test-mread.R b/inst/maintenance/unit/test-mread.R
index 2657e092..b207d2cc 100644
--- a/inst/maintenance/unit/test-mread.R
+++ b/inst/maintenance/unit/test-mread.R
@@ -127,10 +127,26 @@ test_that("Error when code is passed as project", {
 })
 
 test_that("Model name with spaces is error", {
-    expect_error(mcode("ab cd", ""))
+  expect_error(mcode("ab cd", ""))
 })
 
 test_that("Error with duplicate blocks", {
   expect_error(mcode("a", "$MAIN \n $MAIN",compile = FALSE))
   expect_error(mcode("a", "$SET \n $SET",compile = FALSE))
 })
+
+test_that("Recover data when compile fails", {
+  code <- '[main] double a = 2\n[param] b = 5\n'
+  expect_warning(
+    mod <- mcode("fail", code, recover = TRUE), 
+    regexp = "returning object for debugging purposes only"
+  )
+  expect_is(mod, "list")
+  expect_named(mod)
+  expect_true("mod" %in% names(mod))
+  expect_true("build" %in% names(mod))
+  expect_true("out" %in% names(mod))
+  expect_true("spec" %in% names(mod))
+  recov <- mrgsolve:::build_format_recover(data)
+  expect_is(recov, "character")
+})

From f7ce0459690a835cac7c38cf84d035c6fd5797d5 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 22 Jul 2021 21:28:32 -0500
Subject: [PATCH 08/31] doc

---
 R/mread.R    | 5 +++--
 man/mread.Rd | 5 +++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/R/mread.R b/R/mread.R
index 5cd9cb11..578ef56c 100644
--- a/R/mread.R
+++ b/R/mread.R
@@ -48,8 +48,9 @@ NULL
 #' @param quiet don't print messages when compiling
 #' @param preclean logical; if \code{TRUE}, compilation artifacts are 
 #' cleaned up first
-#' @param recover if \code{TRUE}, an object will be returned in case
-#' the model shared object fails to build
+#' @param recover if \code{TRUE}, a list of build will be returned in case
+#' the model shared object fails to compile; use this option to and 
+#' the returned object to collect information assist in debugging
 #' @param capture a character vector or comma-separated string of additional 
 #' model variables to capture; these variables will be added to the capture 
 #' list for the current call to \code{\link{mread}} only
diff --git a/man/mread.Rd b/man/mread.Rd
index aab5223d..4f8a2503 100644
--- a/man/mread.Rd
+++ b/man/mread.Rd
@@ -81,8 +81,9 @@ list for the current call to \code{\link{mread}} only}
 \item{preclean}{logical; if \code{TRUE}, compilation artifacts are 
 cleaned up first}
 
-\item{recover}{if \code{TRUE}, an object will be returned in case
-the model shared object fails to build}
+\item{recover}{if \code{TRUE}, a list of build will be returned in case
+the model shared object fails to compile; use this option to and 
+the returned object to collect information assist in debugging}
 
 \item{...}{passed to \code{\link[mrgsolve]{update}}; also arguments passed
 to mread from \code{\link{mread_cache}}.}

From e37997e9e608d66f4b3849af2d77e24579d98ac7 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Sat, 24 Jul 2021 08:32:19 -0500
Subject: [PATCH 09/31] fix test

---
 inst/maintenance/unit/test-mread.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/inst/maintenance/unit/test-mread.R b/inst/maintenance/unit/test-mread.R
index b207d2cc..414c1de5 100644
--- a/inst/maintenance/unit/test-mread.R
+++ b/inst/maintenance/unit/test-mread.R
@@ -147,6 +147,8 @@ test_that("Recover data when compile fails", {
   expect_true("build" %in% names(mod))
   expect_true("out" %in% names(mod))
   expect_true("spec" %in% names(mod))
-  recov <- mrgsolve:::build_format_recover(data)
+  recov <- mrgsolve:::build_format_recover(mod)
   expect_is(recov, "character")
+  recov_list <- yaml::yaml.load(recov)
+  expect_is(recov_list, "list")
 })

From 77395eae5441ab8a110f74433f5376abe3bc70e6 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Fri, 30 Jul 2021 08:39:55 -0500
Subject: [PATCH 10/31] convert to data frame with Rcpp

---
 R/mrgsim_q.R            |  7 ++++---
 R/mrgsolve.R            | 20 ++++++++------------
 inst/include/mrgsolve.h |  2 ++
 man/qsim.Rd             |  5 +++--
 src/devtran.cpp         |  2 +-
 src/mrgsolve.cpp        | 13 +++++++++++++
 6 files changed, 31 insertions(+), 18 deletions(-)

diff --git a/R/mrgsim_q.R b/R/mrgsim_q.R
index 92e0995a..aeae4003 100644
--- a/R/mrgsim_q.R
+++ b/R/mrgsim_q.R
@@ -157,13 +157,14 @@ mrgsim_q <- function(x,
     PACKAGE = "mrgsolve"
   )[["data"]]
   
-  dimnames(out) <- list(NULL, c("ID", tcol,x@cmtL,x@capL))
+  names(out) <- c("ID", tcol,x@cmtL,x@capL)
   
   if(output=="df") {
-    return(as.data.frame(out))  
+    return(out)  
   }
+  
   if(output=="matrix") {
-    return(out)  
+    return(as.matrix(out))  
   }
   
   new(
diff --git a/R/mrgsolve.R b/R/mrgsolve.R
index 81328676..37b677e6 100644
--- a/R/mrgsolve.R
+++ b/R/mrgsolve.R
@@ -687,12 +687,7 @@ do_mrgsim <- function(x,
     cnames <- new_names
   }
   
-  dimnames(out[["data"]]) <- list(NULL, cnames)
-  
-  ans <- as.data.frame.matrix(
-    out[["data"]], 
-    stringsAsFactors = FALSE
-  )
+  ans <- setNames(out[["data"]], cnames)
   
   if(do_recover_data || do_recover_idata) {
     if(do_recover_data) {
@@ -730,7 +725,8 @@ do_mrgsim <- function(x,
 
 #' Basic, simple simulation from model object
 #' 
-#' This is just a lighter version of [mrgsim], with fewer options.  See `Details`.  
+#' This is just a lighter version of [mrgsim()], with fewer options.  
+#' See `Details`.  
 #' 
 #' @inheritParams mrgsim
 #' 
@@ -758,7 +754,7 @@ do_mrgsim <- function(x,
 #' 
 #' out <- qsim(mod,dose)
 #' 
-#' @seealso [mrgsim_q], [mrgsim], [mrgsim_variants]
+#' @seealso [mrgsim_q()], [mrgsim()], [mrgsim_variants]
 #' 
 #' @md
 #' 
@@ -846,17 +842,17 @@ qsim <- function(x,
   )
   
   if(tad) tcol <- c(tcol,"tad")
-  
-  dimnames(out[["data"]]) <- list(NULL, c("ID", tcol,  x@cmtL, x@capL))
+
+  names(out[["data"]]) <- c("ID", tcol,  x@cmtL, x@capL)
   
   if(output=="df") {
-    return(as.data.frame.matrix(out[["data"]]))
+    return(out[["data"]])
   }
   
   new(
     "mrgsims",
     request=x@cmtL,
-    data=as.data.frame.matrix(out[["data"]]),
+    data=out[["data"]],
     outnames=x@capL,
     mod=x
   )
diff --git a/inst/include/mrgsolve.h b/inst/include/mrgsolve.h
index 857d04f5..b852d7f7 100644
--- a/inst/include/mrgsolve.h
+++ b/inst/include/mrgsolve.h
@@ -61,6 +61,8 @@ Rcpp::NumericMatrix EXPAND_EVENTS(const Rcpp::IntegerVector& idcol_,
                                   const Rcpp::NumericMatrix& events,
                                   const Rcpp::NumericVector& id); 
 
+Rcpp::List mat2df(Rcpp::NumericMatrix& x);
+  
 // Rcpp::NumericMatrix recdata(Rcpp::NumericMatrix& dose,
 //                             Rcpp::NumericMatrix& obs,
 //                             Rcpp::IntegerVector& cols,
diff --git a/man/qsim.Rd b/man/qsim.Rd
index c0382c21..2ece8572 100644
--- a/man/qsim.Rd
+++ b/man/qsim.Rd
@@ -64,7 +64,8 @@ default output object; other options include \code{df} (for data.frame) or
 \code{matrix}}
 }
 \description{
-This is just a lighter version of \link{mrgsim}, with fewer options.  See \code{Details}.
+This is just a lighter version of \code{\link[=mrgsim]{mrgsim()}}, with fewer options.
+See \code{Details}.
 }
 \details{
 There is no pipeline interface for this function; all configuration options
@@ -84,5 +85,5 @@ out <- qsim(mod,dose)
 
 }
 \seealso{
-\link{mrgsim_q}, \link{mrgsim}, \link{mrgsim_variants}
+\code{\link[=mrgsim_q]{mrgsim_q()}}, \code{\link[=mrgsim]{mrgsim()}}, \link{mrgsim_variants}
 }
diff --git a/src/devtran.cpp b/src/devtran.cpp
index 8c8dfb58..1458f67e 100644
--- a/src/devtran.cpp
+++ b/src/devtran.cpp
@@ -640,6 +640,6 @@ Rcpp::List DEVTRAN(const Rcpp::List parin,
   if((tscale != 1) && (tscale >= 0)) {
     ans(Rcpp::_,1) = ans(Rcpp::_,1) * tscale;
   }
-  return Rcpp::List::create(Rcpp::Named("data") = ans,
+  return Rcpp::List::create(Rcpp::Named("data") = mat2df(ans),
                             Rcpp::Named("trannames") = tran_names);
 }
diff --git a/src/mrgsolve.cpp b/src/mrgsolve.cpp
index 42cd032d..6fff131d 100644
--- a/src/mrgsolve.cpp
+++ b/src/mrgsolve.cpp
@@ -388,6 +388,19 @@ Rcpp::List EXPAND_OBSERVATIONS(
                             Rcpp::Named("index") = index);
 }
 
+Rcpp::List mat2df(Rcpp::NumericMatrix& x) {
+  Rcpp::List ret(x.ncol());
+  for(int i = 0; i < x.ncol(); ++i) {
+    ret[i] = x(Rcpp::_,i);
+  }
+  Rcpp::IntegerVector rn(2);
+  rn[0] = NA_INTEGER;
+  rn[1] = x.nrow()*-1;
+  ret.attr("class")  = "data.frame";
+  ret.attr("row.names") = rn;
+  return ret;
+}
+
 #endif
 
 

From c41d7a3477e089b3cdf5da3f6f2919ab731651fb Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 3 Aug 2021 14:19:58 -0500
Subject: [PATCH 11/31] names

---
 R/mrgsolve.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/mrgsolve.R b/R/mrgsolve.R
index 37b677e6..b67dc245 100644
--- a/R/mrgsolve.R
+++ b/R/mrgsolve.R
@@ -637,7 +637,7 @@ do_mrgsim <- function(x,
     capture.output(file=capture, append=TRUE, print(data))
     capture.output(file=capture, append=TRUE, print(carry_out))
   }
-  
+
   out <- .Call(
     `_mrgsolve_DEVTRAN`,
     parin,
@@ -654,11 +654,10 @@ do_mrgsim <- function(x,
     PACKAGE = "mrgsolve"
   )
   
-  
   # out$trannames always comes back lower case in a specific order
   # need to rename to get back to requested case
   # Then, rename again for user-supplied renaming
-  carry.tran <- .ren.rename(rename.carry.tran,out[["trannames"]])
+  carry.tran <- .ren.rename(rename.carry.tran, out[["trannames"]])
   
   if(tad) tcol <- c(tcol,"tad")
   
@@ -686,8 +685,9 @@ do_mrgsim <- function(x,
     }
     cnames <- new_names
   }
-  
-  ans <- setNames(out[["data"]], cnames)
+
+  ans <- out[["data"]]
+  names(ans) <- cnames
   
   if(do_recover_data || do_recover_idata) {
     if(do_recover_data) {

From 8a2f5f9e59543daa080f3e352746f87f549641e3 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 3 Aug 2021 14:21:07 -0500
Subject: [PATCH 12/31] linting

---
 R/mrgsolve.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/mrgsolve.R b/R/mrgsolve.R
index b67dc245..d6bb7998 100644
--- a/R/mrgsolve.R
+++ b/R/mrgsolve.R
@@ -717,9 +717,9 @@ do_mrgsim <- function(x,
   new(
     "mrgsims",
     request = x@cmtL,
-    data=ans,
-    outnames=x@capL,
-    mod=x
+    data = ans,
+    outnames = x@capL,
+    mod = x
   )
 }
 
@@ -851,10 +851,10 @@ qsim <- function(x,
   
   new(
     "mrgsims",
-    request=x@cmtL,
-    data=out[["data"]],
-    outnames=x@capL,
-    mod=x
+    request = x@cmtL,
+    data = out[["data"]],
+    outnames = x@capL,
+    mod = x
   )
 }
 

From 1707ee7746ac29fbb88c50ab06df66ede71d89c7 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 3 Aug 2021 14:40:09 -0500
Subject: [PATCH 13/31] add test for requesting matrix while recovering
 character data

---
 R/mrgsolve.R                    | 18 ++++++++++--------
 tests/testthat/test-carry_out.R |  9 +++++++++
 2 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/R/mrgsolve.R b/R/mrgsolve.R
index d6bb7998..33d4695d 100644
--- a/R/mrgsolve.R
+++ b/R/mrgsolve.R
@@ -686,38 +686,40 @@ do_mrgsim <- function(x,
     cnames <- new_names
   }
 
-  ans <- out[["data"]]
-  names(ans) <- cnames
+  names(out[["data"]]) <- cnames
   
   if(do_recover_data || do_recover_idata) {
     if(do_recover_data) {
       if(!rename.recov$identical) {
         names(join_data) <- .ren.rename(rename.recov,names(join_data))
       }
-      ans <- left_join(ans,join_data,by=".data_row.",suffix=c("", ".recov"))  
-      ans$.data_row. <- NULL
+      out[["data"]] <- left_join(out[["data"]],join_data,by=".data_row.",suffix=c("", ".recov"))  
+      out[["data"]][[".data_row."]] <- NULL
     }
     if(do_recover_idata) {
       if(!rename.recov$identical) {
         names(join_idata) <- .ren.rename(rename.recov,names(join_idata))
       }
-      ans <- left_join(ans,join_idata,by="ID",suffix=c("", ".recov"))
+      out[["data"]] <- left_join(out[["data"]],join_idata,by="ID",suffix=c("", ".recov"))
     }
   }
   
   if(!is.null(output)) {
     if(output=="df") {
-      return(ans)  
+      return(out[["data"]])  
     }
     if(output=="matrix") {
-      return(out[["data"]])  
+      if(!all(sapply(out[["data"]], is.numeric))) {
+        stop("can't return matrix because non-numeric data was found.", call.=FALSE)  
+      }
+      return(data.matrix(out[["data"]]))
     }
   }
   
   new(
     "mrgsims",
     request = x@cmtL,
-    data = ans,
+    data = out[["data"]],
     outnames = x@capL,
     mod = x
   )
diff --git a/tests/testthat/test-carry_out.R b/tests/testthat/test-carry_out.R
index d18de26a..3fd3b68b 100644
--- a/tests/testthat/test-carry_out.R
+++ b/tests/testthat/test-carry_out.R
@@ -106,3 +106,12 @@ test_that("recover input idata-set items", {
   expect_is(out$b,"character")
   expect_error(mrgsim_e(mod,idata,recover="b",carry_out="b"))
 })
+
+test_that("error to request matrix and recover character data", {
+  data <- expand.ev(amt = 100, group = "A")
+  expect_is(mrgsim(mod, data, recover = "group"), "mrgsims")
+  expect_error(
+    mrgsim(mod, data, recover = "group", output = "matrix"), 
+    msg = "can't return matrix because non-numeric data was found"
+  )
+})

From 731947f7c6d183e2c7eabab6214426a9ff23d321 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 3 Aug 2021 14:47:03 -0500
Subject: [PATCH 14/31] some linting

---
 R/mrgsim_q.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/mrgsim_q.R b/R/mrgsim_q.R
index aeae4003..4ef16b3a 100644
--- a/R/mrgsim_q.R
+++ b/R/mrgsim_q.R
@@ -157,7 +157,7 @@ mrgsim_q <- function(x,
     PACKAGE = "mrgsolve"
   )[["data"]]
   
-  names(out) <- c("ID", tcol,x@cmtL,x@capL)
+  names(out) <- c("ID", tcol, x@cmtL, x@capL)
   
   if(output=="df") {
     return(out)  
@@ -169,9 +169,9 @@ mrgsim_q <- function(x,
   
   new(
     "mrgsims",
-    request=x@cmtL,
-    data=as.data.frame(out),
-    outnames=x@capL,
-    mod=x
+    request = x@cmtL,
+    data = out,
+    outnames = x@capL,
+    mod = x
   )
 }

From 82cc71189262ede2d8c03464bb12265dbb5ce88b Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 4 Aug 2021 23:11:00 -0500
Subject: [PATCH 15/31] const matrix to mat2df

---
 inst/include/mrgsolve.h | 2 +-
 src/mrgsolve.cpp        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/include/mrgsolve.h b/inst/include/mrgsolve.h
index b852d7f7..ddf91c5d 100644
--- a/inst/include/mrgsolve.h
+++ b/inst/include/mrgsolve.h
@@ -61,7 +61,7 @@ Rcpp::NumericMatrix EXPAND_EVENTS(const Rcpp::IntegerVector& idcol_,
                                   const Rcpp::NumericMatrix& events,
                                   const Rcpp::NumericVector& id); 
 
-Rcpp::List mat2df(Rcpp::NumericMatrix& x);
+Rcpp::List mat2df(Rcpp::NumericMatrix const& x);
   
 // Rcpp::NumericMatrix recdata(Rcpp::NumericMatrix& dose,
 //                             Rcpp::NumericMatrix& obs,
diff --git a/src/mrgsolve.cpp b/src/mrgsolve.cpp
index 6fff131d..f2ca0818 100644
--- a/src/mrgsolve.cpp
+++ b/src/mrgsolve.cpp
@@ -388,7 +388,7 @@ Rcpp::List EXPAND_OBSERVATIONS(
                             Rcpp::Named("index") = index);
 }
 
-Rcpp::List mat2df(Rcpp::NumericMatrix& x) {
+Rcpp::List mat2df(Rcpp::NumericMatrix const& x) {
   Rcpp::List ret(x.ncol());
   for(int i = 0; i < x.ncol(); ++i) {
     ret[i] = x(Rcpp::_,i);

From 98a6dc1bbffe8bbd3a6e1c7e4d0a6d3a27cc1621 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 25 Aug 2021 07:50:12 -0500
Subject: [PATCH 16/31] fix omega collate issue

---
 R/matlist.R         | 14 +++++++-------
 src/RcppExports.cpp |  5 +++++
 src/mrgsolve.cpp    |  4 ++++
 3 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/R/matlist.R b/R/matlist.R
index 52ea03b6..7784b782 100644
--- a/R/matlist.R
+++ b/R/matlist.R
@@ -200,7 +200,6 @@ setMethod("smat", "mrgsims", function(.x,make=FALSE,...) {
   as.matrix(mod(.x)@sigma)
 })
 
-
 #' Zero out random effects in a model object
 #' 
 #' Sets all elements of the OMEGA or SIGMA matrix to zero
@@ -261,7 +260,7 @@ setMethod("as.list", "matlist", function(x, ...) x@data)
 #' @export
 setMethod("as.matrix", "matlist", function(x, ...) {
   if(length(x@data)==0) return(matrix(nrow=0,ncol=0))
-  SUPERMATRIX(x@data, ...)
+  SUPERMATRIX(x@data, ..., keep_names = FALSE)
 })
 
 #' @rdname matlist
@@ -335,13 +334,14 @@ cumoffset <- function(x) {
 ##' @rdname matlist_ops
 ##' @export
 setMethod("c", "matlist", function(x,...,recursive=FALSE) {
-  what <- c(list(x),list(...))
-  stopifnot(all(sapply(what,is.matlist)))
+  what <- c(list(x), list(...))
+  stopifnot(all(sapply(what, is.matlist)))
+  what <- what[sapply(what, slot, name = "n") > 0]
   if(length(what)==1) return(x)
-  d <- lapply(what,as.matrix)
-  d <- setNames(d,sapply(what,names))
+  d <- lapply(what, as.matrix)
+  d <- setNames(d, sapply(what, names))
   l <- sapply(unname(what), labels)
-  create_matlist(d,labels=l, class=class(x)[1])
+  create_matlist(d, labels = l, class = class(x)[1])
 })
 
 collapse_matrix <- function(x,class) {
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 7b6b645d..e64d5bde 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -7,6 +7,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // DEVTRAN
 Rcpp::List DEVTRAN(const Rcpp::List parin, const Rcpp::NumericVector& inpar, const Rcpp::CharacterVector& parnames, const Rcpp::NumericVector& init, Rcpp::CharacterVector& cmtnames, const Rcpp::IntegerVector& capture, const Rcpp::List& funs, const Rcpp::NumericMatrix& data, const Rcpp::NumericMatrix& idata, Rcpp::NumericMatrix& OMEGA, Rcpp::NumericMatrix& SIGMA, Rcpp::Environment envir);
 RcppExport SEXP _mrgsolve_DEVTRAN(SEXP parinSEXP, SEXP inparSEXP, SEXP parnamesSEXP, SEXP initSEXP, SEXP cmtnamesSEXP, SEXP captureSEXP, SEXP funsSEXP, SEXP dataSEXP, SEXP idataSEXP, SEXP OMEGASEXP, SEXP SIGMASEXP, SEXP envirSEXP) {
diff --git a/src/mrgsolve.cpp b/src/mrgsolve.cpp
index f2ca0818..3e92f126 100644
--- a/src/mrgsolve.cpp
+++ b/src/mrgsolve.cpp
@@ -150,6 +150,10 @@ void dcorr(Rcpp::NumericMatrix& x) {
 //[[Rcpp::export]]
 Rcpp::NumericMatrix SUPERMATRIX(const Rcpp::List& a, bool keep_names) {
   
+  if(a.size()==1) {
+    return a[0];  
+  }
+  
   int j,k;
   Rcpp::NumericMatrix mat;
   

From 5ad2bd644092cdf5d4bb8650ddab3a74d4598d01 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 25 Aug 2021 08:17:02 -0500
Subject: [PATCH 17/31] adding tests for SUPERMATRIX

---
 R/matrix.R                   |  5 +++--
 tests/testthat/test-matrix.R | 19 +++++++++++++++----
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/R/matrix.R b/R/matrix.R
index 87618816..7b56058b 100644
--- a/R/matrix.R
+++ b/R/matrix.R
@@ -1,5 +1,4 @@
-# Copyright (C) 2013 - 2019  Metrum Research Group, LLC
-#
+# Copyright (C) 2013 - 2021  Metrum Research Group
 # This file is part of mrgsolve.
 #
 # mrgsolve is free software: you can redistribute it and/or modify it
@@ -17,6 +16,8 @@
 
 
 SUPERMATRIX <- function(x,keep_names=FALSE) {
+  stopifnot(is.list(x))
+  stopifnot(all(sapply(x, is.matrix)))
   x <- .Call(`_mrgsolve_SUPERMATRIX`,x,keep_names,PACKAGE="mrgsolve")
   if(nrow(x) > 0 & !keep_names) {
     dimnames(x) <- list(paste0(seq_len(nrow(x)), ": "), NULL)
diff --git a/tests/testthat/test-matrix.R b/tests/testthat/test-matrix.R
index c810e5f6..555d54ac 100644
--- a/tests/testthat/test-matrix.R
+++ b/tests/testthat/test-matrix.R
@@ -31,7 +31,18 @@ test_that("Testing modMATRIX", {
     expect_equal(modMATRIX("0 0 0", use=FALSE), matrix(0,nrow=3,ncol=3))
 })
 
-
-
-
-
+test_that("SUPERMATRIX", {
+    ml <- list(matrix(1, 2, 2), matrix(3, 4, 4))
+    dimnames(ml[[1]]) <- list(c("a", "b"), c("A", "B"))
+    ans <- mrgsolve:::SUPERMATRIX(ml)
+    expect_is(ans, "matrix")
+    expect_equal(dim(ans), c(6, 6))
+    ml$a <- "a"
+    expect_error(mrgsolve:::SUPERMATRIX(ml), msg = "is not TRUE")
+    expect_error(mrgsolve:::SUPERMATRIX(ml[[1]]), msg = "is not TRUE")
+    ml$a <- NULL
+    ans <- mrgsolve:::SUPERMATRIX(ml[2])
+    expect_identical(unname(ml[[2]]),unname(ans))
+    ans <- mrgsolve:::SUPERMATRIX(ml[1], keep_names=TRUE)
+    expect_identical(ans, ml[[1]])
+})

From 322e84efbc55a69d7bb8d8b7a450b8e58292af84 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 25 Aug 2021 08:21:49 -0500
Subject: [PATCH 18/31] don't force keep_names

---
 R/matlist.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/matlist.R b/R/matlist.R
index 7784b782..fff1d7cd 100644
--- a/R/matlist.R
+++ b/R/matlist.R
@@ -259,8 +259,10 @@ setMethod("as.list", "matlist", function(x, ...) x@data)
 #' @rdname matlist
 #' @export
 setMethod("as.matrix", "matlist", function(x, ...) {
-  if(length(x@data)==0) return(matrix(nrow=0,ncol=0))
-  SUPERMATRIX(x@data, ..., keep_names = FALSE)
+  if(length(x@data)==0) {
+    return(matrix(nrow = 0, ncol = 0))
+  }
+  SUPERMATRIX(x@data, ...)
 })
 
 #' @rdname matlist

From 18d82af8267ddac98962af2b75158461a5faa10b Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Sun, 29 Aug 2021 07:59:00 -0500
Subject: [PATCH 19/31] SUPERMATRIX tests; clean up

---
 R/class_matlist.R             | 2 +-
 R/matrix.R                    | 1 -
 tests/testthat/test-matlist.R | 8 ++++----
 tests/testthat/test-matrix.R  | 4 ++++
 4 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/R/class_matlist.R b/R/class_matlist.R
index 470d5599..ab8e5201 100644
--- a/R/class_matlist.R
+++ b/R/class_matlist.R
@@ -47,7 +47,7 @@ valid.matlist <- function(object) {
   }
   
   if(!x4) {
-    y <- which(sapply(object@data, det) < 0)
+    y <- which(!sapply(object@data, det) > 0)
     message("Problem with this matrix:")
     print(object@data[y])
     out <- c(out, "Invalid matrix: determinant is less than 0.")
diff --git a/R/matrix.R b/R/matrix.R
index 7b56058b..05b0312f 100644
--- a/R/matrix.R
+++ b/R/matrix.R
@@ -14,7 +14,6 @@
 # You should have received a copy of the GNU General Public License
 # along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
-
 SUPERMATRIX <- function(x,keep_names=FALSE) {
   stopifnot(is.list(x))
   stopifnot(all(sapply(x, is.matrix)))
diff --git a/tests/testthat/test-matlist.R b/tests/testthat/test-matlist.R
index dde2031d..273792b5 100644
--- a/tests/testthat/test-matlist.R
+++ b/tests/testthat/test-matlist.R
@@ -49,10 +49,10 @@ test_that("Indexing SIGMA matrix elements", {
   expect_equivalent(as.matrix(smat(mod))[3,3],0.3)
 })
 
-o1 <- 
-  omat(diag(c(1.1, 2.2, 3.3)), 
-       diag(c(4.4, 5.5, 6.6)), 
-       matrix(seq(91,99),nrow=3, byrow=TRUE))
+a <- diag(c(1.1, 2.2, 3.3))
+b <- diag(c(4.4, 5.5, 6.6))
+c <- matrix(seq(91,99),nrow = 3, byrow = TRUE)
+o1 <- omat(a,b,c)
 
 mat <- as.matrix(o1)
 
diff --git a/tests/testthat/test-matrix.R b/tests/testthat/test-matrix.R
index 555d54ac..18ce57fc 100644
--- a/tests/testthat/test-matrix.R
+++ b/tests/testthat/test-matrix.R
@@ -45,4 +45,8 @@ test_that("SUPERMATRIX", {
     expect_identical(unname(ml[[2]]),unname(ans))
     ans <- mrgsolve:::SUPERMATRIX(ml[1], keep_names=TRUE)
     expect_identical(ans, ml[[1]])
+    ans1 <- mrgsolve:::SUPERMATRIX(list())
+    expect_identical(ans1, matrix(0, nrow = 0, ncol = 0))
+    ans2 <- mrgsolve:::SUPERMATRIX(omat()@data)
+    expect_identical(ans1, ans2)
 })

From be8e4edb30d5b89ed60997d707425946fbc7fe8b Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Mon, 30 Aug 2021 10:45:39 -0500
Subject: [PATCH 20/31] lint

---
 tests/testthat/test-matrix.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-matrix.R b/tests/testthat/test-matrix.R
index 18ce57fc..81b1642d 100644
--- a/tests/testthat/test-matrix.R
+++ b/tests/testthat/test-matrix.R
@@ -43,7 +43,7 @@ test_that("SUPERMATRIX", {
     ml$a <- NULL
     ans <- mrgsolve:::SUPERMATRIX(ml[2])
     expect_identical(unname(ml[[2]]),unname(ans))
-    ans <- mrgsolve:::SUPERMATRIX(ml[1], keep_names=TRUE)
+    ans <- mrgsolve:::SUPERMATRIX(ml[1], keep_names = TRUE)
     expect_identical(ans, ml[[1]])
     ans1 <- mrgsolve:::SUPERMATRIX(list())
     expect_identical(ans1, matrix(0, nrow = 0, ncol = 0))

From ecdc975b0b3b487fcf27d88c95bb895ed1fb6159 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Mon, 30 Aug 2021 10:46:48 -0500
Subject: [PATCH 21/31] lint SUPERMATRIX

---
 R/matrix.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/matrix.R b/R/matrix.R
index 05b0312f..ac742aa9 100644
--- a/R/matrix.R
+++ b/R/matrix.R
@@ -14,10 +14,10 @@
 # You should have received a copy of the GNU General Public License
 # along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
-SUPERMATRIX <- function(x,keep_names=FALSE) {
+SUPERMATRIX <- function(x, keep_names = FALSE) {
   stopifnot(is.list(x))
   stopifnot(all(sapply(x, is.matrix)))
-  x <- .Call(`_mrgsolve_SUPERMATRIX`,x,keep_names,PACKAGE="mrgsolve")
+  x <- .Call(`_mrgsolve_SUPERMATRIX`, x, keep_names, PACKAGE = "mrgsolve")
   if(nrow(x) > 0 & !keep_names) {
     dimnames(x) <- list(paste0(seq_len(nrow(x)), ": "), NULL)
   }

From 988fa3f993841ecfd86c5a416bcda93fc73f7fec Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Mon, 30 Aug 2021 21:15:41 -0500
Subject: [PATCH 22/31] release branch

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ac00ec18..a1eecf0d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 0.11.1.9001
+Version: 0.11.1.9100
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),

From d27de0998c26919bca0ea736701914b9b170489b Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Mon, 30 Aug 2021 21:23:43 -0500
Subject: [PATCH 23/31] fix typo in cmat

---
 NEWS.md                  | 6 ++++++
 R/matrix.R               | 4 ++--
 man/matrix_converters.Rd | 2 +-
 man/matrix_helpers.Rd    | 2 +-
 4 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 0cf226b4..571ed067 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,12 @@
 
 - In `pk2iv`, change scaling volume for `CENT` from `V2` (incorrect) to 
   `V1` (#831, #832, #833)
+  
+- Fix bug collating multiple `$OMEGA` or `$SIGMA` matrices when parsing a 
+  model (#863)
+  
+- Refactor how debugging information is processed when using the `recover` 
+  argument to `mread()` (#853)
 
 # mrgsolve 0.11.1
 
diff --git a/R/matrix.R b/R/matrix.R
index ac742aa9..a8feb18d 100644
--- a/R/matrix.R
+++ b/R/matrix.R
@@ -132,7 +132,7 @@ Diag <- function(x) {
 ##' Create matrices from vector input
 ##'
 ##' @param ... matrix data
-##' @param correlation logical; if TRUE, off diagonal elements are assumed 
+##' @param correlation logical; if TRUE, off-diagonal elements are assumed 
 ##' to be correlations and converted to covariances
 ##' @param digits if greater than zero, matrix is passed to signif (along 
 ##' with digits) prior to returning
@@ -192,7 +192,7 @@ dmat <- function(...) {
 ##' @details
 ##' Use \code{as_dmat} to create a diagonal matrix, \code{as_bmat}
 ##' to create a block matrix, and \code{as_cmat} to create a block 
-##' matrix where diagonal elements are understood to be correlations
+##' matrix where off-diagonal elements are understood to be correlations
 ##' rather than covariances. \code{as_cmat} uses \code{as_bmat} to 
 ##' form the matrix and then converts off-diagonal elements to 
 ##' covariances before returning.
diff --git a/man/matrix_converters.Rd b/man/matrix_converters.Rd
index 94b818ae..22939bb8 100644
--- a/man/matrix_converters.Rd
+++ b/man/matrix_converters.Rd
@@ -58,7 +58,7 @@ matrix (\code{c}).
 \details{
 Use \code{as_dmat} to create a diagonal matrix, \code{as_bmat}
 to create a block matrix, and \code{as_cmat} to create a block 
-matrix where diagonal elements are understood to be correlations
+matrix where off-diagonal elements are understood to be correlations
 rather than covariances. \code{as_cmat} uses \code{as_bmat} to 
 form the matrix and then converts off-diagonal elements to 
 covariances before returning.
diff --git a/man/matrix_helpers.Rd b/man/matrix_helpers.Rd
index 2fbc0810..9759c037 100644
--- a/man/matrix_helpers.Rd
+++ b/man/matrix_helpers.Rd
@@ -16,7 +16,7 @@ dmat(...)
 \arguments{
 \item{...}{matrix data}
 
-\item{correlation}{logical; if TRUE, off diagonal elements are assumed 
+\item{correlation}{logical; if TRUE, off-diagonal elements are assumed 
 to be correlations and converted to covariances}
 
 \item{digits}{if greater than zero, matrix is passed to signif (along 

From 18fe2e9366b905704ece490733f4425b13e8e845 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Mon, 30 Aug 2021 21:23:54 -0500
Subject: [PATCH 24/31] bump

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a1eecf0d..a280022d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 0.11.1.9100
+Version: 0.11.1.9101
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),

From 399fcbda31b8b170650e33e7cf38f1b13a32d4a5 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Mon, 30 Aug 2021 21:27:58 -0500
Subject: [PATCH 25/31] news

---
 NEWS.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 571ed067..ce9b15ef 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -8,6 +8,9 @@
   
 - Refactor how debugging information is processed when using the `recover` 
   argument to `mread()` (#853)
+  
+- Fix typo in documentation for `as_cmat()`; the off-diagonals are assumed
+  to contain correlations (#856)
 
 # mrgsolve 0.11.1
 

From 4d4b09264912d7edf80c06e32ec79d4327f76693 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 31 Aug 2021 08:50:47 -0500
Subject: [PATCH 26/31] bump

---
 DESCRIPTION | 2 +-
 NEWS.md     | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a280022d..e6c7995b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 0.11.1.9101
+Version: 0.11.2
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index ce9b15ef..02b09c28 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# mrgsolve (development version)
+# mrgsolve 0.11.2
 
 - In `pk2iv`, change scaling volume for `CENT` from `V2` (incorrect) to 
   `V1` (#831, #832, #833)
@@ -12,6 +12,9 @@
 - Fix typo in documentation for `as_cmat()`; the off-diagonals are assumed
   to contain correlations (#856)
 
+- Wrote a `as.data.frame.matrix()` function in Rcpp; all simulation results
+  return from the C++ simulation code as a data frame (#857)
+
 # mrgsolve 0.11.1
 
 - `mrgsim()` will now periodically check for user interrupt signal so that 

From 95276bfe7db89ee8aba1f57e65930ca5b1fa5e1e Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 1 Sep 2021 22:45:37 -0500
Subject: [PATCH 27/31] fix capture validation bug

---
 NEWS.md                              |  3 +++
 R/mread.R                            |  3 +--
 inst/maintenance/unit/test-capture.R | 12 +++++++-----
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 02b09c28..61820f83 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -14,6 +14,9 @@
 
 - Wrote a `as.data.frame.matrix()` function in Rcpp; all simulation results
   return from the C++ simulation code as a data frame (#857)
+  
+- Fix bug where dynamic capture (via `mread()`) was not allowed for variables
+  declared in `$GLOBAL` (#868)
 
 # mrgsolve 0.11.1
 
diff --git a/R/mread.R b/R/mread.R
index 578ef56c..4ec0d0b3 100644
--- a/R/mread.R
+++ b/R/mread.R
@@ -283,8 +283,7 @@ mread <- function(model, project = getOption("mrgsolve.project", getwd()),
       unlist(labels(sigma)),
       .eta,
       .eps,
-      mread.env[["move_global"]], 
-      mread.env[["defines"]]
+      build[["cpp_variables"]][["var"]]
     )
     unique(ans)
   }
diff --git a/inst/maintenance/unit/test-capture.R b/inst/maintenance/unit/test-capture.R
index 618fca69..855fb7c0 100644
--- a/inst/maintenance/unit/test-capture.R
+++ b/inst/maintenance/unit/test-capture.R
@@ -52,6 +52,8 @@ test_that("error if cmt in capture issue-555", {
 
 code <- '
 $PARAM CL=1, V2=20,Q=30,V3=200,KA=1
+$GLOBAL
+double z = 5;
 $MAIN  double b = 2;
 $OMEGA 1
 $OMEGA @labels OGA2
@@ -60,15 +62,15 @@ $CAPTURE CL VP = V2
 '
 
 test_that("capture via mread", {
-  mod <- mcode("capture-mread", code, capture = "Q,a=b,OGA2") 
+  mod <- mcode("capture-mread", code, capture = "Q,a=b,OGA2,z") 
   out <- outvars(mod)
-  expect_equal(out$capture, c("CL", "VP", "Q", "a", "OGA2"))
+  expect_equal(out$capture, c("CL", "VP", "Q", "a", "OGA2", "z"))
   expect_error(
-    mread("pk1",modlib(),capture = "mrgsolve"),
+    mread("pk1", modlib(), capture = "mrgsolve"),
     msg = "all requested `capture` variables must exist in the model"
   )
-  mod <- mcode("capture-mread", code, capture="(everything)", compile=FALSE)
-  res <- c("CL","VP", "Q", "V3", "KA", "OGA2", "ETA_1", "ETA_2", "b")
+  mod <- mcode("capture-mread", code, capture="(everything)", compile = FALSE)
+  res <- c("CL","VP", "Q", "V3", "KA", "OGA2", "ETA_1", "ETA_2", "z", "b")
   expect_equal(outvars(mod)$capture, res)
 })
 

From 1588dfd79fd99a1046bdfd6d5e5931fed7b94f68 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Sat, 4 Sep 2021 09:18:18 -0500
Subject: [PATCH 28/31] re-factor cpp_variables

---
 R/mread.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/mread.R b/R/mread.R
index 4ec0d0b3..90fd0c50 100644
--- a/R/mread.R
+++ b/R/mread.R
@@ -277,13 +277,17 @@ mread <- function(model, project = getOption("mrgsolve.project", getwd()),
     } else {
       .eps <- NULL  
     }
+    cppv <- NULL
+    if(is.data.frame(build[["cpp_variables"]])) {
+      cppv <-  build[["cpp_variables"]][["var"]] 
+    }
     ans <- c(
       names(param), 
       unlist(labels(omega)), 
       unlist(labels(sigma)),
       .eta,
       .eps,
-      build[["cpp_variables"]][["var"]]
+      cppv
     )
     unique(ans)
   }

From 08bde8de1fe0e1dd62e1ba5b40a6b7064d3bf4dc Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Sat, 4 Sep 2021 11:22:56 -0500
Subject: [PATCH 29/31] sort pp directive capture test

---
 inst/maintenance/unit/test-capture.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/inst/maintenance/unit/test-capture.R b/inst/maintenance/unit/test-capture.R
index 855fb7c0..138dccb8 100644
--- a/inst/maintenance/unit/test-capture.R
+++ b/inst/maintenance/unit/test-capture.R
@@ -76,6 +76,5 @@ test_that("capture via mread", {
 
 test_that("capture pp directive via mread", {
   mod <- modlib("irm3", capture = "STIM", compile = FALSE)  
-  expect_equal(outvars(mod)$capture, c("CP", "STIM"))
+  expect_equal(sort(outvars(mod)$capture), sort(c("CP", "STIM")))
 })
-

From d2b155b27ef9bba8d703d4ca722a392c6dafe696 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Sat, 4 Sep 2021 12:07:50 -0500
Subject: [PATCH 30/31] stringsAsFactors ... again

---
 R/modspec.R | 9 +++++++--
 R/mread.R   | 6 +-----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/R/modspec.R b/R/modspec.R
index fde6b472..fd9e774a 100644
--- a/R/modspec.R
+++ b/R/modspec.R
@@ -328,7 +328,7 @@ get_c_vars2 <- function(y,context) {
   if(length(regm)==0) return(data.frame())
   vars <- gsub(pattern="\\s*=$", replacement = "", x = regm, perl=TRUE)
   vars <- token_space(vars)
-  ans <- as.data.frame(do.call(rbind,vars),stringsAsFactors = FALSE)
+  ans <- as.data.frame(do.call(rbind,vars), stringsAsFactors = FALSE)
   names(ans) <- c("type", "var")
   if(nrow(ans) > 0) ans$context <- context
   ans
@@ -354,7 +354,12 @@ pp_defs <- function(x,context) {
   code <- s_pick(x, 3)
   list(
     vars = vars, code = code, n = length(x), 
-    tab = data.frame(type = "define", var = vars, context = "global")
+    tab = data.frame(
+      type = "define", 
+      var = vars, 
+      context = "global", 
+      stringsAsFactors = FALSE
+    )
   )
 }
 
diff --git a/R/mread.R b/R/mread.R
index 90fd0c50..4ec0d0b3 100644
--- a/R/mread.R
+++ b/R/mread.R
@@ -277,17 +277,13 @@ mread <- function(model, project = getOption("mrgsolve.project", getwd()),
     } else {
       .eps <- NULL  
     }
-    cppv <- NULL
-    if(is.data.frame(build[["cpp_variables"]])) {
-      cppv <-  build[["cpp_variables"]][["var"]] 
-    }
     ans <- c(
       names(param), 
       unlist(labels(omega)), 
       unlist(labels(sigma)),
       .eta,
       .eps,
-      cppv
+      build[["cpp_variables"]][["var"]]
     )
     unique(ans)
   }

From 9bad8adaad2d4c3c72e6ceccdd98c636b38101bd Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Sat, 4 Sep 2021 12:09:57 -0500
Subject: [PATCH 31/31] remove sorting in test

---
 inst/maintenance/unit/test-capture.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/maintenance/unit/test-capture.R b/inst/maintenance/unit/test-capture.R
index 138dccb8..91489619 100644
--- a/inst/maintenance/unit/test-capture.R
+++ b/inst/maintenance/unit/test-capture.R
@@ -76,5 +76,5 @@ test_that("capture via mread", {
 
 test_that("capture pp directive via mread", {
   mod <- modlib("irm3", capture = "STIM", compile = FALSE)  
-  expect_equal(sort(outvars(mod)$capture), sort(c("CP", "STIM")))
+  expect_equal(outvars(mod)$capture, c("CP", "STIM"))
 })