Merge pull request #392 from metrumresearchgroup/dev

Implementation of $PRED

.travis.yml

@@ -1,4 +1,4 @@
-language: r
+language: R
 sudo: false
 dist: trusty
 cache: packages
@@ -10,10 +10,11 @@ binary_packages:
   - dplyr
 
 env:
-  - R_KEEP_PKG_SOURCE=yes
-  - _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_=true
-  - _R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_=true  
-  - _R_CHECK_FORCE_SUGGESTS=0
+  global: 
+    - R_KEEP_PKG_SOURCE=yes
+    - _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_=true
+    - _R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_=true  
+    - _R_CHECK_FORCE_SUGGESTS=0
 
 pandoc: false
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mrgsolve
 Type: Package
-Version: 0.8.12
+Version: 0.8.12.9000
 Title: Simulate from ODE-Based Population PK/PD and Systems Pharmacology
     Models
 Authors@R: c(

Makefile

@@ -13,6 +13,10 @@ CHKDIR=Rchecks
 gut_check:
 	Rscript "inst/maintenance/gut_check.R"
 
+everything:
+	make all
+	make pkgdown
+
 pkgdown:
 	Rscript "inst/maintenance/pkgdown.R"
 	cp -r DOCS/ ../../mrgsolve/docs/

NAMESPACE

@@ -23,6 +23,7 @@ S3method(handle_spec_block,specOMEGA)
 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)
@@ -114,6 +115,7 @@ export(mrgsim_ei)
 export(mrgsim_i)
 export(mutate_sims)
 export(mvgauss)
+export(numerics_only)
 export(obsaug)
 export(obsonly)
 export(omat)

NEWS.md

@@ -1,3 +1,23 @@
+# mrgsolve 0.8.12.9000
+
+## New functions
+- Added `numerics_only` function to drop non-numeric columns from 
+the input data set after optionally converting logical columns
+to integer
+
+## New features
+- Added `$PRED` block for models that don't utilize any compartments
+- Added `pred1` to the `modlib`
+
+## New behavior
+- `time/TIME` is no longer required in a data set when `$PRED` is in use
+- `cmt/CMT` is no longer required in a data set; a default value of 0 will 
+be assigned in case it is missing and an error will continue to be generated
+when dosing into an invalid compartment (0 is always an invalid index
+for dosing compartment)
+
+# mrgsolve 0.8.12
+- Minor changes to namespace for CRAN
 # mrgsove 0.8.11
 - Internal release
 - Removed the function `s` and replaced with `s_`; this was not a problem 

R/Aaaa.R

@@ -72,7 +72,7 @@ block_list <- c("ENV", "PROB", "PARAM", "INIT",
                 "FIXED", "CMTN", "THETA", "NMXML", "VCMT",
                 "PKMODEL", "PLUGIN", "INCLUDE", "NAMESPACE",
                 "OMEGA", "SIGMA", "SET","GLOBAL", "CAPTURE", 
-                "PREAMBLE")
+                "PREAMBLE", "PRED")
 
 Reserved_cvar <- c("SOLVERTIME","table","ETA","EPS",
                    "ID", "TIME", "EVID","simeps", "self", "simeta",

R/annot.R

@@ -88,13 +88,24 @@ parse_annot_line <- function(x, novalue=FALSE, noname=FALSE,context="not given")
   list(name=a[1],value=a[2],unit=units,options=options,descr=b)
 }
 
-##' Extract model details.
+##' Extract model details
 ##' 
 ##' @param x a model object
-##' @param complete logical; if \code{TRUE}, un-annotated parameters and compartments will be added to the output
-##' @param values logical; if \code{TRUE}, a values column will be added to the output
+##' @param complete logical; if \code{TRUE}, un-annotated parameters and 
+##' compartments will be added to the output
+##' @param values logical; if \code{TRUE}, a values column will be added to 
+##' the output
 ##' @param ... not used
 ##' 
+##' @details
+##' This function is not exported.  You will have to call it 
+##' with \code{mrgsolve:::details()}. 
+##' 
+##' @examples
+##' mod <- mrgsolve:::house()
+##' 
+##' mrgsolve:::details(mod)
+##' 
 details <- function(x,complete=FALSE,values=FALSE,...) {
 
   stopifnot(is.mrgmod(x))

R/class_ev.R

@@ -40,6 +40,7 @@ select.ev <- function(.data, ...) {
   .data@data <- as.data.frame(dplyr::select(.data@data,...))
   .data 
 }
+
 ##' @rdname ev_dplyr
 ##' @export
 filter_.ev <-  function(.data, ...) {

R/class_mrgmod.R

@@ -32,6 +32,7 @@ check_names <- function(x,par,cmt) {
   dups <- any(duplicated(x))
   us <-  any(charthere(x,"_"))
   res <- any(is.element(x,Reserved))
+  alph <- !all(grepl("^[[:alpha:]]",x))
 
   ans <- character(0)
 
@@ -42,9 +43,14 @@ check_names <- function(x,par,cmt) {
   }
   ## Look for names in the Reserved word list
   if(res) {
-    tmp <- paste(x[is.element(x,Reserved)],collapse=" ")
+    tmp <- paste0(x[is.element(x,Reserved)],collapse=" ")
     ans <- c(ans,paste0("Reserved words in model names: ",tmp))
   }
+  ## names that don't start with alpha
+  if(alph) {
+    tmp <- paste0(x[!grepl("^[[:alpha:]]", x)], collapse = " ")
+    ans <- c(ans, paste0("Names without leading alpha character: ", tmp))
+  }
   ## Scan for names with underscores
   ## Leading underscores are not allowed
   ## Also, look for any name that conflicts with
@@ -138,12 +144,12 @@ valid.mrgmod <- function(object) {
   tags <- unlist(names(object), use.names=FALSE)
   x <- check_names(tags,Pars(object),Cmt(object))
   x1 <- length(x)==0
-  x2 <- object@advan %in% c(1,2,3,4,13)
+  x2 <- object@advan %in% c(0,1,2,3,4,13)
   fun <- valid_funs(object@funs)
   cool <- x1 & x2 & fun[[1]]
   if(cool) return(TRUE)
   x <- c(x,fun[[2]])
-  if(!x2) x <- c(x,"Advan must be 1, 2, 3, 4, or 13")
+  if(!x2) x <- c(x,"advan must be 1, 2, 3, 4, or 13")
   return(x)
 }
 

R/data_set.R

@@ -17,7 +17,6 @@
 
 ##' Select and modify a data set for simulation
 ##'
-##'
 ##' @param x model object
 ##' @param data data set
 ##' @param .subset an unquoted expression passed to 
@@ -46,23 +45,32 @@
 ##'
 ##' Input data set may include the following columns related to 
 ##' PK dosing events: \code{time}, \code{cmt}, \code{amt}, \code{rate},
-##' \code{ii}, \code{addl}, \code{ss}.  \code{time} and \code{cmt} 
-##' (and \code{ID}) are required columns in the input data set. 
+##' \code{ii}, \code{addl}, \code{ss}.  Along with \code{ID}, \code{time} 
+##' is a required column in the input data set unless \code{$PRED} is in 
+##' use.  Upper case PK dosing column names including
+##' \code{TIME}, \code{CMT}, \code{AMT}, \code{RATE}, \code{II},
+##' \code{ADDL}, \code{SS} are also recognized.  However, an 
+##' error will be generated if a mix of upper case and lower
+##' case columns in this family are found.
+##'  
 ##' \code{time} is the observation or event time, \code{cmt} 
 ##' is the compartment number (see \code{\link{init}}), \code{amt} 
 ##' is the dosing amount, \code{rate} is the infusion rate, 
 ##' \code{ii} is the dosing interval, \code{addl} specifies 
 ##' additional doses to administer, and \code{ss} is a flag 
 ##' for steady state dosing.  These column names operate 
 ##' similarly to other non-linear mixed effects modeling 
-##' software.  Upper case PK dosing column names including
-##' \code{TIME}, \code{CMT}, \code{AMT}, \code{RATE}, \code{II},
-##' \code{ADDL}, \code{SS} are also recognized.  However, an 
-##' error will be generated if a mix of upper case and lower
-##' case columns are found.
-##'
+##' software. 
+##' 
+##' An error will be generate when mrgsolve detects that the data set
+##' is not sorted by \code{time} within an individual.  Also, an error 
+##' will be generated in case mrgsolve finds negative values for 
+##' \code{time}, unless \code{$PRED} is in use.
+##' 
 ##' Only numeric data can be brought in to the problem.  
-##' Any non-numeric data columns will be dropped with warning.
+##' Any non-numeric data columns will be dropped with warning.  
+##' See \code{\link{numerics_only}}, which is used 
+##' to prepare the data set. 
 ##'
 ##' See \code{\link{exdatasets}} for different example data sets.
 ##' 

R/events.R

@@ -26,12 +26,15 @@
 ##' ways.
 ##'
 ##' @param x a model object
+##' @param time event time
+##' @param amt dose amount
 ##' @param evid event ID
+##' @param cmt compartment
+
 ##' @param ID subject ID
-##' @param time event time
 ##' @param replicate logical; if \code{TRUE}, events will be replicated for 
 ##' each individual in \code{ID}
-##' @param cmt compartment
+
 ##' @param until the expected maximum \bold{observation} time for this regimen
 ##' @param realize_addl if \code{FALSE} (default), no change to \code{addl} 
 ##' doses.  If \code{TRUE}, \code{addl} doses are made explicit with 
@@ -43,11 +46,14 @@
 ##' 
 ##' @details
 ##' \itemize{
-##' \item Required input for creating events objects include 
-##' \code{time} and \code{cmt}
+##' \item Required items in events objects include 
+##' \code{time}, \code{amt}, \code{evid} and \code{cmt}.
 ##' \item If not supplied, \code{evid} is assumed to be 1.
 ##' \item If not supplied, \code{cmt}  is assumed to be 1.
 ##' \item If not supplied, \code{time} is assumed to be 0.
+##' \item If \code{amt} is not supplied, an error will be generated.
+##' \item Other items can include \code{ii}, \code{ss}, and \code{addl}
+##' (see \code{\link{data_set}} for details on all of these items).
 ##' \item \code{ID} may be specified as a vector.
 ##' \item If replicate is \code{TRUE} (default), thenthe events 
 ##' regimen is replicated for each \code{ID}; otherwise, the number of
@@ -93,9 +99,8 @@ setMethod("ev", "mrgmod", function(x,object=NULL,...) {
 
 ##' @rdname ev
 ##' @export
-setMethod("ev", "missing", function(time=0, evid=1, ID=numeric(0), 
-                                    cmt=1, replicate=TRUE, until=NULL,
-                                    realize_addl=FALSE,...) {
+setMethod("ev", "missing", function(time=0, amt, evid=1, cmt=1, ID=numeric(0), 
+                                    replicate=TRUE, until=NULL, realize_addl=FALSE, ...) {
 
   if(length(match.call())==1) { 
     return(new("ev", data=data.frame()[0,]))
@@ -105,7 +110,7 @@ setMethod("ev", "missing", function(time=0, evid=1, ID=numeric(0),
     stop("evid cannot be 0 (observation)")
   }
 
-  data <- as_data_frame(list(..., time = time, cmt = cmt, evid = evid))
+  data <- as_data_frame(list(time=time, cmt=cmt, amt=amt, evid=evid, ...))
 
   data <- as.data.frame(data)
 
@@ -180,6 +185,10 @@ setMethod("ev", "ev", function(x, realize_addl=FALSE,...) {
 ##' the result
 ##' @param ... not used
 ##' 
+##' @examples
+##' data <- data.frame(amt = 100) 
+##' 
+##' as.ev(data)
 ##' 
 ##' @export
 setGeneric("as.ev", function(x,...) {

R/generics.R

@@ -98,5 +98,7 @@ setGeneric("ex", function(x,...) standardGeneric("ex"))
 ##'
 ##' @param x mrgsims object
 ##' @param ... passed along
+##' 
+##' 
 ##' @rdname mod
 setGeneric("mod", function(x,...) standardGeneric("mod"))

R/idata_set.R

@@ -36,7 +36,7 @@
 ##' data for the problem.  An  \code{ID} column is required and there 
 ##' can be no more than one row in the data frame for each individual.  
 ##' 
-##' In most cases, the columns in the `idata_set` have the same names
+##' In most cases, the columns in the \code{idata_set} have the same names
 ##' as parameters in the \code{\link{param}} list.  When this is the case, 
 ##' the parameter set is updated as the simulation proceeds once at the 
 ##' start of each individual.  The `idata_set` can also be used to 
@@ -65,11 +65,18 @@
 ##' 
 ##' exidata
 ##' 
-##' mod %>% idata_set(exidata, ID <= 2) %>% mrgsim %>% plot
+##' mod %>% 
+##'   idata_set(exidata, ID <= 2) %>% 
+##'   ev(amt = 100) %>%
+##'   mrgsim() %>% 
+##'   plot()
 ##' 
-##' mod %>% idata_set(exidata) %>% mrgsim
+##' mod %>% 
+##'   idata_set(exidata) %>% 
+##'   ev(amt = 100) %>%
+##'   mrgsim()
 ##' 
-##' mod %>% mrgsim(idata=exidata) 
+##' mod %>% ev(amt = 100) %>% mrgsim(idata=exidata) 
 ##' 
 ##' @seealso \code{\link{data_set}}, \code{\link{ev}}
 ##' 

R/modlib.R

@@ -16,7 +16,7 @@
 # along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
 
-##' Internal model library.
+##' Internal model library
 ##' 
 ##' @param list list available models
 ##' @export
@@ -48,6 +48,7 @@
 ##' mod <- mread("tmdd",   modlib())
 ##' mod <- mread("viral1", modlib())
 ##' mod <- mread("viral2", modlib())
+##' mod <- mread("pred1",  modlib())
 ##' 
 ##' mrgsolve:::code(mod)
 ##' }