dt2mat returns matrix objects

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.7.903
+Version: 0.1.7.904
 Authors@R:
   c(person(given="Philip", family="Delff",
      email = "philip@delff.dk",

NEWS.md

@@ -20,6 +20,9 @@
 * NMscanMultiple would sometimes print a bit of a messy overview of
   the results. That has been fixed without implications on the results
   returned.
+
+* dt2mat() now returns actual matrix objects. This provides
+  compatibility with the simpar package.
 
 # NMdata 0.1.7
 

R/dt2mat.R

@@ -8,7 +8,10 @@
 ##' @param dt.subset Specifies whether pars contains only a lower or
 ##'     upper triangle of an assumed symmetric matrix (most often the
 ##'     case for variance-covariance matrices), or it contains the
-##'     full matrix.
+##'     full matrix. `dt.subset="unique"` (default) means that `pars` only
+##'     contains either upper or lower diagonal matrix (including
+##'     diagonal), `dt.subset="all"` means `pars` contains both upper
+##'     and lower triangles. See details.
 ##' @param max.i By default, the maximum row number is derived as he
 ##'     maximum value in the `i` column. If more (empty ones) are
 ##'     needed, specify the maximum row number with `max.i`. This can
@@ -21,9 +24,9 @@
 ##'     output from `NMreadExt()`.
 ##' @details If pars does not contain all `i` values, they will be
 ##'     imputed with zeros. The desired matrix dimension is inferred
-##'     from `min(i)` and `max(i)`.  In case `dt.subset=="unique"`
+##'     from `min(i)` and `max(i)`. In case `dt.subset=="unique"`
 ##'     missing `j` elements will also give imputations of missing
-##'     elements.
+##'     elements. 
 ##' @import data.table
 ##' @return a matrix
 ##' @export
@@ -62,8 +65,21 @@ dt2mat <- function(pars,dt.subset="unique",max.i,fill=0,col.value) {
     i.missing <- setdiff(min(pars$i):max.i,pars$i)
     pars.mat <- rbind(pars.mat,data.table(i=i.missing,j=i.missing),fill=TRUE)
 
+
+
     ## note, dcast returns a keyed data.table (keys are LHS vars) so it is always ordered by i.
-    matrix.pars <- as.matrix(dcast(pars.mat,i~j,value.var="value")[,!("i")])
+    pars.matshape <- dcast(pars.mat,i~j,value.var="value")[,!("i")]
+    matrix.pars <- matrix(unlist(pars.matshape),ncol=nrow(pars.matshape))
+
+    if(F){
+        if(nrow(pars.matshape)==1){
+            ## matrix.pars <- matrix(pars.matshape)
+            matrix.pars <- matrix(as.numeric(unlist(pars.matshape)))
+        } else {
+            matrix.pars <- as.matrix(pars.matshape)
+        }
+    }
+
     if(!isFALSE(fill)){
         matrix.pars[is.na(matrix.pars)] <- fill
     }

devel/scripts/dsCreate_1.R

@@ -15,6 +15,7 @@ library(ggplot2)
 ## install_github("philipdelff/NMdata")
 ## library(NMdata)
 
+setwd("~/wdirs/NMdata/devel/scripts/")
 library(devtools)
 load_all("~/wdirs/NMdata")
 
@@ -310,3 +311,13 @@ NMwriteSection(file.nm("xgxr001dir/input.txt"),section="DATA",newlines=sec.data.
 
 ###  Section end: Create xgxr001dir
 
+#### Section start: Version with AMT in microgram ####
+
+### xgxgr002: CYCLE=DROP, BBW for WEIGHTB
+pk2 <- copy(pk)
+pk2[,AMT:=AMT*1000]
+nmcode <- NMwriteData(pk2,file=file.data.test("xgxr12.csv"),script=script.1,args.stamp = list(description="AMT in micrograms"))
+
+
+### Section end: Version with AMT in microgram
+