add OMEGA and SIGMA block info to ext pars output

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.6.915
+Version: 0.1.6.921
 Authors@R:
   c(person(given="Philip", family="Delff",
      email = "philip@delff.dk",

NEWS.md

@@ -1,5 +1,6 @@
 
 # 0.1.7
+
 ## New features
 * `NMreadPartab()` has been generalized to support comment formats very
   generally. `NMreadPartab()` reads the comments in `$THETA`, `$OMEGA`
@@ -24,6 +25,27 @@
 * `mergeCheck()` has additional features available in the common.cols
   argument.
 
+* `NMreadExt()` separates objective function values into a separate list
+  element. The `return` argument is used to control what data to
+  retrieve. Use one of "pars" (default, parameter estimates),
+  "iterations" (parameter estimates for each iteration), "obj" for
+  objective funtion value, or "all" for a list with all of those.
+
+* `NMreadExt()` adds block information to `OMEGA` and `SIGMA` elements
+  based on off-diagonal values.
+
+* `NMreadExt()` adds a `par.name` column which is provides consistent
+  parameter naming. Instead of Nonmem's `THETA1` which is found in the
+  `parameter` column, the `par.name` column will contain `THETA(1)`
+  consistent with the `OMEGA` and `SIGMA` naming like `OMEGA(1,1)`
+
+* `NMreadExt()` recognizes Laplacian estimation steps in addition to
+  the already supported FO, FOCE(i), SAEM, and IMP.
+
+* A new option `nc` can be controlled with NMdataConf(). This is to
+  serve `NMsim`. Please see `NMsim::NMexec`. `NMsim::NMsim()` does not
+  adhere to this setting because it does not parallellize by default.
+
 ## Bugfixes
 * `NMscanInput()` and `NMreadCsv()` could fail if file names had no
   extensions. Fixed.

R/NMreadExt.R

@@ -6,7 +6,9 @@
 ##'     \code{return="pars"} (default) the final estimates are
 ##'     returned in addition to what other parameter-level information
 ##'     is found, like FIX, sd etc. as columns. If
-##'     \code{return="iterations"}, the iterations are returned. If
+##'     \code{return="iterations"}, the iterations are returned
+##'     (including objective function value). If \code{return="obj"}
+##'     objective function value at final estimate is returned. If
 ##'     \code{return="all"}, all er returned, though in separate
 ##'     data.frames compiled in a list.
 ##' @param as.fun The default is to return data as a data.frame. Pass
@@ -121,7 +123,7 @@ NMreadExt <- function(file,return,as.fun,modelname,col.model,auto.ext,tableno="m
 
     if(missing(return)||is.null(return)) return <- "pars"
     return <- tolower(return)
-
+    
     allowed.return <- c("pars","iterations","obj","all")
     if(!return %in% allowed.return){
         stop("Argument return has to be one of: ", paste(allowed.return,collapse =", "))
@@ -195,12 +197,26 @@ NMreadExt <- function(file,return,as.fun,modelname,col.model,auto.ext,tableno="m
         obj[,(cols.drop):=NULL]
         pars <- pars[!parameter%in%c("SAEMOBJ","OBJ")]
 
-        ### this setorder call doesnt work - unsure why
+### this setorder call doesnt work - unsure why
         ## setorder(pars,match(par.type,c("THETA","OMEGA","SIGMA")),i,j)
         pars <- pars[order(model,match(par.type,c("THETA","OMEGA","SIGMA")),i,j)]
         ## est is just a copy of value for backward compatibility
         pars[,est:=value]
 
+### add OMEGA block information based on off diagonal values
+        tab.blocks <- rbind(pars[par.type%in%c("OMEGA","SIGMA"),.(par.type,i=i,j=j,value)],
+                            pars[par.type%in%c("OMEGA","SIGMA"),.(par.type,i=j,j=i,value)])[
+            abs(value)>1e-9,.(iblock=min(i,j),blocksize=max(abs(j-i))+1),by=.(par.type,i)]
+
+        tab.blocks
+
+        pars <- mergeCheck(pars,tab.blocks,by=cc(par.type,i),all.x=T)
+        pars[abs(i-j)>(blocksize-1),(c("iblock","blocksize")):=list(NA,NA)]
+
+        pars[par.type%in%c("OMEGA","SIGMA")&i==j&is.na(iblock),iblock:=i]
+        pars[par.type%in%c("OMEGA","SIGMA")&i==j&iblock==i,blocksize:=1]
+### done add OMEGA/SIGMA blocks
+
     }
 
     ## what to do about OBJ? Disregard? And keep in a iteration table instead?