R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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> # Preliminaries
> setwd("C:/Users/James/Documents/pharmacometrics/testing")
> system2(ls())
Warning message:
running command '""' had status 127 
> system2(dir())
Warning message:
running command '""' had status 127 
> shell(dir())
> #  Folder is empty.
> library(nlmixr)
Loading required package: nlme
Loading required package: RxODE
> str(theo_sd)  # like Theoph but with ID instead of Subject, also other NONMEM-like
'data.frame':	144 obs. of  7 variables:
 $ ID  : int  1 1 1 1 1 1 1 1 1 1 ...
 $ TIME: num  0 0 0.25 0.57 1.12 2.02 3.82 5.1 7.03 9.05 ...
 $ DV  : num  0 0.74 2.84 6.57 10.5 9.66 8.58 8.36 7.47 6.89 ...
 $ AMT : num  4.02 0 0 0 0 0 0 0 0 0 ...
 $ EVID: int  101 0 0 0 0 0 0 0 0 0 ...
 $ CMT : int  1 2 2 2 2 2 2 2 2 2 ...
 $ WT  : num  79.6 79.6 79.6 79.6 79.6 79.6 79.6 79.6 79.6 79.6 ...
> # 'uif' for Unified Interface Function, 1 compartment, lin for linCmt()
> uif.1cm.lin <- function() {
+   ini({
+     logtcl <- -3.2      # log typical value Cl (L/hr)
+     logtka <-  0.5      # log typical value Ka (1/hr)
+     logtv  <- -1        # log typical value V  (L)
+     
+     # error model
+     add.err <- 0.1
+     
+     # Initial estimates for IIV variances
+     # Labels work for single parameters.
+     eta.cl ~ 2
+     eta.ka ~ 1    ## BSV Ka
+     eta.v  ~ 1
+   })
+   model({
+     cl <- exp(logtcl + eta.cl)
+     ka <- exp(logtka + eta.ka)
+     v  <- exp(logtv  + eta.v)
+     linCmt() ~ add(add.err)
+   })
+ }
> # NLME fittings
> 
> fit.nlme.1cm.lin.theo_sd     <- nlmixr(uif.1cm.lin, theo_sd, est="nlme")

**Iteration 1
LME step: Loglik: -182.2318, nlminb iterations: 1
reStruct  parameters:
      ID1       ID2       ID3 
1.0022617 0.2783009 2.0758984 
PNLS step: RSS =  63.14922 
 fixed effects: -3.211937  0.4479979  -0.7859318  
 iterations: 7 
Convergence crit. (must all become <= tolerance = 1e-05):
   fixed reStruct 
0.272375 3.267309 

**Iteration 2
LME step: Loglik: -179.291, nlminb iterations: 9
reStruct  parameters:
       ID1        ID2        ID3 
0.96385527 0.08333435 1.63552295 
PNLS step: RSS =  63.28221 
 fixed effects: -3.211535  0.4441505  -0.7863391  
 iterations: 7 
Convergence crit. (must all become <= tolerance = 1e-05):
      fixed    reStruct 
0.008662381 0.172135330 

**Iteration 3
LME step: Loglik: -179.3381, nlminb iterations: 8
reStruct  parameters:
       ID1        ID2        ID3 
0.96129928 0.07085834 1.63885629 
PNLS step: RSS =  63.2196 
 fixed effects: -3.211732  0.4458486  -0.7861743  
 iterations: 7 
Convergence crit. (must all become <= tolerance = 1e-05):
      fixed    reStruct 
0.003808629 0.082919683 

**Iteration 4
LME step: Loglik: -179.3201, nlminb iterations: 7
reStruct  parameters:
       ID1        ID2        ID3 
0.96243507 0.07618717 1.63736945 
PNLS step: RSS =  63.22991 
 fixed effects: -3.211823  0.4451494  -0.7862432  
 iterations: 7 
Convergence crit. (must all become <= tolerance = 1e-05):
      fixed    reStruct 
0.001570583 0.013884126 

**Iteration 5
LME step: Loglik: -179.3277, nlminb iterations: 4
reStruct  parameters:
       ID1        ID2        ID3 
0.96197111 0.07396744 1.63796900 
PNLS step: RSS =  63.24112 
 fixed effects: -3.211722  0.4454457  -0.7862145  
 iterations: 6 
Convergence crit. (must all become <= tolerance = 1e-05):
       fixed     reStruct 
0.0006651255 0.0147544693 

**Iteration 6
LME step: Loglik: -179.3246, nlminb iterations: 1
reStruct  parameters:
       ID1        ID2        ID3 
0.96215433 0.07487426 1.63772430 
PNLS step: RSS =  63.24112 
 fixed effects: -3.211722  0.4454457  -0.7862145  
 iterations: 1 
Convergence crit. (must all become <= tolerance = 1e-05):
       fixed     reStruct 
0.000000e+00 3.910435e-10 
Using sympy via SnakeCharmR
C:/RTools/3.4/mingw_64/bin/gcc  -I"C:/R/R-34~1.3/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mtune=generic -c rx_920cdb7f8c8c7b5e42b1a8db66863398_x64.c -o rx_920cdb7f8c8c7b5e42b1a8db66863398_x64.o
C:/RTools/3.4/mingw_64/bin/gcc -shared -s -static-libgcc -o rx_920cdb7f8c8c7b5e42b1a8db66863398_x64.dll tmp.def rx_920cdb7f8c8c7b5e42b1a8db66863398_x64.o -LC:/R/R-34~1.3/bin/x64 -lRblas -LC:/R/R-34~1.3/bin/x64 -lRlapack -lgfortran -lm -lquadmath -LC:/R/R-34~1.3/bin/x64 -lR
The model has been setup to calculate residuals.
It will be cached for future runs.
Diagonal form: sqrt
     [,1]
[1,]    1
Calculate symbolic inverse...done
Calculate symbolic determinant of inverse...done
Calculate d(Omega)/d(Est) and d(Omega^-1)/d(Est)...
.0
...done.
Calculating Table Variables...
done
Warning message:
In nlmixrUI.nlme.var(obj) :
  Initial condition for additive error ignored with nlme
nlmixr UI combined dataset and properties
 $ par.hist         : Parameter history (if available)
 $ par.hist.stacked : Parameter history in stacked form for easy plotting (if available)
 $ par.fixed        : Fixed Effect Parameter Table
 $ eta              : Individual Parameter Estimates
 $ seed             : Seed (if applicable)
 $ model.name       : Model name (from R function)
 $ data.name        : Name of R data input
> # Object x now appears:
> ls()
[1] "fit.nlme.1cm.lin.theo_sd" "uif.1cm.lin"              "x"                       
> # Now exit session and repeat above steps.
> # This output will be stored as 'first_output.txt'.