Questions relating to the R Template Model Builder package
Questions relating to the R Template Model Builder package:
https://github.com/kaskr/adcomp
https://cran.r-project.org/web/packages/TMB/index.html
Questions tagged [tmb]
32 questions
4
votes
1 answer
TMB c++ code in R package and CRAN checks
I am working on an R package to include c++ templates created in TMB. Using the helpful guidelines shared in this suggestion, I managed to come a very long way.
At the moment, I'm using 2 c++ templates ("kglmer.cpp" and "nglmer.cpp") and the…
Stefan Vriend
- 43
- 5
4
votes
1 answer
How do I see and replicate the R default Makevars configuration?
I do not have a ~/.R/Makevars file and
> tools::makevars_user()
character(0)
> tools::makevars_site()
character(0)
Yet, R must be reading the configuration from somewhere as .cpp files containing Rcpp exports in the package src subdirectory…
Alex
- 15,186
- 15
- 73
- 127
3
votes
2 answers
Guidelines for including TMB c++ code in an R package
I've recently discovered the wonders of TMB and I'm working on a package which would ideally include TMB c++ templates in it for rather computationally expensive models.
I'm assuming that there's a possibility of:
Automatically compiling the TMB…
RTbecard
- 868
- 1
- 8
- 23
2
votes
0 answers
Using splines in TMB models
I have a nonlinear mixed-effects model that I have implemented in nlme that I would like to implement in TMB to decrease computation times and hopefully some occasional convergence issues.
In its simplest form, the model is given by
y_ij = f((1 -…
Lars Lau Raket
- 1,905
- 20
- 35
2
votes
0 answers
Why does calling dyn.load in a for loop crash my R session?
R (3.3.2, Windows 7) crashes after about 1000 iterations of dyn.load() being used in a for loop. This does not happen in Ubuntu. This behaviour is observed for dll files created from Rcpp and TMB code, but I don't think it is related to either of…
Alex
- 15,186
- 15
- 73
- 127
2
votes
0 answers
Distributing TMB functions in R package and CRAN checks
I have 9 cpp files in /src - 8 from Rcpp and 1 from TMB. I can compile all and run code successfully OR get passed the CRAN checks. But not both.
Method 1
Let R compile all cpp files and generate a single DLL: 'mypackage.dll' and TMB::MakeADfun(...,…
Adrian
- 684
- 3
- 20
2
votes
2 answers
Exporting g++ compilation error messages from TMB library to a text file
I'm trying to compile a model with gcc (c++) in R (using the TMB package). The errors are so numerous that in Rstudio, I can't even scroll up to see the beginning of them. Therefore, I would like to print everything in the console (messages, errors…
Wave
- 1,216
- 1
- 9
- 22
1
vote
1 answer
glmmTMB_phylo: Error in Matrix::rankMatrix(TMBStruc$data.tmb[[whichX]]) : length(d <- dim(x)) == 2 is not TRUE
I am trying to run the following model:
mod1<- phylo_glmmTMB(response ~ sv1 + # sampling variables
sv2 + sv3 + sv4 + sv5 +
sv6 + sv7 +
(1|phylo) + (1|reference_id), #random effects
ziformula = ~ 0,
#ar1(pos + 0| group) # spatial autocorrelation…
Non_Praying_Mantis
- 25
- 6
1
vote
1 answer
Why am getting the following error when adjusting a glmm with the "glmmTMB" function and I try to obtain the confidence intervals?
I am trying to run the following model:
Mm3znb<-glmmTMB(total~ Geopolitical-1 + offset(logha) + YearCollected + tmn + (tmn|Site/Plot), ziformula = ~1, data = mc3m, family="nbinom2")
but when I try to obtain the confidence intervals am getting this…
1
vote
1 answer
How to do a matrix * vector multiplication and pass this result to a vector in TMB in R?
I need to do a matrix * vector multiplication, which generates only a single number, and pass it to a vector (but it doesn't work in the commented code below). What I have so far is:
cpp code
#include
template
Type…
Guilherme Parreira
- 944
- 9
- 29
1
vote
0 answers
How to debug my .cpp file using `gdbsource` function in TMB in R?
I am writing to implement a Simplex regression in this file (simplex_reg.cpp):
// Simplex Regression
#include
template
Type objective_function::operator() ()
{
// Data provided from user
DATA_VECTOR(Y);
…
Guilherme Parreira
- 944
- 9
- 29
1
vote
1 answer
C++ for TMB but not Rcpp in knitr
I'm writting a document using knitr that includes C++ code. This code is to be used with the R package TMB. I am using a .Rnw document.
My main problem is that I do not know what to specify for the code chunk engine. I have read a few questions…
Marie Auger-Methe
- 808
- 1
- 8
- 20
1
vote
1 answer
What is this outermgc message while optimising with TMB?
After producing the objective function and gradient with TMB, and calling the optim function, I get a sequence of reports printed in my console that seems to of the form "outer mgc: ":
outer mgc: 56.54273
outer mgc: 56.51064
outer mgc: 56.96065…
Alex
- 15,186
- 15
- 73
- 127
1
vote
2 answers
How do I include more objective functions in my TMB .cpp file?
The TMB objective functions are seemingly defined in one function block that is saved to a .cpp file. Then, after compiling the file, each objective function is accessed by loading with the command dyn.load(dynlib()).
Is it possible to…
Alex
- 15,186
- 15
- 73
- 127
0
votes
0 answers
Possible bias when fitting linear regression with errors in variables using TMB
I am new to template model builder (TMB), and I am trying to use it to fit a simple linear regression with errors in variables as a learning exercise. My ultimate goal is to apply this to more complex models. I am using the formulation:
Formulae
and…
Darren G
- 1
- 2