interpolated variables undeclared in delay blocks

[OJWatson]

Following is an example of where the interpolated variables are not correctly included within delay blocks. Sorry it's a little long, but tried to remake it with just one delay and couldn't seem to

mod <- odin::odin({
  
  deriv(A) <- 2 * A * cov2 
  initial(A) <- 1  
  lagB <- A * 2
  B <- delay(lagB, 10)
  
  ###
  
  deriv(C) <- C * B
  initial(C) <- 1 
  lagD <- C * cov[1]
  D <- delay(lagD, 12) 

 ###
  
  flux <- interpolate(flux_t, flux_y, "linear")
  dim(cov) <- 2
  cov[1] <- 1 - flux
  cov[2] <- flux
  cov2 <- sum(cov) * D
  
  ###
  
  flux_t[] <- user()
  flux_y[] <- user()
  dim(flux_t) <- user()
  dim(flux_y) <- user()
  
})

which yields

Compiling shared library
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mtune=generic -c odin.c -o odin.o
odin.c: In function 'odin_deriv':
odin.c:220:86: error: 'interpolate_flux' undeclared (first use in this function)
     double flux = "linear"(odin_p->flux_t, odin_p->flux_y, 0, 1, odin_p->dim_flux_t, interpolate_flux);
                                                                                      ^
odin.c:220:86: note: each undeclared identifier is reported only once for each function it appears in
odin.c:220:19: error: called object is not a function or function pointer
     double flux = "linear"(odin_p->flux_t, odin_p->flux_y, 0, 1, odin_p->dim_flux_t, interpolate_flux);
                   ^
make: *** [odin.o] Error 1

Error in handle_compiler_output(output, verbose, compiler_warnings) : 
  Error compiling source

and the compiled c code (as file):

odin.c.txt

[OJWatson]

@richfitz am just checking in on this.

[richfitz]

Fix for this on the i130 branch now

[richfitz]

this is fixed!

[OJWatson]

@richfitz think i've found something similar when trying to use an interpolated matrix. For example this works fine:

mod <- odin::odin({
  
  deriv(A) <- 2 * A * D
  initial(A) <- 1  
  lagB <- A * 2
  B <- delay(lagB, 10)
  
  ###
  
  deriv(C) <- C * B
  initial(C) <- 1 
  lagD <- C * cov_interp
  D <- delay(lagD, 12)

  ###
  
  int_times[] <- user()
  dim(int_times) <- user()
  cov_vec[] <- user()
  dim(cov_vec) <- length(int_times)
  cov_interp <- interpolate(int_times, cov_vec, "constant")

})

But the following where make cov_vec into a matrix to be interpolated errors:

mod <- odin::odin({
  
  deriv(A) <- 2 * A * D
  initial(A) <- 1  
  lagB <- A * 2
  B <- delay(lagB, 10)
  
  ###
  
  deriv(C) <- C * B
  initial(C) <- 1 
  lagD <- C * cov_interp[1]
  D <- delay(lagD, 12)
  
  ###
  
  int_times[] <- user()
  dim(int_times) <- user()

  cov_mat[,] <- user()
  dim(cov_mat) <- c(length(int_times),2)

  cov_interp[] <- interpolate(int_times, cov_mat, "constant")
  dim(cov_interp) <- 2
  

})

gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i39faS/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c odin.c -o odin.o
odin.c: In function ‘odin_deriv’:
odin.c:272:37: error: ‘constant’ undeclared (first use in this function); did you mean ‘long int’?
       odin_p->delay_cov_interp[i] = constant;
                                     ^~~~~~~~
                                     long int
odin.c:272:37: note: each undeclared identifier is reported only once for each function it appears in
/usr/lib/R/etc/Makeconf:162: recipe for target 'odin.o' failed
make: *** [odin.o] Error 1

odin.c.txt

Let me know if there is anything else that would be useful to know

[richfitz]

can you give initialisation parameters for this model too please?

[OJWatson]

Sure so for the first model:

mod <- odin::odin({
  
  deriv(A) <- 0.1 * A * D
  initial(A) <- 1  
  lagB <- A * 2
  B <- delay(lagB, 10)
  ###
  
  deriv(C) <- C * B * 0.001
  initial(C) <- 1 
  lagD <- C * cov_interp
  D <- delay(lagD, 12)
  ###
  
  int_times[] <- user()
  dim(int_times) <- user()
  cov_vec[] <- user()
  dim(cov_vec) <- length(int_times)
  cov_interp <- interpolate(int_times, cov_vec, "constant")
  
})

m <- mod(int_times = c(-20,20,40),cov_vec = c(0,0.3,0.6))
m$run(t = 0:60)

and then the second one that doesn't

mod <- odin::odin({
  
  deriv(A) <- 0.1 * A * D
  initial(A) <- 1  
  lagB <- A * 2
  B <- delay(lagB, 10)
  ###
  
  deriv(C) <- C * B * 0.001
  initial(C) <- 1 
  lagD <- C * cov_interp[1]
  D <- delay(lagD, 12)
  ###
  
  int_times[] <- user()
  dim(int_times) <- user()
  
  cov_mat[,] <- user()
  dim(cov_mat) <- c(length(int_times),2)
  
  cov_interp[] <- interpolate(int_times, cov_mat, "constant")
  dim(cov_interp) <- 2
  
  
})

m <- mod(int_times = c(-20,20,40),cov_mat = matrix(rep(c(0,0.3,0.6),2),nrow=3))
m$run(t = 0:60)

[richfitz]

thanks, very useful. this won't move until I get the new interface working I'm afraid, but I will probably look at rolling this into that work

[OJWatson]

Cool - and yeah no rush from me so that sounds great.

[richfitz]

This is fixed on the i139_ir branch - please give it a go if you get a chance