Add/Create C functions for use in rxode2
Arguments
- name
This can either give the name of the user function or be a simple R function that you wish to convert to C. If you have rxode2 convert the R function to C, the name of the function will match the function name provided and the number of arguments will match the R function provided. Hence, if you are providing an R function for conversion to C, the rest of the arguments are implied.
- args
This gives the arguments of the user function
- cCode
This is the C-code for the new function
Examples
# \donttest{
## Right now rxode2 is not aware of the function fun
## Therefore it cannot translate it to symengine or
## Compile a model with it.
try(rxode2("a=fun(a,b,c)"))
#>
#>
#> Error : syntax errors (see above)
## Note for this approach to work, it cannot interfere with C
## function names or reserved rxode2 special terms. Therefore
## f(x) would not work since f is an alias for bioavailability.
fun <- "
double fun(double a, double b, double c) {
return a*a+b*a+c;
}
" ## C-code for function
rxFun("fun", c("a", "b", "c"), fun) ## Added function
## Now rxode2 knows how to translate this function to symengine
rxToSE("fun(a,b,c)")
#> [1] "fun(a,b,c)"
## And will take a central difference when calculating derivatives
rxFromSE("Derivative(fun(a,b,c),a)")
#> [1] "(fun((a)+6.05545445239334e-06,b,c)-fun(a,b,c))/6.05545445239334e-06"
## Of course, you could specify the derivative table manually
rxD("fun", list(
function(a, b, c) {
paste0("2*", a, "+", b)
},
function(a, b, c) {
return(a)
},
function(a, b, c) {
return("0.0")
}
))
rxFromSE("Derivative(fun(a,b,c),a)")
#> [1] "2*a+b"
# You can also remove the functions by `rxRmFun`
rxRmFun("fun")
# you can also use R functions directly in rxode2
gg <- function(x, y) {
x + y
}
f <- rxode2({
z = gg(x, y)
})
#>
#>
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
e <- et(1:10) |> as.data.frame()
e$x <- 1:10
e$y <- 21:30
rxSolve(f, e)
#> Warning: not thread safe method, using 1 core
#> ── Solved rxode2 object ──
#> ── Parameters ($params): ──
#> # A tibble: 1 × 0
#> ── Initial Conditions ($inits): ──
#> named numeric(0)
#> ── First part of data (object): ──
#> # A tibble: 10 × 4
#> time z x y
#> <dbl> <dbl> <dbl> <dbl>
#> 1 1 22 1 21
#> 2 2 24 2 22
#> 3 3 26 3 23
#> 4 4 28 4 24
#> 5 5 30 5 25
#> 6 6 32 6 26
#> # ℹ 4 more rows
# Note that since it touches R, it can only run single-threaded.
# There are also requirements for the function:
#
# 1. It accepts one value per argument (numeric)
#
# 2. It returns one numeric value
# If it is a simple function (like gg) you can also convert it to C
# using rxFun and load it into rxode2
rxFun(gg)
#> → finding duplicate expressions in d(gg)/d(x)...
#> → finding duplicate expressions in d(gg)/d(y)...
#> converted R function 'gg' to C (will now use in rxode2)
#> converted R function 'rx_gg_d_x' to C (will now use in rxode2)
#> converted R function 'rx_gg_d_y' to C (will now use in rxode2)
#> Added derivative table for 'gg'
rxSolve(f, e)
#> compiled with R user function 'gg'; now there is a clashing C user function
#> triggered a recompile to use the C user function (they are always preferred)
#>
#>
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> ── Solved rxode2 object ──
#> ── Parameters ($params): ──
#> # A tibble: 1 × 0
#> ── Initial Conditions ($inits): ──
#> named numeric(0)
#> ── First part of data (object): ──
#> # A tibble: 10 × 4
#> time z x y
#> <dbl> <dbl> <dbl> <dbl>
#> 1 1 22 1 21
#> 2 2 24 2 22
#> 3 3 26 3 23
#> 4 4 28 4 24
#> 5 5 30 5 25
#> 6 6 32 6 26
#> # ℹ 4 more rows
# to stop the recompile simply reassign the function
f <- rxode2(f)
#>
#>
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rxSolve(f, e)
#> ── Solved rxode2 object ──
#> ── Parameters ($params): ──
#> # A tibble: 1 × 0
#> ── Initial Conditions ($inits): ──
#> named numeric(0)
#> ── First part of data (object): ──
#> # A tibble: 10 × 4
#> time z x y
#> <dbl> <dbl> <dbl> <dbl>
#> 1 1 22 1 21
#> 2 2 24 2 22
#> 3 3 26 3 23
#> 4 4 28 4 24
#> 5 5 30 5 25
#> 6 6 32 6 26
#> # ℹ 4 more rows
rxRmFun("gg")
rm(gg)
rm(f)
# You can also automatically convert a R function to R code (and
# calculate first derivatives)
fun <- function(a, b, c) {
a^2+b*a+c
}
rxFun(fun)
#> → finding duplicate expressions in d(fun)/d(a)...
#> → finding duplicate expressions in d(fun)/d(b)...
#> → finding duplicate expressions in d(fun)/d(c)...
#> converted R function 'fun' to C (will now use in rxode2)
#> converted R function 'rx_fun_d_a' to C (will now use in rxode2)
#> converted R function 'rx_fun_d_b' to C (will now use in rxode2)
#> converted R function 'rx_fun_d_c' to C (will now use in rxode2)
#> Added derivative table for 'fun'
# You can see the R code if you want with rxC
message(rxC("fun"))
#> double fun(double a, double b, double c) {
#> double _lastValue=NA_REAL;
#> _lastValue = R_pow_di(a,2)+b*a+c;
#> return _lastValue;
#> }
# you can also remove both the function and the
# derivatives with rxRmFun("fun")
rxRmFun("fun")
# }