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Modified Yasso model Fortran source code and R runscript
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Jarmo Mäkelä
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Jan 18, 2021
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| #' Run the YASSO model | ||
| #' | ||
| #' \code{run_yasso()} runs the YASSO model and returns simulated soil carbon. | ||
| #' | ||
| #' \code{run_yasso()} wraps the Fortran90-release of the soil carbon model | ||
| #' YASSO15 into a simple R-function. The function is a convenient way to call | ||
| #' the Fortran-release. | ||
| #' | ||
| #' The function provides YASSO with the initial soil carbon values in the vector | ||
| #' \code{init} and runs the model one time step at a time. The simulated | ||
| #' carbon of the current time step is used as the initial value of the next time | ||
| #' step. The model runs until it has looped over all the time steps. | ||
| #' | ||
| #' @param par A numeric vector of YASSO parameters. | ||
| #' @param n_runs Input data. Refer to \code{\link{sample_data_run}} for now. | ||
| #' @param time -||- | ||
| #' @param temp -||- | ||
| #' @param prec -||- | ||
| #' @param init -||- | ||
| #' @param litter -||- | ||
| #' @param wsize -||- | ||
| #' @param leac -||- | ||
| #' @param sspred Optional integer, should steady state mode be used (1 = yes). | ||
| #' | ||
| #' @return A matrix containing the initial soil carbon on the first row and | ||
| #' simulated soil carbon on the following rows. | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' soil_c <- run_yasso( | ||
| #' par = sample_parameters, | ||
| #' n_runs = sample_data_run$n_runs, | ||
| #' time = sample_data_run$time, | ||
| #' temp = sample_data_run$temp, | ||
| #' prec = sample_data_run$prec, | ||
| #' init = sample_data_run$init, | ||
| #' litter = sample_data_run$litter, | ||
| #' wsize = sample_data_run$wsize, | ||
| #' leac = sample_data_run$leac | ||
| #' ) | ||
|
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| run_yasso_c13 <- function(par, par_c13, n_runs, time, temp, prec, soil_c, init, litter, wsize, leac, | ||
| sspred = 0L) { | ||
|
|
||
| # Typeset parameters | ||
| par <- as.double(par) | ||
| par_c13 <- as.double(par_c13) | ||
|
|
||
| # Initialize, typeset an array for the results | ||
| soil_c13 <- matrix(rep(0, len = (n_runs) * 5), nrow = n_runs) | ||
| soil_c13 <- rbind(init, soil_c13) | ||
| soil_c13 <- unname(as.matrix(soil_c13)) | ||
|
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||
| # Call the fortran model | ||
| xx <- .Fortran( | ||
| "runyasso_c13", | ||
| par = par, | ||
| par_c13 = par_c13, | ||
| n_runs = n_runs, | ||
| time = time, | ||
| temp = temp, | ||
| prec = prec, | ||
| litter = litter, | ||
| wsize = wsize, | ||
| leac = leac, | ||
| soil_c = soil_c, | ||
| soil_c13 = soil_c13, | ||
| sspred = sspred | ||
| ) | ||
|
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||
| # Return simulated soil carbon | ||
| return(xx$soil_c13) | ||
| } |
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