diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinfit.R | 9 | ||||
| -rw-r--r-- | R/mkinmod.R | 46 |
2 files changed, 22 insertions, 33 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index 1c409569..5c092612 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -378,8 +378,9 @@ mkinfit <- function(mkinmod, observed, if (parmname == "r") parms.ini[parmname] = 0.2 } # Default values for formation fractions in case they are present - for (box in mod_vars) { - f_names <- mkinmod$parms[grep(paste0("^f_", box), mkinmod$parms)] + for (obs_var in obs_vars) { + origin <- mkinmod$map[[obs_var]][[1]] + f_names <- mkinmod$parms[grep(paste0("^f_", origin), mkinmod$parms)] if (length(f_names) > 0) { # We need to differentiate between default and specified fractions # and set the unspecified to 1 - sum(specified)/n_unspecified @@ -388,9 +389,9 @@ mkinfit <- function(mkinmod, observed, sum_f_specified = sum(parms.ini[f_specified_names]) if (sum_f_specified > 1) { stop("Starting values for the formation fractions originating from ", - box, " sum up to more than 1.") + origin, " sum up to more than 1.") } - if (mkinmod$spec[[box]]$sink) n_unspecified = length(f_default_names) + 1 + if (mkinmod$spec[[obs_var]]$sink) n_unspecified = length(f_default_names) + 1 else { n_unspecified = length(f_default_names) } diff --git a/R/mkinmod.R b/R/mkinmod.R index 62f16e73..4587e210 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -182,7 +182,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb "are only supported with formation fractions (use_of_ff = 'max')") } if(spec[[varname]]$sink) { - # If sink is required, add first-order/IORE sink term + # If sink is requested, add first-order/IORE sink term k_compound_sink <- paste("k", box_1, "sink", sep = "_") if(spec[[varname]]$type == "IORE") { k_compound_sink <- paste("k__iore", box_1, "sink", sep = "_") @@ -197,7 +197,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb } else { # otherwise no decline term needed here decline_term = "0" } - } else { + } else { # Maximum use of formation fractions k_compound <- paste("k", box_1, sep = "_") if(spec[[varname]]$type == "IORE") { k_compound <- paste("k__iore", box_1, sep = "_") @@ -236,26 +236,13 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb diffs[[box_1]] <- paste(diffs[[box_1]], "-", decline_term)#}}} if(spec[[varname]]$type == "SFORB") { # {{{ Add SFORB reversible binding terms box_2 = map[[varname]][[2]] - if (use_of_ff == "min") { # Minimum use of formation fractions - k_free_bound <- paste("k", varname, "free", "bound", sep = "_") - k_bound_free <- paste("k", varname, "bound", "free", sep = "_") - parms <- c(parms, k_free_bound, k_bound_free) - reversible_binding_term_1 <- paste("-", k_free_bound, "*", box_1, "+", - k_bound_free, "*", box_2) - reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-", - k_bound_free, "*", box_2) - } else { # Use formation fractions also for the free compartment - stop("The maximum use of formation fractions is not supported for SFORB models") - # The problems were: Calculation of dissipation times did not work in this case - # and the coefficient matrix is not generated correctly by the code present - # in this file in this case - #f_free_bound <- paste("f", varname, "free", "bound", sep = "_") - #k_bound_free <- paste("k", varname, "bound", "free", sep = "_") - #parms <- c(parms, f_free_bound, k_bound_free) - #reversible_binding_term_1 <- paste("+", k_bound_free, "*", box_2) - #reversible_binding_term_2 <- paste("+", f_free_bound, "*", k_compound, "*", box_1, "-", - # k_bound_free, "*", box_2) - } + k_free_bound <- paste("k", varname, "free", "bound", sep = "_") + k_bound_free <- paste("k", varname, "bound", "free", sep = "_") + parms <- c(parms, k_free_bound, k_bound_free) + reversible_binding_term_1 <- paste("-", k_free_bound, "*", box_1, "+", + k_bound_free, "*", box_2) + reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-", + k_bound_free, "*", box_2) diffs[[box_1]] <- paste(diffs[[box_1]], reversible_binding_term_1) diffs[[box_2]] <- paste(diffs[[box_2]], reversible_binding_term_2) } #}}} @@ -286,7 +273,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb k_from_to, "*", origin_box) } else { # Do not introduce a formation fraction if this is the only target - if (spec[[origin_box]]$sink == FALSE && n_targets == 1) { + if (spec[[varname]]$sink == FALSE && n_targets == 1) { diffs[[target_box]] <- paste(diffs[[target_box]], "+", decline_term) } else { @@ -302,7 +289,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff) - # Create coefficient matrix if appropriate#{{{ + # Create coefficient matrix if possible #{{{ if (mat) { boxes <- names(diffs) n <- length(boxes) @@ -321,12 +308,12 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb } else { # off-diagonal elements k.candidate = paste("k", from, to, sep = "_") - if (sub("_free$", "", from) == sub("_bound$", "", to)) { + if (sub("_free$", "", from) == sub("_bound$", "", to)) { k.candidate = paste("k", sub("_free$", "_free_bound", from), sep = "_") - } - if (sub("_bound$", "", from) == sub("_free$", "", to)) { + } + if (sub("_bound$", "", from) == sub("_free$", "", to)) { k.candidate = paste("k", sub("_bound$", "_bound_free", from), sep = "_") - } + } k.effective = intersect(model$parms, k.candidate) m[to, from] = ifelse(length(k.effective) > 0, k.effective, "0") @@ -350,7 +337,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb } else { # off-diagonal elements f.candidate = paste("f", from, "to", to, sep = "_") k.candidate = paste("k", from, to, sep = "_") - # SFORB with maximum use of formation fractions not implemented, see above + k.candidate = sub("free.*bound", "free_bound", k.candidate) + k.candidate = sub("bound.*free", "bound_free", k.candidate) m[to, from] = ifelse(f.candidate %in% model$parms, paste(f.candidate, " * k_", from, sep = ""), ifelse(k.candidate %in% model$parms, k.candidate, "0")) |