# Copyright (C) 2010-2013 Johannes Ranke {{{ # Contact: jranke@uni-bremen.de # This file is part of the R package mkin # mkin is free software: you can redistribute it and/or modify it under the # terms of the GNU General Public License as published by the Free Software # Foundation, either version 3 of the License, or (at your option) any later # version. # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more # details. # You should have received a copy of the GNU General Public License along with # this program. If not, see <http://www.gnu.org/licenses/> }}} mkinmod <- function(..., use_of_ff = "min", speclist = NULL) { if (is.null(speclist)) spec <- list(...) else spec <- speclist obs_vars <- names(spec) # Check if any of the names of the observed variables contains any other for (obs_var in obs_vars) { if (length(grep(obs_var, obs_vars)) > 1) stop("Sorry, variable names can not contain each other") if (grepl("_to_", obs_var)) stop("Sorry, names of observed variables can not contain _to_") } if (!use_of_ff %in% c("min", "max")) stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'") # The returned model will be a list of character vectors, containing {{{ # differential equations, parameter names and a mapping from model variables # to observed variables. If possible, a matrix representation of the # differential equations is included parms <- vector() diffs <- vector() map <- list() # }}} # Give a warning when a model with time dependent degradation uses formation {{{ # fractions if(spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) { mat = FALSE } else mat = TRUE #}}} # Establish a list of differential equations as well as a map from observed {{{ # compartments to differential equations for (varname in obs_vars) { # Check the type component of the compartment specification {{{ if(is.null(spec[[varname]]$type)) stop( "Every part of the model specification must be a list containing a type component") if(!spec[[varname]]$type %in% c("SFO", "FOMC", "DFOP", "HS", "SFORB")) stop( "Available types are SFO, FOMC, DFOP, HS and SFORB only") if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) { stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,", "which is assumed to be the source compartment")) } #}}} # New (sub)compartments (boxes) needed for the model type {{{ new_boxes <- switch(spec[[varname]]$type, SFO = varname, FOMC = varname, DFOP = varname, HS = varname, SFORB = paste(varname, c("free", "bound"), sep="_") ) map[[varname]] <- new_boxes names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes)) #}}} # Start a new differential equation for each new box {{{ new_diffs <- paste("d_", new_boxes, " =", sep="") names(new_diffs) <- new_boxes diffs <- c(diffs, new_diffs) #}}} } #}}} # Create content of differential equations and build parameter list {{{ for (varname in obs_vars) { # Get the name of the box(es) we are working on for the decline term(s) box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB # Turn on sink if this is not explicitly excluded by the user by # specifying sink=FALSE if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE if(spec[[varname]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term if (use_of_ff == "min") { # Minimum use of formation fractions if(spec[[varname]]$sink) { # If sink is required, add first-order sink term k_compound_sink <- paste("k", box_1, "sink", sep="_") parms <- c(parms, k_compound_sink) decline_term <- paste(k_compound_sink, "*", box_1) } else { # otherwise no decline term needed here decline_term = "0" } } else { k_compound <- paste("k", box_1, sep="_") parms <- c(parms, k_compound) decline_term <- paste(k_compound, "*", box_1) } } #}}} if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term # From p. 53 of the FOCUS kinetics report decline_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1) parms <- c(parms, "alpha", "beta") } #}}} if(spec[[varname]]$type == "DFOP") { # {{{ Add DFOP decline term # From p. 57 of the FOCUS kinetics report decline_term <- paste("((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) *", box_1) parms <- c(parms, "k1", "k2", "g") } #}}} if(spec[[varname]]$type == "HS") { # {{{ Add HS decline term # From p. 55 of the FOCUS kinetics report decline_term <- paste("ifelse(time <= tb, k1, k2)", "*", box_1) parms <- c(parms, "k1", "k2", "tb") } #}}} # Add origin decline term to box 1 (usually the only box, unless type is SFORB)#{{{ diffs[[box_1]] <- paste(diffs[[box_1]], "-", decline_term)#}}} if(spec[[varname]]$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) } diffs[[box_1]] <- paste(diffs[[box_1]], reversible_binding_term_1) diffs[[box_2]] <- paste(diffs[[box_2]], reversible_binding_term_2) } #}}} # Transfer between compartments#{{{ to <- spec[[varname]]$to if(!is.null(to)) { # Name of box from which transfer takes place origin_box <- box_1 # Add transfer terms to listed compartments for (target in to) { target_box <- switch(spec[[target]]$type, SFO = target, SFORB = paste(target, "free", sep="_")) if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO", "SFORB")) { k_from_to <- paste("k", origin_box, target_box, sep="_") parms <- c(parms, k_from_to) diffs[[origin_box]] <- paste(diffs[[origin_box]], "-", k_from_to, "*", origin_box) diffs[[target_box]] <- paste(diffs[[target_box]], "+", k_from_to, "*", origin_box) } else { if (!spec[[varname]]$sink) { stop("Turning off the sink when using formation fractions is not supported") } fraction_to_target = paste("f", origin_box, "to", target, sep="_") parms <- c(parms, fraction_to_target) diffs[[target_box]] <- paste(diffs[[target_box]], "+", fraction_to_target, "*", decline_term) } } } #}}} } #}}} model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff) # Create coefficient matrix if appropriate#{{{ if (mat) { boxes <- names(diffs) n <- length(boxes) m <- matrix(nrow=n, ncol=n, dimnames=list(boxes, boxes)) if (use_of_ff == "min") { # {{{ Minimum use of formation fractions for (from in boxes) { for (to in boxes) { if (from == to) { # diagonal elements k.candidate = paste("k", from, c(boxes, "sink"), sep="_") k.candidate = sub("free.*bound", "free_bound", k.candidate) k.candidate = sub("bound.*free", "bound_free", k.candidate) k.effective = intersect(model$parms, k.candidate) m[from,to] = ifelse(length(k.effective) > 0, paste("-", k.effective, collapse = " "), "0") } else { # off-diagonal elements k.candidate = paste("k", from, to, sep="_") if (sub("_free$", "", from) == sub("_bound$", "", to)) { k.candidate = paste("k", sub("_free$", "_free_bound", from), sep="_") } 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") } } } # }}} } else { # {{{ Use formation fractions where possible for (from in boxes) { for (to in boxes) { if (from == to) { # diagonal elements k.candidate = paste("k", from, sep="_") m[from,to] = ifelse(k.candidate %in% model$parms, paste("-", k.candidate), "0") if(grepl("_free", from)) { # add transfer to bound compartment for SFORB m[from,to] = paste(m[from,to], "-", paste("k", from, "bound", sep="_")) } if(grepl("_bound", from)) { # add backtransfer to free compartment for SFORB m[from,to] = paste("- k", from, "free", sep="_") } m[from,to] = m[from,to] } else { # off-diagonal elements f.candidate = paste("f", from, "to", to, sep="_") k.candidate = paste("k", from, to, sep="_") # SFORB with maximum use of formation fractions not implemented, see above m[to, from] = ifelse(f.candidate %in% model$parms, paste(f.candidate, " * k_", from, sep=""), ifelse(k.candidate %in% model$parms, k.candidate, "0")) } } } } # }}} model$coefmat <- m }#}}} class(model) <- "mkinmod" return(model) } # vim: set foldmethod=marker ts=2 sw=2 expandtab: