diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/IORE.solution.R | 4 | ||||
| -rw-r--r-- | R/endpoints.R | 2 | ||||
| -rw-r--r-- | R/mkinerrmin.R | 6 | ||||
| -rw-r--r-- | R/mkinfit.R | 23 | ||||
| -rw-r--r-- | R/mkinmod.R | 95 | ||||
| -rw-r--r-- | R/mkinpredict.R | 50 | ||||
| -rw-r--r-- | R/plot.mkinfit.R | 2 | ||||
| -rw-r--r-- | R/transform_odeparms.R | 12 |
8 files changed, 115 insertions, 79 deletions
diff --git a/R/IORE.solution.R b/R/IORE.solution.R index 9546ce56..5405be96 100644 --- a/R/IORE.solution.R +++ b/R/IORE.solution.R @@ -1,4 +1,4 @@ -IORE.solution <- function(t, parent.0, k.iore, N)
+IORE.solution <- function(t, parent.0, k__iore, N)
{
- parent = (parent.0^(1 - N) - (1 - N) * k.iore * t)^(1/(1 - N))
+ parent = (parent.0^(1 - N) - (1 - N) * k__iore * t)^(1/(1 - N))
}
diff --git a/R/endpoints.R b/R/endpoints.R index ae9aa3ec..001595bc 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -50,7 +50,7 @@ endpoints <- function(fit) { ep$distimes[obs_var, c("DT50back")] = DT50_back
}
if (type == "IORE") {
- k_names = grep(paste("k.iore", obs_var, sep="_"), names(parms.all), value=TRUE)
+ k_names = grep(paste("k__iore", obs_var, sep="_"), names(parms.all), value=TRUE)
k_tot = sum(parms.all[k_names])
# From the NAFTA kinetics guidance, p. 5
n = parms.all[paste("N", obs_var, sep = "_")]
diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R index b28235a6..6103dd1d 100644 --- a/R/mkinerrmin.R +++ b/R/mkinerrmin.R @@ -61,8 +61,8 @@ mkinerrmin <- function(fit, alpha = 0.05) n.k.optim <- length(grep(paste("^k", obs_var, sep="_"), names(parms.optim))) n.k.optim <- n.k.optim + length(grep(paste("^log_k", obs_var, sep="_"), names(parms.optim))) - n.k.iore.optim <- length(grep(paste("^k.iore", obs_var, sep="_"), names(parms.optim))) - n.k.iore.optim <- n.k.iore.optim + length(grep(paste("^log_k.iore", obs_var, + n.k__iore.optim <- length(grep(paste("^k__iore", obs_var, sep="_"), names(parms.optim))) + n.k__iore.optim <- n.k__iore.optim + length(grep(paste("^log_k__iore", obs_var, sep = "_"), names(parms.optim))) @@ -82,7 +82,7 @@ mkinerrmin <- function(fit, alpha = 0.05) } } - n.optim <- sum(n.initials.optim, n.k.optim, n.k.iore.optim, n.N.optim, n.ff.optim) + n.optim <- sum(n.initials.optim, n.k.optim, n.k__iore.optim, n.N.optim, n.ff.optim) # FOMC, DFOP and HS parameters are only counted if we are looking at the # first variable in the model which is always the source variable diff --git a/R/mkinfit.R b/R/mkinfit.R index 5118519a..ce380243 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -26,9 +26,8 @@ mkinfit <- function(mkinmod, observed, state.ini = "auto",
fixed_parms = NULL,
fixed_initials = names(mkinmod$diffs)[-1],
- solution_type = c("auto", "analytical", "eigen", "deSolve"),
+ solution_type = c("auto", "analytical", "eigen", "deSolve", "odeintr"),
method.ode = "lsoda",
- use_compiled = "auto",
method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"),
maxit.modFit = "auto",
control.modFit = list(),
@@ -208,8 +207,7 @@ mkinfit <- function(mkinmod, observed, # Decide if the solution of the model can be based on a simple analytical
# formula, the spectral decomposition of the matrix (fundamental system)
# or a numeric ode solver from the deSolve package
- # Prefer deSolve over eigen if a compiled model is present and use_compiled
- # is not set to FALSE
+ # Prefer odeintr if a compiled model is present
solution_type = match.arg(solution_type)
if (solution_type == "analytical" && length(mkinmod$spec) > 1)
stop("Analytical solution not implemented for models with metabolites.")
@@ -219,8 +217,11 @@ mkinfit <- function(mkinmod, observed, if (length(mkinmod$spec) == 1) {
solution_type = "analytical"
} else {
- if (!is.null(mkinmod$compiled) & use_compiled[1] != FALSE) {
- solution_type = "deSolve"
+ if (!is.null(mkinmod$e$m)) {
+ solution_type = "odeintr"
+ if (!missing(atol) | !missing(rtol)) {
+ message("When fitting with solution type odeintr, atol and rtol can only be set in the call to mkinmod()")
+ }
} else {
if (is.matrix(mkinmod$coefmat)) {
solution_type = "eigen"
@@ -269,9 +270,8 @@ mkinfit <- function(mkinmod, observed, out <- mkinpredict(mkinmod, parms,
odeini, outtimes,
solution_type = solution_type,
- use_compiled = use_compiled,
method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
+ atol.deSolve = atol, rtol.deSolve = rtol, ...)
assign("out_predicted", out, inherits=TRUE)
@@ -289,9 +289,8 @@ mkinfit <- function(mkinmod, observed, out_plot <- mkinpredict(mkinmod, parms,
odeini, outtimes_plot,
solution_type = solution_type,
- use_compiled = use_compiled,
method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
+ atol.deSolve = atol, rtol.deSolve = rtol, ...)
plot(0, type="n",
xlim = range(observed$time), ylim = c(0, max(observed$value, na.rm=TRUE)),
@@ -319,8 +318,8 @@ mkinfit <- function(mkinmod, observed, if (!transform_rates) {
index_k <- grep("^k_", names(lower))
lower[index_k] <- 0
- index_k.iore <- grep("^k.iore_", names(lower))
- lower[index_k.iore] <- 0
+ index_k__iore <- grep("^k__iore_", names(lower))
+ lower[index_k__iore] <- 0
other_rate_parms <- intersect(c("alpha", "beta", "k1", "k2", "tb"), names(lower))
lower[other_rate_parms] <- 0
}
diff --git a/R/mkinmod.R b/R/mkinmod.R index e865fa27..4991be22 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -16,12 +16,17 @@ # 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, quiet = FALSE)
+mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE,
+ odeintr_compile = c("auto", "no", "yes"),
+ odeintr_method = "rk5_i",
+ odeintr_atol = 1e-8, odeintr_rtol = 1e-10)
{
if (is.null(speclist)) spec <- list(...)
else spec <- speclist
obs_vars <- names(spec)
+ odeintr_compile <- match.arg(odeintr_compile)
+
# 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")
@@ -99,7 +104,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) # If sink is required, add first-order/IORE sink term
k_compound_sink <- paste("k", box_1, "sink", sep = "_")
if(spec[[varname]]$type == "IORE") {
- k_compound_sink <- paste("k.iore", box_1, "sink", sep = "_")
+ k_compound_sink <- paste("k__iore", box_1, "sink", sep = "_")
}
parms <- c(parms, k_compound_sink)
decline_term <- paste(k_compound_sink, "*", box_1)
@@ -114,7 +119,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) } else {
k_compound <- paste("k", box_1, sep = "_")
if(spec[[varname]]$type == "IORE") {
- k_compound <- paste("k.iore", box_1, sep = "_")
+ k_compound <- paste("k__iore", box_1, sep = "_")
}
parms <- c(parms, k_compound)
decline_term <- paste(k_compound, "*", box_1)
@@ -127,17 +132,18 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) } #}}}
if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term
# From p. 53 of the FOCUS kinetics report, without the power function so it works in C
- decline_term <- paste("(alpha/beta) * 1/((time/beta) + 1) *", box_1)
+ decline_term <- paste("(alpha/beta) * 1/(( time /beta) + 1) *", box_1)
parms <- c(parms, "alpha", "beta")
} #}}}
if(spec[[varname]]$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)
+ 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")
} #}}}
+ HS_decline <- "ifelse(time <= tb, k1, k2)" # Used below for automatic translation to C++
if(spec[[varname]]$type == "HS") { # {{{ Add HS decline term
# From p. 55 of the FOCUS kinetics report
- decline_term <- paste("ifelse(time <= tb, k1, k2)", "*", box_1)
+ decline_term <- paste(HS_decline, "*", box_1)
parms <- c(parms, "k1", "k2", "tb")
} #}}}
# Add origin decline term to box 1 (usually the only box, unless type is SFORB)#{{{
@@ -272,35 +278,58 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) model$coefmat <- m
}#}}}
- # Create a function compiled from C code if more than one observed variable and ccSolve is available #{{{
- if (length(obs_vars) > 1 & requireNamespace("ccSolve", quietly = TRUE)) {
- diffs.C <- paste(diffs, collapse = ";\n")
- diffs.C <- paste0(diffs.C, ";")
- for (i in seq_along(diffs)) {
- obs_var <- names(diffs)[i]
+ # Try to create a function compiled from C code if more than one observed variable and g++ can be called #{{{
+ if (length(obs_vars) > 1) {
+ try(gcc_version <- system("g++ -v 2>&1", intern = TRUE))
+ if (!inherits(gcc_version, "try-error") & odeintr_compile != "no") {
- # Replace d_... terms by f[i-1]
- # First line
- pattern <- paste0("^d_", obs_var)
- replacement <- paste0("\nf[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
- # Other lines
- pattern <- paste0("\\nd_", obs_var)
- replacement <- paste0("\nf[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
+ if ((odeintr_compile == "auto" & mat == FALSE) | odeintr_compile == "yes") {
+ # HS
+ diffs <- gsub(HS_decline, "(t <= tb ? k1 : k2)", diffs, fixed = TRUE)
- # Replace names of observed variables by y[i],
- # making the implicit assumption that the observed variables only occur after "* "
- pattern <- paste0("\\* ", obs_var)
- replacement <- paste0("* y[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
- }
- if (sum(sapply(spec, function(x) x$type %in%
- c("SFO", "FOMC", "DFOP", "SFORB"))) == length(spec)) {
- if (!quiet) message("Compiling differential equation model from auto-generated C code...")
- model$compiled <- ccSolve::compile.ode(diffs.C, language = "C",
- parms = parms,
- declaration = "double time = *t;")
+ diffs.C <- paste(diffs, collapse = ";\n")
+ diffs.C <- paste0(diffs.C, ";")
+
+ for (i in seq_along(diffs)) {
+ state_var <- names(diffs)[i]
+
+ # IORE
+ if (state_var %in% obs_vars) {
+ if (spec[[state_var]]$type == "IORE") {
+ diffs.C <- gsub(paste0(state_var, "^N_", state_var),
+ paste0("pow(x[", i - 1, "], N_", state_var, ")"),
+ diffs.C, fixed = TRUE)
+ }
+ }
+
+ # Replace d_... terms by dxdt[i-1]
+ # First line
+ pattern <- paste0("^d_", state_var)
+ replacement <- paste0("\ndxdt[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+ # Other lines
+ pattern <- paste0("\\nd_", state_var)
+ replacement <- paste0("\ndxdt[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+
+ # Replace names of observed variables by x[i],
+ # making the implicit assumption that the observed variables only occur after "* "
+ pattern <- paste0("\\* ", state_var)
+ replacement <- paste0("* x[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+
+ # Handle time, which needs to be enclosed by spaces (except for HS which is handled separately)
+ diffs.C <- gsub(" time ", " t ", diffs.C)
+ }
+ if (!quiet) message("Compiling differential equation model from auto-generated C++ code...")
+ model$e <- new.env()
+ model$e$code <- try(compile_sys("m", diffs.C, pars = parms, method = odeintr_method,
+ atol = odeintr_atol, rtol = odeintr_rtol, env = model$e))
+
+ if (inherits(model$e$code, "try-error")) {
+ if (!quiet) message("Compilation failed, model solution will be slower than necessary")
+ }
+ }
}
}
# }}}
diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 3121f1d7..d91e87df 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -18,11 +18,12 @@ # this program. If not, see <http://www.gnu.org/licenses/> mkinpredict <- function(mkinmod, odeparms, odeini, - outtimes, solution_type = "deSolve", - use_compiled = "auto", - method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, + outtimes, solution_type = c("deSolve", "analytical", "eigen", "odeintr"), + method.ode = "lsoda", atol.deSolve = 1e-8, rtol.deSolve = 1e-10, map_output = TRUE, ...) { + solution_type = match.arg(solution_type) + # Get the names of the state variables in the model mod_vars <- names(mkinmod$diffs) @@ -54,8 +55,8 @@ mkinpredict <- function(mkinmod, odeparms, odeini, IORE = IORE.solution(outtimes, evalparse(parent.name), ifelse(mkinmod$use_of_ff == "min", - evalparse(paste("k.iore", parent.name, "sink", sep="_")), - evalparse(paste("k.iore", parent.name, sep="_"))), + evalparse(paste("k__iore", parent.name, "sink", sep="_")), + evalparse(paste("k__iore", parent.name, sep="_"))), evalparse("N_parent")), DFOP = DFOP.solution(outtimes, evalparse(parent.name), @@ -88,30 +89,26 @@ mkinpredict <- function(mkinmod, odeparms, odeini, names(out) <- c("time", mod_vars) } if (solution_type == "deSolve") { - if (!is.null(mkinmod$compiled) & use_compiled[1] != FALSE) { - mkindiff <- mkinmod$compiled - } else { - mkindiff <- function(t, state, parms) { + mkindiff <- function(t, state, parms) { - time <- t - diffs <- vector() - for (box in names(mkinmod$diffs)) - { - diffname <- paste("d", box, sep="_") - diffs[diffname] <- with(as.list(c(time, state, parms)), - eval(parse(text=mkinmod$diffs[[box]]))) - } - return(list(c(diffs))) + time <- t + diffs <- vector() + for (box in names(mkinmod$diffs)) + { + diffname <- paste("d", box, sep="_") + diffs[diffname] <- with(as.list(c(time, state, parms)), + eval(parse(text=mkinmod$diffs[[box]]))) } - } + return(list(c(diffs))) + } out <- ode( y = odeini, times = outtimes, func = mkindiff, parms = odeparms[mkinmod$parms], # Order matters when using compiled models method = method.ode, - atol = atol, - rtol = rtol, + atol = atol.deSolve, + rtol = rtol.deSolve, ... ) if (sum(is.na(out)) > 0) { @@ -119,6 +116,17 @@ mkinpredict <- function(mkinmod, odeparms, odeini, "NaN values occurred in output from ode()") } } + if (solution_type == "odeintr") { + if (is.null(mkinmod$e$m)) stop("Method odeintr can not be used as no compiled version of the model is available") + odeparms_argstring = "" + for (parname in names(odeparms)) { + odeparms_argstring = paste0(odeparms_argstring, parname, " = ", odeparms[parname], ", ") + } + odeparms_argstring = gsub(", $", "", odeparms_argstring) + with(as.list(odeparms_argstring), eval(parse(text=paste0("mkinmod$e$m_set_params(", odeparms_argstring, ")")))) + out <- mkinmod$e$m_at(init = odeini, times = outtimes) + names(out) <- c("time", names(mkinmod$diffs)) + } if (map_output) { # Output transformation for models with unobserved compartments like SFORB out_mapped <- data.frame(time = out[,"time"]) diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 31746fb8..1523be7d 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -55,7 +55,7 @@ plot.mkinfit <- function(x, fit = x, odeparms <- parms.all[odenames] out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, - solution_type = solution_type, atol = fit$atol, rtol = fit$rtol) + solution_type = solution_type, atol.deSolve = fit$atol, rtol.deSolve = fit$rtol) # Set up the plot if not to be added to an existing plot if (add == FALSE) { diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R index aa70a0b3..0946ff14 100644 --- a/R/transform_odeparms.R +++ b/R/transform_odeparms.R @@ -33,8 +33,8 @@ transform_odeparms <- function(parms, mkinmod, # Log transformation for rate constants if requested
k <- parms[grep("^k_", names(parms))]
- k.iore <- parms[grep("^k.iore_", names(parms))]
- k <- c(k, k.iore)
+ k__iore <- parms[grep("^k__iore_", names(parms))]
+ k <- c(k, k__iore)
if (length(k) > 0) {
if(transform_rates) {
transparms[paste0("log_", names(k))] <- log(k)
@@ -113,8 +113,8 @@ backtransform_odeparms <- function(transparms, mkinmod, # Exponential transformation for rate constants
if(transform_rates) {
trans_k <- transparms[grep("^log_k_", names(transparms))]
- trans_k.iore <- transparms[grep("^log_k.iore_", names(transparms))]
- trans_k = c(trans_k, trans_k.iore)
+ trans_k__iore <- transparms[grep("^log_k__iore_", names(transparms))]
+ trans_k = c(trans_k, trans_k__iore)
if (length(trans_k) > 0) {
k_names <- gsub("^log_k", "k", names(trans_k))
parms[k_names] <- exp(trans_k)
@@ -122,8 +122,8 @@ backtransform_odeparms <- function(transparms, mkinmod, } else {
trans_k <- transparms[grep("^k_", names(transparms))]
parms[names(trans_k)] <- trans_k
- trans_k.iore <- transparms[grep("^k.iore_", names(transparms))]
- parms[names(trans_k.iore)] <- trans_k.iore
+ trans_k__iore <- transparms[grep("^k__iore_", names(transparms))]
+ parms[names(trans_k__iore)] <- trans_k__iore
}
# Do not transform exponents in IORE models
|