diff options
| -rw-r--r-- | R/saemix.R | 146 | ||||
| -rw-r--r-- | R/summary.saem.mmkin.R | 2 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 27839 -> 1011 bytes | |||
| -rw-r--r-- | docs/dev/reference/saem.html | 80 | ||||
| -rw-r--r-- | man/saem.Rd | 23 |
6 files changed, 183 insertions, 70 deletions
@@ -40,7 +40,7 @@ #' f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) #' f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) #' -#' # The returned saem.mmkin object contains an SaemixObject, we can use +#' # The returned saem.mmkin object contains an SaemixObject, therefore we can use #' # functions from saemix #' library(saemix) #' compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) @@ -49,17 +49,26 @@ #' f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ]) #' compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) #' +#' sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), +#' A1 = mkinsub("SFO")) +#' fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), +#' A1 = mkinsub("SFO")) #' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), #' A1 = mkinsub("SFO")) -#' f_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "analytical") -#' # This takes about 4 minutes on my system -#' f_saem <- saem(f_mmkin) +#' # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, +#' # and compiled ODEs for FOMC, both are fast +#' f_mmkin <- mmkin(list( +#' "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), +#' ds, quiet = TRUE) +#' # These take about five seconds each on this system, as we use +#' # analytical solutions written for saemix. When using the analytical +#' # solutions written for mkin this took around four minutes +#' f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ]) +#' f_saem_dfop_sfo <- saem(f_mmkin["SFO-SFO", ]) #' -#' f_mmkin_des <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "deSolve") #' # Using a single core, the following takes about 6 minutes, using 10 cores #' # it is slower instead of faster -#' f_saem_des <- saem(f_mmkin_des, cores = 1) -#' compare.saemix(list(f_saem$so, f_saem_des$so)) +#' f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) #' } #' @export saem <- function(object, control, ...) UseMethod("saem") @@ -83,7 +92,12 @@ saem.mmkin <- function(object, } fit_time <- system.time({ f_saemix <- saemix::saemix(m_saemix, d_saemix, control) - f_saemix <- try(saemix::saemix.predict(f_saemix), silent = TRUE) + f_pred <- try(saemix::saemix.predict(f_saemix), silent = TRUE) + if (!inherits(f_pred, "try-error")) { + f_saemix <- f_pred + } else { + warning("Creating predictions from the saemix model failed") + } }) if (suppressPlot) { grDevices::dev.off() @@ -145,37 +159,43 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { model_function <- FALSE - if (length(mkin_model$spec) == 1 & mkin_model$use_of_ff == "max") { - parent_type <- mkin_model$spec[[1]]$type - if (length(odeini_fixed) == 1) { - if (parent_type == "SFO") { - stop("saemix needs at least two parameters to work on.") - } - if (parent_type == "FOMC") { - model_function <- function(psi, id, xidep) { - odeini_fixed / (xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, 1]) + # Model functions with analytical solutions + # Fixed parameters, use_of_ff = "min" and turning off sinks currently not supported here + # In general, we need to consider exactly how the parameters in mkinfit were specified, + # as the parameters are currently mapped by position in these solutions + sinks <- sapply(mkin_model$spec, function(x) x$sink) + if (length(odeparms_fixed) == 0 & mkin_model$use_of_ff == "max" & all(sinks)) { + # Parent only + if (length(mkin_model$spec) == 1) { + parent_type <- mkin_model$spec[[1]]$type + if (length(odeini_fixed) == 1) { + if (parent_type == "SFO") { + stop("saemix needs at least two parameters to work on.") } - } - if (parent_type == "DFOP") { - model_function <- function(psi, id, xidep) { - g <- plogis(psi[id, 3]) - t = xidep[, "time"] - odeini_fixed * (g * exp(- exp(psi[id, 1]) * t) + - (1 - g) * exp(- exp(psi[id, 2]) * t)) + if (parent_type == "FOMC") { + model_function <- function(psi, id, xidep) { + odeini_fixed / (xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, 1]) + } } - } - if (parent_type == "HS") { - model_function <- function(psi, id, xidep) { - tb <- exp(psi[id, 3]) - t = xidep[, "time"] - k1 = exp(psi[id, 1]) - odeini_fixed * ifelse(t <= tb, - exp(- k1 * t), - exp(- k1 * t) * exp(- exp(psi[id, 2]) * (t - tb))) + if (parent_type == "DFOP") { + model_function <- function(psi, id, xidep) { + g <- plogis(psi[id, 3]) + t <- xidep[, "time"] + odeini_fixed * (g * exp(- exp(psi[id, 1]) * t) + + (1 - g) * exp(- exp(psi[id, 2]) * t)) + } } - } - } else { - if (length(odeparms_fixed) == 0) { + if (parent_type == "HS") { + model_function <- function(psi, id, xidep) { + tb <- exp(psi[id, 3]) + t <- xidep[, "time"] + k1 = exp(psi[id, 1]) + odeini_fixed * ifelse(t <= tb, + exp(- k1 * t), + exp(- k1 * t) * exp(- exp(psi[id, 2]) * (t - tb))) + } + } + } else { if (parent_type == "SFO") { model_function <- function(psi, id, xidep) { psi[id, 1] * exp( - exp(psi[id, 2]) * xidep[, "time"]) @@ -189,7 +209,7 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { if (parent_type == "DFOP") { model_function <- function(psi, id, xidep) { g <- plogis(psi[id, 4]) - t = xidep[, "time"] + t <- xidep[, "time"] psi[id, 1] * (g * exp(- exp(psi[id, 2]) * t) + (1 - g) * exp(- exp(psi[id, 3]) * t)) } @@ -197,7 +217,7 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { if (parent_type == "HS") { model_function <- function(psi, id, xidep) { tb <- exp(psi[id, 4]) - t = xidep[, "time"] + t <- xidep[, "time"] k1 = exp(psi[id, 2]) psi[id, 1] * ifelse(t <= tb, exp(- k1 * t), @@ -206,9 +226,57 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { } } } + + # Parent with one metabolite + # Parameter names used in the model functions are as in + # https://nbviewer.jupyter.org/urls/jrwb.de/nb/Symbolic%20ODE%20solutions%20for%20mkin.ipynb + if (length(mkin_model$spec) == 2) { + types <- unname(sapply(mkin_model$spec, function(x) x$type)) + # Initial value for the metabolite (n20) must be fixed + if (names(odeini_fixed) == names(mkin_model$spec)[2]) { + n20 <- odeini_fixed + parent_name <- names(mkin_model$spec)[1] + if (identical(types, c("SFO", "SFO"))) { + model_function <- function(psi, id, xidep) { + t <- xidep[, "time"] + n10 <- psi[id, 1] + k1 <- exp(psi[id, 2]) + k2 <- exp(psi[id, 3]) + f12 <- plogis(psi[id, 4]) + ifelse(xidep[, "name"] == parent_name, + n10 * exp(- k1 * t), + (((k2 - k1) * n20 - f12 * k1 * n10) * exp(- k2 * t)) / (k2 - k1) + + (f12 * k1 * n10 * exp(- k1 * t)) / (k2 - k1) + ) + } + } + if (identical(types, c("DFOP", "SFO"))) { + model_function <- function(psi, id, xidep) { + t <- xidep[, "time"] + n10 <- psi[id, 1] + k2 <- exp(psi[id, 2]) + f12 <- plogis(psi[id, 3]) + l1 <- exp(psi[id, 4]) + l2 <- exp(psi[id, 5]) + g <- plogis(psi[id, 6]) + ifelse(xidep[, "name"] == parent_name, + n10 * (g * exp(- l1 * t) + (1 - g) * exp(- l2 * t)), + ((f12 * g - f12) * l2 * n10 * exp(- l2 * t)) / (l2 - k2) - + (f12 * g * l1 * n10 * exp(- l1 * t)) / (l1 - k2) + + ((((l1 - k2) * l2 - k2 * l1 + k2^2) * n20 + + ((f12 * l1 + (f12 * g - f12) * k2) * l2 - + f12 * g * k2 * l1) * n10) * exp( - k2 * t)) / + ((l1 - k2) * l2 - k2 * l1 + k2^2) + ) + } + } + } + } } - if (!is.function(model_function)) { + if (is.function(model_function)) { + solution_type = "analytical saemix" + } else { model_function <- function(psi, id, xidep) { uid <- unique(id) diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R index f7110dd0..4c9776a6 100644 --- a/R/summary.saem.mmkin.R +++ b/R/summary.saem.mmkin.R @@ -96,7 +96,7 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = colnames(confint_ranef)[1] <- "est." # Error model - enames <- object$so@results@name.sigma + enames <- if (object$err_mod == "const") "a.1" else c("a.1", "b.1") confint_errmod <- as.matrix(conf.int[enames, c("estimate", "lower", "upper")]) colnames(confint_errmod)[1] <- "est." diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index d9720761..8d117fb1 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-11-08T02:20Z +last_built: 2020-11-09T06:03Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex cfc5bc2b..17a35806 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 06fcfaa7..25608fc8 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -229,28 +229,28 @@ using <a href='mmkin.html'>mmkin</a>.</p> state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sun Nov 8 02:44:42 2020" +#> [1] "Mon Nov 9 07:04:09 2020" #> .... #> Minimisation finished -#> [1] "Sun Nov 8 02:44:43 2020"</div><div class='input'> +#> [1] "Mon Nov 9 07:04:11 2020"</div><div class='input'> <span class='va'>f_mmkin_parent</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sun Nov 8 02:44:45 2020" +#> [1] "Mon Nov 9 07:04:12 2020" #> .... #> Minimisation finished -#> [1] "Sun Nov 8 02:44:46 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 07:04:13 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sun Nov 8 02:44:47 2020" +#> [1] "Mon Nov 9 07:04:14 2020" #> .... #> Minimisation finished -#> [1] "Sun Nov 8 02:44:49 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 07:04:16 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sun Nov 8 02:44:49 2020" +#> [1] "Mon Nov 9 07:04:16 2020" #> .... #> Minimisation finished -#> [1] "Sun Nov 8 02:44:52 2020"</div><div class='input'> -<span class='co'># The returned saem.mmkin object contains an SaemixObject, we can use</span> +#> [1] "Mon Nov 9 07:04:19 2020"</div><div class='input'> +<span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span> <span class='co'># functions from saemix</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Package saemix, version 3.1.9000</span> @@ -262,33 +262,69 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sun Nov 8 02:44:54 2020" +#> [1] "Mon Nov 9 07:04:21 2020" #> .... #> Minimisation finished -#> [1] "Sun Nov 8 02:44:59 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Mon Nov 9 07:04:26 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC #> 1 467.7644 465.0305 #> 2 469.4862 466.3617</div><div class='input'> -<span class='va'>dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, +<span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>f_mmkin</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span> -<span class='co'># This takes about 4 minutes on my system</span> -<span class='va'>f_saem</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>fomc_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, + A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, + A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span> +<span class='co'># and compiled ODEs for FOMC, both are fast</span> +<span class='va'>f_mmkin</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span> + <span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>sfo_sfo</span>, <span class='st'>"FOMC-SFO"</span> <span class='op'>=</span> <span class='va'>fomc_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, + <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='co'># These take about five seconds each on this system, as we use</span> +<span class='co'># analytical solutions written for saemix. When using the analytical</span> +<span class='co'># solutions written for mkin this took around four minutes</span> +<span class='va'>f_saem_sfo_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Mon Nov 9 07:04:28 2020" +#> .... +#> Minimisation finished +#> [1] "Mon Nov 9 07:04:33 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sun Nov 8 02:45:00 2020" +#> [1] "Mon Nov 9 07:04:33 2020" #> .... #> Minimisation finished -#> [1] "Sun Nov 8 02:49:01 2020"</div><div class='output co'>#> <span class='error'>Error in exp(trans_k): non-numeric argument to mathematical function</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 317.7 169.9 258.9</span></div><div class='input'> -<span class='va'>f_mmkin_des</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span> +#> [1] "Mon Nov 9 07:04:39 2020"</div><div class='input'> <span class='co'># Using a single core, the following takes about 6 minutes, using 10 cores</span> <span class='co'># it is slower instead of faster</span> -<span class='va'>f_saem_des</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_des</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +<span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sun Nov 8 02:49:20 2020" +#> [1] "Mon Nov 9 07:04:39 2020" +#> DLSODA- At current T (=R1), MXSTEP (=I1) steps +#> taken on this call before reaching TOUT +#> In above message, I1 = 5000 +#> +#> In above message, R1 = 0.00156238 +#> +#> DLSODA- At T (=R1) and step size H (=R2), the +#> corrector convergence failed repeatedly +#> or with ABS(H) = HMIN +#> In above message, R1 = 0, R2 = 1.1373e-10 +#> +#> DLSODA- At current T (=R1), MXSTEP (=I1) steps +#> taken on this call before reaching TOUT +#> In above message, I1 = 5000 +#> +#> In above message, R1 = 2.24752e-06 +#> +#> DLSODA- At current T (=R1), MXSTEP (=I1) steps +#> taken on this call before reaching TOUT +#> In above message, I1 = 5000 +#> +#> In above message, R1 = 0.000585935 +#> #> .... #> Minimisation finished -#> [1] "Sun Nov 8 02:57:30 2020"</div><div class='output co'>#> <span class='error'>Error in exp(trans_k): non-numeric argument to mathematical function</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 591.7 205.6 521.4</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_des</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in compare.saemix(list(f_saem$so, f_saem_des$so)): object 'f_saem' not found</span></div><div class='input'><span class='co'># }</span> +#> [1] "Mon Nov 9 07:11:24 2020"</div><div class='output co'>#> <span class='warning'>Warning: Creating predictions from the saemix model failed</span></div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> diff --git a/man/saem.Rd b/man/saem.Rd index 96b8b55a..b2daf419 100644 --- a/man/saem.Rd +++ b/man/saem.Rd @@ -77,7 +77,7 @@ f_saem_sfo <- saem(f_mmkin_parent["SFO", ]) f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) -# The returned saem.mmkin object contains an SaemixObject, we can use +# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) @@ -86,17 +86,26 @@ f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ]) compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), + A1 = mkinsub("SFO")) +fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), + A1 = mkinsub("SFO")) dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), A1 = mkinsub("SFO")) -f_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "analytical") -# This takes about 4 minutes on my system -f_saem <- saem(f_mmkin) +# The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, +# and compiled ODEs for FOMC, both are fast +f_mmkin <- mmkin(list( + "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), + ds, quiet = TRUE) +# These take about five seconds each on this system, as we use +# analytical solutions written for saemix. When using the analytical +# solutions written for mkin this took around four minutes +f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ]) +f_saem_dfop_sfo <- saem(f_mmkin["SFO-SFO", ]) -f_mmkin_des <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "deSolve") # Using a single core, the following takes about 6 minutes, using 10 cores # it is slower instead of faster -f_saem_des <- saem(f_mmkin_des, cores = 1) -compare.saemix(list(f_saem$so, f_saem_des$so)) +f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) } } \seealso{ |
