diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 09:18:58 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 09:18:58 +0100 |
| commit | a3e058f8bceca903e7952e66abb4744f66115921 (patch) | |
| tree | f029eded457914459ecc111511e468905d56172d | |
| parent | e2cb0d4668f17f57c65f3ff94a7e17c784eaf4ba (diff) | |
Some work on example code, pkgdown update
| -rw-r--r-- | R/saemix.R | 9 | ||||
| -rw-r--r-- | R/summary.saem.mmkin.R | 39 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/Rplot003.png | bin | 15451 -> 52903 bytes | |||
| -rw-r--r-- | docs/dev/reference/Rplot004.png | bin | 13203 -> 49175 bytes | |||
| -rw-r--r-- | docs/dev/reference/saem-1.png | bin | 0 -> 48512 bytes | |||
| -rw-r--r-- | docs/dev/reference/saem-2.png | bin | 0 -> 48630 bytes | |||
| -rw-r--r-- | docs/dev/reference/saem-3.png | bin | 0 -> 82018 bytes | |||
| -rw-r--r-- | docs/dev/reference/saem-4.png | bin | 0 -> 128571 bytes | |||
| -rw-r--r-- | docs/dev/reference/saem.html | 180 | ||||
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin-1.png | bin | 0 -> 7742 bytes | |||
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin.html | 385 | ||||
| -rw-r--r-- | man/saem.Rd | 9 | ||||
| -rw-r--r-- | man/summary.saem.mmkin.Rd | 39 |
14 files changed, 451 insertions, 212 deletions
@@ -44,6 +44,10 @@ #' # functions from saemix #' library(saemix) #' compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) +#' plot(f_saem_fomc$so, plot.type = "convergence") +#' plot(f_saem_fomc$so, plot.type = "individual.fit") +#' plot(f_saem_fomc$so, plot.type = "npde") +#' plot(f_saem_fomc$so, plot.type = "vpc") #' #' f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") #' f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ]) @@ -64,11 +68,12 @@ #' # 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_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#' summary(f_saem_dfop_sfo, data = FALSE) #' #' # Using a single core, the following takes about 6 minutes, using 10 cores #' # it is slower instead of faster -#' f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) +#' #f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) #' } #' @export saem <- function(object, control, ...) UseMethod("saem") diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R index 4c9776a6..a8917144 100644 --- a/R/summary.saem.mmkin.R +++ b/R/summary.saem.mmkin.R @@ -34,25 +34,34 @@ #' @author Johannes Ranke for the mkin specific parts #' saemix authors for the parts inherited from saemix. #' @examples -#' # Generate five datasets following SFO kinetics +#' # Generate five datasets following DFOP-SFO kinetics #' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) -#' dt50_sfo_in_pop <- 50 -#' k_in_pop <- log(2) / dt50_sfo_in_pop +#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"), +#' m1 = mkinsub("SFO"), quiet = TRUE) #' set.seed(1234) -#' k_in <- rlnorm(5, log(k_in_pop), 0.5) -#' SFO <- mkinmod(parent = mkinsub("SFO")) +#' k1_in <- rlnorm(5, log(0.1), 0.3) +#' k2_in <- rlnorm(5, log(0.02), 0.3) +#' g_in <- plogis(rnorm(5, qlogis(0.5), 0.3)) +#' f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3)) +#' k_m1_in <- rlnorm(5, log(0.02), 0.3) #' -#' pred_sfo <- function(k) { -#' mkinpredict(SFO, -#' c(k_parent = k), -#' c(parent = 100), +#' pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) { +#' mkinpredict(dfop_sfo, +#' c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1), +#' c(parent = 100, m1 = 0), #' sampling_times) #' } #' -#' ds_sfo_mean <- lapply(k_in, pred_sfo) -#' names(ds_sfo_mean) <- paste("ds", 1:5) +#' ds_mean_dfop_sfo <- lapply(1:5, function(i) { +#' mkinpredict(dfop_sfo, +#' c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i], +#' f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]), +#' c(parent = 100, m1 = 0), +#' sampling_times) +#' }) +#' names(ds_mean_dfop_sfo) <- paste("ds", 1:5) #' -#' ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) { +#' ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) { #' add_err(ds, #' sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), #' n = 1)[[1]] @@ -60,9 +69,9 @@ #' #' \dontrun{ #' # Evaluate using mmkin and saem -#' f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1) -#' f_saem <- saem(f_mmkin) -#' summary(f_saem, data = TRUE) +#' f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = "tc", cores = 5) +#' f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo) +#' summary(f_saem_dfop_sfo, data = TRUE) #' } #' #' @export diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 8d117fb1..0b40dd02 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: 2020-11-09T06:03Z +last_built: 2020-11-09T08:10Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png Binary files differindex dd7e24f3..7514f1a4 100644 --- a/docs/dev/reference/Rplot003.png +++ b/docs/dev/reference/Rplot003.png diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png Binary files differindex 2057f883..2a90c6ee 100644 --- a/docs/dev/reference/Rplot004.png +++ b/docs/dev/reference/Rplot004.png diff --git a/docs/dev/reference/saem-1.png b/docs/dev/reference/saem-1.png Binary files differnew file mode 100644 index 00000000..9c3421bd --- /dev/null +++ b/docs/dev/reference/saem-1.png diff --git a/docs/dev/reference/saem-2.png b/docs/dev/reference/saem-2.png Binary files differnew file mode 100644 index 00000000..bc975b79 --- /dev/null +++ b/docs/dev/reference/saem-2.png diff --git a/docs/dev/reference/saem-3.png b/docs/dev/reference/saem-3.png Binary files differnew file mode 100644 index 00000000..5744b722 --- /dev/null +++ b/docs/dev/reference/saem-3.png diff --git a/docs/dev/reference/saem-4.png b/docs/dev/reference/saem-4.png Binary files differnew file mode 100644 index 00000000..b020dbbc --- /dev/null +++ b/docs/dev/reference/saem-4.png diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 25608fc8..26f4c3e3 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -229,27 +229,27 @@ 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] "Mon Nov 9 07:04:09 2020" +#> [1] "Mon Nov 9 09:03:11 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:11 2020"</div><div class='input'> +#> [1] "Mon Nov 9 09:03:13 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] "Mon Nov 9 07:04:12 2020" +#> [1] "Mon Nov 9 09:03:14 2020" #> .... #> Minimisation finished -#> [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> +#> [1] "Mon Nov 9 09:03:16 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] "Mon Nov 9 07:04:14 2020" +#> [1] "Mon Nov 9 09:03:16 2020" #> .... #> Minimisation finished -#> [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> +#> [1] "Mon Nov 9 09:03:18 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] "Mon Nov 9 07:04:16 2020" +#> [1] "Mon Nov 9 09:03:19 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:19 2020"</div><div class='input'> +#> [1] "Mon Nov 9 09:03:22 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> @@ -258,14 +258,47 @@ using <a href='mmkin.html'>mmkin</a>.</p> </div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC #> 1 624.2428 622.2900 #> 2 467.7644 465.0305 -#> 3 491.3541 487.8391</div><div class='input'> +#> 3 491.3541 487.8391</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> +</div><div class='output co'>#> Plotting convergence plots</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span> +</div><div class='img'><img src='saem-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Plotting individual fits</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span> +</div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#> Simulating data using nsim = 1000 simulated datasets +#> Computing WRES and npde . +#> Plotting npde</div><div class='img'><img src='saem-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> --------------------------------------------- +#> Distribution of npde: +#> mean= -0.01736 (SE= 0.098 ) +#> variance= 0.8562 (SE= 0.13 ) +#> skewness= 0.513 +#> kurtosis= 1.202 +#> --------------------------------------------- +#> +#> Statistical tests +#> Wilcoxon signed rank test : 0.652 +#> Fisher variance test : 0.338 +#> SW test of normality : 0.0757 . +#> Global adjusted p-value : 0.227 +#> --- +#> Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 +#> ---------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"vpc"</span><span class='op'>)</span> +</div><div class='output co'>#> Performing simulations under the model. +#> Plotting VPC +#> Method used for VPC: binning by quantiles on X , dividing into the following intervals +#> Interval Centered.On +#> 1 (-1,3] 1.3 +#> 2 (3,8] 7.4 +#> 3 (8,14] 13.2 +#> 4 (14,21] 20.5 +#> 5 (21,37.7] 29.5 +#> 6 (37.7,60] 50.4 +#> 7 (60,90] 76.6 +#> 8 (90,120] 109.0 +#> 9 (120,180] 156.0 </div><div class='img'><img src='saem-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:21 2020" +#> [1] "Mon Nov 9 09:03:24 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:26 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Mon Nov 9 09:03:29 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</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'> @@ -285,46 +318,105 @@ using <a href='mmkin.html'>mmkin</a>.</p> <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" +#> [1] "Mon Nov 9 09:03:31 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> +#> [1] "Mon Nov 9 09:03:36 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'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:33 2020" +#> [1] "Mon Nov 9 09:03:37 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:39 2020"</div><div class='input'> +#> [1] "Mon Nov 9 09:03:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +</div><div class='output co'>#> saemix version used for fitting: 3.1.9000 +#> mkin version used for pre-fitting: 0.9.50.4 +#> R version used for fitting: 4.0.3 +#> Date of fit: Mon Nov 9 09:03:47 2020 +#> Date of summary: Mon Nov 9 09:03:47 2020 +#> +#> Equations: +#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * +#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) +#> * parent +#> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) +#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * +#> exp(-k2 * time))) * parent - k_A1 * A1 +#> +#> Data: +#> 170 observations of 2 variable(s) grouped in 5 datasets +#> +#> Model predictions using solution type analytical +#> +#> Fitted in 9.758 s using 300, 100 iterations +#> +#> Variance model: Constant variance +#> +#> Mean of starting values for individual parameters: +#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 +#> 93.8101519 -9.7647455 -0.9711148 -1.8799371 -4.2708142 +#> g_qlogis +#> 0.1356441 +#> +#> Fixed degradation parameter values: +#> None +#> +#> Results: +#> +#> Likelihood computed by importance sampling +#> AIC BIC logLik +#> 841.3208 836.2435 -407.6604 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> est. lower upper +#> parent_0 93.7514328489 91.113651 96.3892150 +#> log_k_A1 -6.1262333211 -8.432492 -3.8199749 +#> f_parent_qlogis -0.9739851652 -1.371984 -0.5759863 +#> log_k1 -2.4818388836 -3.746899 -1.2167788 +#> log_k2 -3.6138616567 -5.294149 -1.9335743 +#> g_qlogis -0.0004613666 -1.063179 1.0622564 +#> +#> Correlation: +#> prnt_0 lg__A1 f_prn_ log_k1 log_k2 +#> log_k_A1 -0.013 +#> f_parent_qlogis -0.025 0.050 +#> log_k1 0.030 0.000 -0.005 +#> log_k2 0.013 0.005 -0.003 0.037 +#> g_qlogis -0.068 -0.016 0.011 -0.181 -0.181 +#> +#> Random effects: +#> est. lower upper +#> SD.parent_0 2.7857084 0.7825105 4.7889063 +#> SD.log_k_A1 2.1412505 0.4425207 3.8399803 +#> SD.f_parent_qlogis 0.4463087 0.1609059 0.7317116 +#> SD.log_k1 1.4097204 0.5240566 2.2953842 +#> SD.log_k2 1.8739067 0.6979362 3.0498773 +#> SD.g_qlogis 0.4559301 -0.8149852 1.7268453 +#> +#> Variance model: +#> est. lower upper +#> a.1 1.882757 1.665681 2.099832 +#> +#> Backtransformed parameters with asymmetric confidence intervals: +#> est. lower upper +#> parent_0 93.751432849 9.111365e+01 96.38921497 +#> k_A1 0.002184795 2.176784e-04 0.02192835 +#> f_parent_to_A1 0.274086887 2.022995e-01 0.35985666 +#> k1 0.083589373 2.359079e-02 0.29618269 +#> k2 0.026947583 5.020885e-03 0.14463032 +#> g 0.499884658 2.567024e-01 0.74312150 +#> +#> Resulting formation fractions: +#> ff +#> parent_A1 0.2741 +#> parent_sink 0.7259 +#> +#> Estimated disappearance times: +#> DT50 DT90 DT50back DT50_k1 DT50_k2 +#> parent 13.91 60.89 18.33 8.292 25.72 +#> A1 317.26 1053.91 NA NA NA</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_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] "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] "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> +<span class='co'>#f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)</span> +<span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> diff --git a/docs/dev/reference/summary.saem.mmkin-1.png b/docs/dev/reference/summary.saem.mmkin-1.png Binary files differnew file mode 100644 index 00000000..e3538cb6 --- /dev/null +++ b/docs/dev/reference/summary.saem.mmkin-1.png diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 01e8eb12..75ede09f 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -156,7 +156,7 @@ endpoints such as formation fractions and DT50 values. Optionally </div> <pre class="usage"><span class='co'># S3 method for saem.mmkin</span> -<span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span> <span class='co'># S3 method for summary.saem.mmkin</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</span>, <span class='va'>...</span><span class='op'>)</span></pre> @@ -220,25 +220,34 @@ The print method is called for its side effect, i.e. printing the summary. saemix authors for the parts inherited from saemix.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Generate five datasets following SFO kinetics</span> + <pre class="examples"><div class='input'><span class='co'># Generate five datasets following DFOP-SFO kinetics</span> <span class='va'>sampling_times</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='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> -<span class='va'>dt50_sfo_in_pop</span> <span class='op'><-</span> <span class='fl'>50</span> -<span class='va'>k_in_pop</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in_pop</span> +<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'>"m1"</span><span class='op'>)</span>, + m1 <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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</span><span class='op'>)</span> -<span class='va'>k_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='va'>k_in_pop</span><span class='op'>)</span>, <span class='fl'>0.5</span><span class='op'>)</span> -<span class='va'>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='op'>)</span><span class='op'>)</span> - -<span class='va'>pred_sfo</span> <span class='op'><-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><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>, +<span class='va'>k1_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.1</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span> +<span class='va'>k2_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.02</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span> +<span class='va'>g_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>qlogis</a></span><span class='op'>(</span><span class='fl'>0.5</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>f_parent_to_m1_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>qlogis</a></span><span class='op'>(</span><span class='fl'>0.3</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>k_m1_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.02</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span> + +<span class='va'>pred_dfop_sfo</span> <span class='op'><-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>g</span>, <span class='va'>f_parent_to_m1</span>, <span class='va'>k_m1</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='va'>k1</span>, k2 <span class='op'>=</span> <span class='va'>k2</span>, g <span class='op'>=</span> <span class='va'>g</span>, f_parent_to_m1 <span class='op'>=</span> <span class='va'>f_parent_to_m1</span>, k_m1 <span class='op'>=</span> <span class='va'>k_m1</span><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>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> <span class='op'>}</span> -<span class='va'>ds_sfo_mean</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span> +<span class='va'>ds_mean_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='va'>k1_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, k2 <span class='op'>=</span> <span class='va'>k2_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, g <span class='op'>=</span> <span class='va'>g_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, + f_parent_to_m1 <span class='op'>=</span> <span class='va'>f_parent_to_m1_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, k_m1 <span class='op'>=</span> <span class='va'>k_m1_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span><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>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, + <span class='va'>sampling_times</span><span class='op'>)</span> +<span class='op'>}</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_mean_dfop_sfo</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span> -<span class='va'>ds_sfo_syn</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span> +<span class='va'>ds_syn_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_mean_dfop_sfo</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> @@ -246,34 +255,41 @@ saemix authors for the parts inherited from saemix.</p> <span class='co'># \dontrun{</span> <span class='co'># Evaluate using mmkin and saem</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='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -<span class='va'>f_saem</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> +<span class='va'>f_mmkin_dfop_sfo</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='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_syn_dfop_sfo</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span> +<span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sun Nov 8 02:58:03 2020" +#> [1] "Mon Nov 9 09:11:04 2020" #> .... #> Minimisation finished -#> [1] "Sun Nov 8 02:58:07 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +#> [1] "Mon Nov 9 09:11:16 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Sun Nov 8 02:58:07 2020 -#> Date of summary: Sun Nov 8 02:58:07 2020 +#> Date of fit: Mon Nov 9 09:11:17 2020 +#> Date of summary: Mon Nov 9 09:11:17 2020 #> #> Equations: -#> d_parent/dt = - k_parent * parent +#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * +#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) +#> * parent +#> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) +#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * +#> exp(-k2 * time))) * parent - k_m1 * m1 #> #> Data: -#> 90 observations of 1 variable(s) grouped in 5 datasets +#> 171 observations of 2 variable(s) grouped in 5 datasets #> #> Model predictions using solution type analytical #> -#> Fitted in 4.175 s using 300, 100 iterations +#> Fitted in 13.497 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> #> Mean of starting values for individual parameters: -#> parent_0 log_k_parent -#> 97.849556 -4.455036 +#> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 +#> 101.65644697 -4.05368181 -0.94310703 -2.35943247 -4.07006293 +#> g_qlogis +#> -0.01132621 #> #> Fixed degradation parameter values: #> None @@ -281,129 +297,232 @@ saemix authors for the parts inherited from saemix.</p> #> Results: #> #> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 555.6718 553.3284 -271.8359 +#> AIC BIC logLik +#> 828.8639 823.396 -400.432 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> est. lower upper -#> parent_0 97.840291 94.701895 100.978686 -#> log_k_parent -4.464246 -5.001413 -3.927078 +#> est. lower upper +#> parent_0 101.35835807 97.8846505 104.8320657 +#> log_k_m1 -4.06644838 -4.1861445 -3.9467523 +#> f_parent_qlogis -0.94818070 -1.3124706 -0.5838908 +#> log_k1 -2.92096208 -3.7684319 -2.0734922 +#> log_k2 -3.54529352 -4.2532018 -2.8373852 +#> g_qlogis -0.09254475 -0.9675848 0.7824953 #> #> Correlation: -#> prnt_0 -#> log_k_parent 0.022 +#> prnt_0 lg_k_1 f_prn_ log_k1 log_k2 +#> log_k_m1 -0.217 +#> f_parent_qlogis -0.153 0.203 +#> log_k1 0.066 -0.067 -0.035 +#> log_k2 0.002 0.010 0.001 -0.041 +#> g_qlogis -0.014 0.005 0.015 -0.163 -0.106 #> #> Random effects: -#> est. lower upper -#> SD.parent_0 3.0805465 0.4960170 5.6650760 -#> SD.log_k_parent 0.6109508 0.2301398 0.9917617 +#> est. lower upper +#> SD.parent_0 2.70034095 -0.7003441 6.1010260 +#> SD.log_k_m1 0.08269959 -0.0456860 0.2110852 +#> SD.f_parent_qlogis 0.39452161 0.1376650 0.6513782 +#> SD.log_k1 0.90605744 0.2946394 1.5174755 +#> SD.log_k2 0.77604374 0.2646031 1.2874844 +#> SD.g_qlogis 0.37531563 -0.6836568 1.4342881 #> #> Variance model: #> est. lower upper -#> a.1 1.06249961 0.23012265 1.89487657 -#> b.1 0.04649661 0.03060849 0.06238473 +#> a.1 0.65736042 0.48750246 0.82721839 +#> b.1 0.06424086 0.05011127 0.07837046 #> #> Backtransformed parameters with asymmetric confidence intervals: -#> est. lower upper -#> parent_0 97.84029088 94.701895315 100.97868644 -#> k_parent 0.01151338 0.006728434 0.01970115 +#> est. lower upper +#> parent_0 101.35835807 97.88465048 104.83206565 +#> k_m1 0.01713815 0.01520479 0.01931734 +#> f_parent_to_m1 0.27925085 0.21207372 0.35803781 +#> k1 0.05388182 0.02308824 0.12574588 +#> k2 0.02886015 0.01421864 0.05857864 +#> g 0.47688031 0.27536216 0.68621766 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.2793 +#> parent_sink 0.7207 #> #> Estimated disappearance times: -#> DT50 DT90 -#> parent 60.2 200 +#> DT50 DT90 DT50back DT50_k1 DT50_k2 +#> parent 17.57 63.28 19.05 12.86 24.02 +#> m1 40.44 134.35 NA NA NA #> #> Data: -#> ds name time observed predicted residual standardized -#> ds 1 parent 0 103.6 97.303 6.297361 -1.12720 -#> ds 1 parent 0 95.9 97.303 -1.402639 0.25107 -#> ds 1 parent 1 95.4 96.599 -1.198705 0.21583 -#> ds 1 parent 1 95.3 96.599 -1.298705 0.23383 -#> ds 1 parent 3 91.6 95.206 -3.606076 0.65693 -#> ds 1 parent 3 94.5 95.206 -0.706076 0.12863 -#> ds 1 parent 7 88.1 92.481 -4.380761 0.81692 -#> ds 1 parent 7 89.6 92.481 -2.880761 0.53720 -#> ds 1 parent 14 90.3 87.898 2.402166 -0.46649 -#> ds 1 parent 14 96.0 87.898 8.102166 -1.57340 -#> ds 1 parent 28 80.2 79.402 0.797948 -0.16783 -#> ds 1 parent 28 77.9 79.402 -1.502052 0.31593 -#> ds 1 parent 60 59.3 62.940 -3.639829 0.91247 -#> ds 1 parent 60 59.6 62.940 -3.339829 0.83726 -#> ds 1 parent 90 59.4 50.620 8.779547 -2.56999 -#> ds 1 parent 90 51.0 50.620 0.379547 -0.11110 -#> ds 1 parent 120 38.8 40.712 -1.912380 0.64706 -#> ds 1 parent 120 38.9 40.712 -1.812380 0.61323 -#> ds 2 parent 0 103.2 97.185 6.015158 -1.07774 -#> ds 2 parent 0 95.1 97.185 -2.084842 0.37354 -#> ds 2 parent 1 88.3 95.609 -7.309466 1.32706 -#> ds 2 parent 1 102.4 95.609 6.790534 -1.23285 -#> ds 2 parent 3 88.4 92.535 -4.134911 0.77071 -#> ds 2 parent 3 95.2 92.535 2.665089 -0.49675 -#> ds 2 parent 7 83.5 86.679 -3.179231 0.62426 -#> ds 2 parent 7 96.4 86.679 9.720769 -1.90873 -#> ds 2 parent 14 77.3 77.309 -0.009268 0.00199 -#> ds 2 parent 14 76.0 77.309 -1.309268 0.28113 -#> ds 2 parent 28 61.7 61.499 0.201491 -0.05137 -#> ds 2 parent 28 56.5 61.499 -4.998509 1.27449 -#> ds 2 parent 60 35.1 36.454 -1.353571 0.49087 -#> ds 2 parent 60 32.2 36.454 -4.253571 1.54256 -#> ds 2 parent 90 21.2 22.326 -1.125996 0.53604 -#> ds 2 parent 90 23.3 22.326 0.974004 -0.46368 -#> ds 2 parent 120 14.1 13.674 0.426440 -0.25110 -#> ds 2 parent 120 16.9 13.674 3.226440 -1.89983 -#> ds 3 parent 0 92.4 93.838 -1.437848 0.26501 -#> ds 3 parent 0 94.0 93.838 0.162152 -0.02989 -#> ds 3 parent 1 95.7 91.709 3.991384 -0.74932 -#> ds 3 parent 1 90.8 91.709 -0.908616 0.17058 -#> ds 3 parent 3 86.7 87.594 -0.893997 0.17409 -#> ds 3 parent 3 85.8 87.594 -1.793997 0.34934 -#> ds 3 parent 7 77.1 79.910 -2.810299 0.58817 -#> ds 3 parent 7 81.5 79.910 1.589701 -0.33271 -#> ds 3 parent 14 69.1 68.050 1.050102 -0.24845 -#> ds 3 parent 14 62.4 68.050 -5.649898 1.33675 -#> ds 3 parent 28 49.1 49.349 -0.248837 0.07412 -#> ds 3 parent 28 47.2 49.349 -2.148837 0.64010 -#> ds 3 parent 60 21.9 23.676 -1.775776 0.82085 -#> ds 3 parent 60 23.6 23.676 -0.075776 0.03503 -#> ds 3 parent 90 12.4 11.892 0.507660 -0.31425 -#> ds 3 parent 90 13.8 11.892 1.907660 -1.18088 -#> ds 3 parent 120 4.9 5.974 -1.073521 0.80099 -#> ds 3 parent 120 7.5 5.974 1.526479 -1.13895 -#> ds 4 parent 0 91.8 102.087 -10.287197 1.77084 -#> ds 4 parent 0 104.6 102.087 2.512803 -0.43256 -#> ds 4 parent 1 117.5 101.632 15.867689 -2.74145 -#> ds 4 parent 1 99.3 101.632 -2.332311 0.40295 -#> ds 4 parent 3 94.0 100.729 -6.728610 1.17100 -#> ds 4 parent 3 98.7 100.729 -2.028610 0.35304 -#> ds 4 parent 7 109.2 98.945 10.254756 -1.81080 -#> ds 4 parent 7 89.2 98.945 -9.745244 1.72083 -#> ds 4 parent 14 103.3 95.900 7.400009 -1.34021 -#> ds 4 parent 14 103.0 95.900 7.100009 -1.28588 -#> ds 4 parent 28 90.8 90.088 0.712227 -0.13563 -#> ds 4 parent 28 88.7 90.088 -1.387773 0.26427 -#> ds 4 parent 60 74.8 78.091 -3.291273 0.70124 -#> ds 4 parent 60 75.3 78.091 -2.791273 0.59471 -#> ds 4 parent 90 71.1 68.300 2.800407 -0.66075 -#> ds 4 parent 90 78.0 68.300 9.700407 -2.28880 -#> ds 4 parent 120 59.1 59.736 -0.635668 0.16554 -#> ds 4 parent 120 53.8 59.736 -5.935668 1.54574 -#> ds 5 parent 0 94.9 98.353 -3.452694 0.61266 -#> ds 5 parent 0 101.8 98.353 3.447306 -0.61171 -#> ds 5 parent 1 96.1 96.722 -0.621996 0.11187 -#> ds 5 parent 1 97.1 96.722 0.378004 -0.06799 -#> ds 5 parent 3 93.8 93.541 0.258738 -0.04781 -#> ds 5 parent 3 85.8 93.541 -7.741262 1.43043 -#> ds 5 parent 7 87.6 87.490 0.109848 -0.02141 -#> ds 5 parent 7 94.0 87.490 6.509848 -1.26885 -#> ds 5 parent 14 82.5 77.827 4.672679 -0.99818 -#> ds 5 parent 14 81.7 77.827 3.872679 -0.82728 -#> ds 5 parent 28 60.0 61.585 -1.585419 0.40382 -#> ds 5 parent 28 61.0 61.585 -0.585419 0.14911 -#> ds 5 parent 60 32.5 36.068 -3.568284 1.30251 -#> ds 5 parent 60 35.5 36.068 -0.568284 0.20744 -#> ds 5 parent 90 21.8 21.842 -0.042136 0.02028 -#> ds 5 parent 90 24.4 21.842 2.557864 -1.23088 -#> ds 5 parent 120 14.1 13.227 0.872898 -0.52035 -#> ds 5 parent 120 12.1 13.227 -1.127102 0.67189</div><div class='input'><span class='co'># }</span> +#> ds name time observed predicted residual standardized +#> ds 1 parent 0 89.8 9.848e+01 -8.68339 1.243323 +#> ds 1 parent 0 104.1 9.848e+01 5.61661 -0.804209 +#> ds 1 parent 1 88.7 9.403e+01 -5.32943 0.795687 +#> ds 1 parent 1 95.5 9.403e+01 1.47057 -0.219557 +#> ds 1 parent 3 81.8 8.584e+01 -4.04129 0.654791 +#> ds 1 parent 3 94.5 8.584e+01 8.65871 -1.402929 +#> ds 1 parent 7 71.5 7.196e+01 -0.46034 0.087182 +#> ds 1 parent 7 70.3 7.196e+01 -1.66034 0.314448 +#> ds 1 parent 14 54.2 5.384e+01 0.36125 -0.087766 +#> ds 1 parent 14 49.6 5.384e+01 -4.23875 1.029821 +#> ds 1 parent 28 31.5 3.220e+01 -0.69922 0.256514 +#> ds 1 parent 28 28.8 3.220e+01 -3.39922 1.247025 +#> ds 1 parent 60 12.1 1.264e+01 -0.53539 0.364441 +#> ds 1 parent 60 13.6 1.264e+01 0.96461 -0.656614 +#> ds 1 parent 90 6.2 6.081e+00 0.11929 -0.113824 +#> ds 1 parent 90 8.3 6.081e+00 2.21929 -2.117659 +#> ds 1 parent 120 2.2 3.055e+00 -0.85531 1.001955 +#> ds 1 parent 120 2.4 3.055e+00 -0.65531 0.767664 +#> ds 1 m1 1 0.3 1.115e+00 -0.81540 1.118502 +#> ds 1 m1 1 0.2 1.115e+00 -0.91540 1.255673 +#> ds 1 m1 3 2.2 3.111e+00 -0.91095 1.062691 +#> ds 1 m1 3 3.0 3.111e+00 -0.11095 0.129432 +#> ds 1 m1 7 6.5 6.292e+00 0.20799 -0.195930 +#> ds 1 m1 7 5.0 6.292e+00 -1.29201 1.217079 +#> ds 1 m1 14 10.2 9.886e+00 0.31362 -0.242650 +#> ds 1 m1 14 9.5 9.886e+00 -0.38638 0.298948 +#> ds 1 m1 28 12.2 1.259e+01 -0.39388 0.268603 +#> ds 1 m1 28 13.4 1.259e+01 0.80612 -0.549726 +#> ds 1 m1 60 11.8 1.092e+01 0.87659 -0.644982 +#> ds 1 m1 60 13.2 1.092e+01 2.27659 -1.675083 +#> ds 1 m1 90 6.6 7.814e+00 -1.21445 1.047509 +#> ds 1 m1 90 9.3 7.814e+00 1.48555 -1.281347 +#> ds 1 m1 120 3.5 5.275e+00 -1.77526 1.781944 +#> ds 1 m1 120 5.4 5.275e+00 0.12474 -0.125213 +#> ds 2 parent 0 118.0 1.045e+02 13.54366 -1.838241 +#> ds 2 parent 0 99.8 1.045e+02 -4.65634 0.631992 +#> ds 2 parent 1 90.2 9.872e+01 -8.51733 1.216927 +#> ds 2 parent 1 94.6 9.872e+01 -4.11733 0.588270 +#> ds 2 parent 3 96.1 8.872e+01 7.38009 -1.160975 +#> ds 2 parent 3 78.4 8.872e+01 -10.31991 1.623443 +#> ds 2 parent 7 77.9 7.337e+01 4.52584 -0.842647 +#> ds 2 parent 7 77.7 7.337e+01 4.32584 -0.805409 +#> ds 2 parent 14 56.0 5.616e+01 -0.15795 0.037034 +#> ds 2 parent 14 54.7 5.616e+01 -1.45795 0.341841 +#> ds 2 parent 28 36.6 3.859e+01 -1.99435 0.635813 +#> ds 2 parent 28 36.8 3.859e+01 -1.79435 0.572052 +#> ds 2 parent 60 22.1 2.113e+01 0.97273 -0.482843 +#> ds 2 parent 60 24.7 2.113e+01 3.57273 -1.773425 +#> ds 2 parent 90 12.4 1.258e+01 -0.17909 0.122205 +#> ds 2 parent 90 10.8 1.258e+01 -1.77909 1.214019 +#> ds 2 parent 120 6.8 7.509e+00 -0.70864 0.621767 +#> ds 2 parent 120 7.9 7.509e+00 0.39136 -0.343380 +#> ds 2 m1 1 1.3 1.466e+00 -0.16566 0.220431 +#> ds 2 m1 3 3.7 3.947e+00 -0.24719 0.271357 +#> ds 2 m1 3 4.7 3.947e+00 0.75281 -0.826421 +#> ds 2 m1 7 8.1 7.501e+00 0.59910 -0.525881 +#> ds 2 m1 7 7.9 7.501e+00 0.39910 -0.350323 +#> ds 2 m1 14 10.1 1.082e+01 -0.71564 0.529253 +#> ds 2 m1 14 10.3 1.082e+01 -0.51564 0.381342 +#> ds 2 m1 28 10.7 1.248e+01 -1.78322 1.221977 +#> ds 2 m1 28 12.2 1.248e+01 -0.28322 0.194082 +#> ds 2 m1 60 10.7 1.058e+01 0.12295 -0.091967 +#> ds 2 m1 60 12.5 1.058e+01 1.92295 -1.438427 +#> ds 2 m1 90 9.1 8.029e+00 1.07074 -0.912688 +#> ds 2 m1 90 7.4 8.029e+00 -0.62926 0.536381 +#> ds 2 m1 120 6.1 5.816e+00 0.28391 -0.275375 +#> ds 2 m1 120 4.5 5.816e+00 -1.31609 1.276529 +#> ds 3 parent 0 106.2 1.048e+02 1.43237 -0.193885 +#> ds 3 parent 0 106.9 1.048e+02 2.13237 -0.288636 +#> ds 3 parent 1 107.4 9.616e+01 11.23530 -1.643774 +#> ds 3 parent 1 96.1 9.616e+01 -0.06470 0.009466 +#> ds 3 parent 3 79.4 8.238e+01 -2.97800 0.500554 +#> ds 3 parent 3 82.6 8.238e+01 0.22200 -0.037315 +#> ds 3 parent 7 63.9 6.427e+01 -0.36601 0.076477 +#> ds 3 parent 7 62.4 6.427e+01 -1.86601 0.389900 +#> ds 3 parent 14 51.0 4.825e+01 2.74941 -0.731807 +#> ds 3 parent 14 47.1 4.825e+01 -1.15059 0.306250 +#> ds 3 parent 28 36.1 3.501e+01 1.09474 -0.376700 +#> ds 3 parent 28 36.6 3.501e+01 1.59474 -0.548750 +#> ds 3 parent 60 20.1 2.050e+01 -0.40214 0.203675 +#> ds 3 parent 60 19.8 2.050e+01 -0.70214 0.355617 +#> ds 3 parent 90 11.3 1.257e+01 -1.27210 0.868328 +#> ds 3 parent 90 10.7 1.257e+01 -1.87210 1.277883 +#> ds 3 parent 120 8.2 7.710e+00 0.48984 -0.424960 +#> ds 3 parent 120 7.3 7.710e+00 -0.41016 0.355837 +#> ds 3 m1 0 0.8 -1.421e-13 0.80000 -1.216988 +#> ds 3 m1 1 1.8 1.928e+00 -0.12842 0.164382 +#> ds 3 m1 1 2.3 1.928e+00 0.37158 -0.475623 +#> ds 3 m1 3 4.2 4.925e+00 -0.72511 0.744654 +#> ds 3 m1 3 4.1 4.925e+00 -0.82511 0.847349 +#> ds 3 m1 7 6.8 8.542e+00 -1.74215 1.444429 +#> ds 3 m1 7 10.1 8.542e+00 1.55785 -1.291627 +#> ds 3 m1 14 11.4 1.096e+01 0.44492 -0.326877 +#> ds 3 m1 14 12.8 1.096e+01 1.84492 -1.355438 +#> ds 3 m1 28 11.5 1.122e+01 0.27920 -0.202587 +#> ds 3 m1 28 10.6 1.122e+01 -0.62080 0.450442 +#> ds 3 m1 60 7.5 8.912e+00 -1.41171 1.147867 +#> ds 3 m1 60 8.6 8.912e+00 -0.31171 0.253453 +#> ds 3 m1 90 7.3 6.683e+00 0.61657 -0.567369 +#> ds 3 m1 90 8.1 6.683e+00 1.41657 -1.303536 +#> ds 3 m1 120 5.3 4.825e+00 0.47527 -0.491339 +#> ds 3 m1 120 3.8 4.825e+00 -1.02473 1.059361 +#> ds 4 parent 0 104.7 9.956e+01 5.14415 -0.729366 +#> ds 4 parent 0 88.3 9.956e+01 -11.25585 1.595915 +#> ds 4 parent 1 94.2 9.639e+01 -2.19462 0.320391 +#> ds 4 parent 1 94.6 9.639e+01 -1.79462 0.261995 +#> ds 4 parent 3 78.1 9.044e+01 -12.34368 1.908558 +#> ds 4 parent 3 96.5 9.044e+01 6.05632 -0.936418 +#> ds 4 parent 7 76.2 7.988e+01 -3.67799 0.635364 +#> ds 4 parent 7 77.8 7.988e+01 -2.07799 0.358968 +#> ds 4 parent 14 70.8 6.492e+01 5.88059 -1.218059 +#> ds 4 parent 14 67.3 6.492e+01 2.38059 -0.493097 +#> ds 4 parent 28 43.1 4.442e+01 -1.32411 0.377111 +#> ds 4 parent 28 45.1 4.442e+01 0.67589 -0.192494 +#> ds 4 parent 60 21.3 2.136e+01 -0.06143 0.030267 +#> ds 4 parent 60 23.5 2.136e+01 2.13857 -1.053671 +#> ds 4 parent 90 11.8 1.187e+01 -0.06548 0.046122 +#> ds 4 parent 90 12.1 1.187e+01 0.23452 -0.165204 +#> ds 4 parent 120 7.0 6.864e+00 0.13645 -0.124240 +#> ds 4 parent 120 6.2 6.864e+00 -0.66355 0.604171 +#> ds 4 m1 0 1.6 8.811e-13 1.60000 -2.433977 +#> ds 4 m1 1 0.9 6.943e-01 0.20568 -0.293006 +#> ds 4 m1 3 3.7 1.964e+00 1.73568 -2.215152 +#> ds 4 m1 3 2.0 1.964e+00 0.03568 -0.045539 +#> ds 4 m1 7 3.6 4.082e+00 -0.48184 0.523977 +#> ds 4 m1 7 3.8 4.082e+00 -0.28184 0.306486 +#> ds 4 m1 14 7.1 6.694e+00 0.40571 -0.373099 +#> ds 4 m1 14 6.6 6.694e+00 -0.09429 0.086710 +#> ds 4 m1 28 9.5 9.147e+00 0.35343 -0.283895 +#> ds 4 m1 28 9.3 9.147e+00 0.15343 -0.123245 +#> ds 4 m1 60 8.3 8.788e+00 -0.48803 0.399399 +#> ds 4 m1 60 9.0 8.788e+00 0.21197 -0.173474 +#> ds 4 m1 90 6.6 6.644e+00 -0.04431 0.040866 +#> ds 4 m1 90 7.7 6.644e+00 1.05569 -0.973711 +#> ds 4 m1 120 3.7 4.667e+00 -0.96735 1.010605 +#> ds 4 m1 120 3.5 4.667e+00 -1.16735 1.219548 +#> ds 5 parent 0 110.4 1.020e+02 8.37855 -1.161863 +#> ds 5 parent 0 112.1 1.020e+02 10.07855 -1.397604 +#> ds 5 parent 1 93.5 9.494e+01 -1.43722 0.212725 +#> ds 5 parent 1 91.0 9.494e+01 -3.93722 0.582755 +#> ds 5 parent 3 71.0 8.280e+01 -11.80256 1.974773 +#> ds 5 parent 3 89.7 8.280e+01 6.89744 -1.154061 +#> ds 5 parent 7 60.4 6.485e+01 -4.45291 0.923157 +#> ds 5 parent 7 59.1 6.485e+01 -5.75291 1.192667 +#> ds 5 parent 14 56.5 4.626e+01 10.24038 -2.821727 +#> ds 5 parent 14 47.0 4.626e+01 0.74038 -0.204011 +#> ds 5 parent 28 30.2 3.034e+01 -0.13506 0.051824 +#> ds 5 parent 28 23.9 3.034e+01 -6.43506 2.469220 +#> ds 5 parent 60 17.0 1.795e+01 -0.95206 0.525822 +#> ds 5 parent 60 18.7 1.795e+01 0.74794 -0.413085 +#> ds 5 parent 90 11.3 1.186e+01 -0.56163 0.395692 +#> ds 5 parent 90 11.9 1.186e+01 0.03837 -0.027033 +#> ds 5 parent 120 9.0 7.866e+00 1.13427 -0.975579 +#> ds 5 parent 120 8.1 7.866e+00 0.23427 -0.201493 +#> ds 5 m1 0 0.7 -4.263e-14 0.70000 -1.064865 +#> ds 5 m1 1 3.0 3.169e+00 -0.16908 0.196384 +#> ds 5 m1 1 2.6 3.169e+00 -0.56908 0.660990 +#> ds 5 m1 3 5.1 8.455e+00 -3.35479 2.794486 +#> ds 5 m1 3 7.5 8.455e+00 -0.95479 0.795325 +#> ds 5 m1 7 16.5 1.577e+01 0.73235 -0.438460 +#> ds 5 m1 7 19.0 1.577e+01 3.23235 -1.935208 +#> ds 5 m1 14 22.9 2.202e+01 0.88393 -0.426673 +#> ds 5 m1 14 23.2 2.202e+01 1.18393 -0.571482 +#> ds 5 m1 28 22.2 2.399e+01 -1.79091 0.814583 +#> ds 5 m1 28 24.4 2.399e+01 0.40909 -0.186073 +#> ds 5 m1 60 15.5 1.872e+01 -3.21988 1.731175 +#> ds 5 m1 60 19.8 1.872e+01 1.08012 -0.580725 +#> ds 5 m1 90 14.9 1.383e+01 1.06749 -0.690500 +#> ds 5 m1 90 14.2 1.383e+01 0.36749 -0.237710 +#> ds 5 m1 120 10.9 1.004e+01 0.85568 -0.656897 +#> ds 5 m1 120 10.4 1.004e+01 0.35568 -0.273054</div><div class='input'><span class='co'># }</span> </div></pre> </div> diff --git a/man/saem.Rd b/man/saem.Rd index b2daf419..56b54fbf 100644 --- a/man/saem.Rd +++ b/man/saem.Rd @@ -81,6 +81,10 @@ f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) # functions from saemix library(saemix) compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) +plot(f_saem_fomc$so, plot.type = "convergence") +plot(f_saem_fomc$so, plot.type = "individual.fit") +plot(f_saem_fomc$so, plot.type = "npde") +plot(f_saem_fomc$so, plot.type = "vpc") f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ]) @@ -101,11 +105,12 @@ f_mmkin <- mmkin(list( # 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_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +summary(f_saem_dfop_sfo, data = FALSE) # Using a single core, the following takes about 6 minutes, using 10 cores # it is slower instead of faster -f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) +#f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) } } \seealso{ diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd index 0f0d8264..828691e6 100644 --- a/man/summary.saem.mmkin.Rd +++ b/man/summary.saem.mmkin.Rd @@ -51,25 +51,34 @@ endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full. } \examples{ -# Generate five datasets following SFO kinetics +# Generate five datasets following DFOP-SFO kinetics sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) -dt50_sfo_in_pop <- 50 -k_in_pop <- log(2) / dt50_sfo_in_pop +dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"), + m1 = mkinsub("SFO"), quiet = TRUE) set.seed(1234) -k_in <- rlnorm(5, log(k_in_pop), 0.5) -SFO <- mkinmod(parent = mkinsub("SFO")) +k1_in <- rlnorm(5, log(0.1), 0.3) +k2_in <- rlnorm(5, log(0.02), 0.3) +g_in <- plogis(rnorm(5, qlogis(0.5), 0.3)) +f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3)) +k_m1_in <- rlnorm(5, log(0.02), 0.3) -pred_sfo <- function(k) { - mkinpredict(SFO, - c(k_parent = k), - c(parent = 100), +pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) { + mkinpredict(dfop_sfo, + c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1), + c(parent = 100, m1 = 0), sampling_times) } -ds_sfo_mean <- lapply(k_in, pred_sfo) -names(ds_sfo_mean) <- paste("ds", 1:5) +ds_mean_dfop_sfo <- lapply(1:5, function(i) { + mkinpredict(dfop_sfo, + c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i], + f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]), + c(parent = 100, m1 = 0), + sampling_times) +}) +names(ds_mean_dfop_sfo) <- paste("ds", 1:5) -ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) { +ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) { add_err(ds, sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), n = 1)[[1]] @@ -77,9 +86,9 @@ ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) { \dontrun{ # Evaluate using mmkin and saem -f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1) -f_saem <- saem(f_mmkin) -summary(f_saem, data = TRUE) +f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = "tc", cores = 5) +f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo) +summary(f_saem_dfop_sfo, data = TRUE) } } |
