## R version 4.0.0 (2020-04-24) diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 167a8d06..6473cdce 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -71,7 +71,7 @@ diff --git a/docs/dev/index.html b/docs/dev/index.html index 4a71b99b..37cd7d50 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ @@ -127,7 +127,7 @@

Documentation

The HTML documentation is available at jrwb.de, at github and at R-Forge.

The HTML documentation of the latest version released to CRAN is available at jrwb.de and github. Documentation of the development version is found in the ‘dev’ subdirectory.

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 36f7025a..7e39aa46 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 0.9.50.3 + 0.9.50.3

diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 0dbb110e..31ffe2ad 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: NAFTA_examples: web_only/NAFTA_examples.html benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html -last_built: 2020-05-27T03:53Z +last_built: 2020-05-27T05:43Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index a03ecea8..074bed3e 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> @@ -281,12 +281,12 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, use_of_ff = "max", quiet = TRUE) f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE) system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))

#> user system elapsed -#> 3.707 1.077 3.444

# Using more cores does not save much time here, as parent_0 takes up most of the time +#> 3.610 1.071 3.378

# Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of # minor interest), we get a nice performance improvement from about 50 # seconds to about 12 seconds if we use at least four cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", - c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))

#> Profiling the likelihood

#> Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected

#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent

#> Timing stopped at: 0.011 0.026 0.207

ci_profile

#> 2.5% 97.5% + c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))

#> Profiling the likelihood

#> Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected

#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent

#> Timing stopped at: 0.005 0.04 0.206

ci_profile

#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent 0.090911032 1.071578e-01 #> k_m1 0.003892605 6.702778e-03 diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 906bc2f8..f1ab22e6 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -71,7 +71,7 @@

diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index 49e896fc..e1e75767 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -80,7 +80,7 @@ likelihood function." /> @@ -424,15 +424,15 @@ Degradation Data. Environments 6(12) 124 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)

#> mkin version used for fitting: 0.9.50.3 #> R version used for fitting: 4.0.0 -#> Date of fit: Wed May 27 05:54:13 2020 -#> Date of summary: Wed May 27 05:54:13 2020 +#> Date of fit: Wed May 27 07:43:45 2020 +#> Date of summary: Wed May 27 07:43:45 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.043 s +#> Fitted using 222 model solutions performed in 0.044 s #> #> Error model: Constant variance #> @@ -509,7 +509,7 @@ Degradation Data. Environments 6(12) 124 m1 = mkinsub("SFO"))

#> Successfully compiled differential equation model from auto-generated C code.

# Fit the model to the FOCUS example dataset D using defaults print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))

#> Warning: Observations with value of zero were removed from the data

#> user system elapsed -#> 0.414 0.000 0.418

parms(fit)

#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.405 0.001 0.407

parms(fit)

#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598481046 0.098697740 0.005260651 0.514475962 3.125503875

endpoints(fit)

#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -599,7 +599,7 @@ Degradation Data. Environments 6(12) 124 #> Sum of squared residuals at call 165: 371.2134 #> Sum of squared residuals at call 167: 371.2134 #> Negative log-likelihood at call 177: 97.22429

#> Optimisation successfully terminated.

#> user system elapsed -#> 0.371 0.001 0.370

parms(fit.deSolve)

#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.361 0.000 0.361

parms(fit.deSolve)

#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598480300 0.098697739 0.005260651 0.514475968 3.125503874

endpoints(fit.deSolve)

#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -633,8 +633,8 @@ Degradation Data. Environments 6(12) 124 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max")

#> Successfully compiled differential equation model from auto-generated C code.

f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)

#> Warning: Observations with value of zero were removed from the data

summary(f.noweight)

#> mkin version used for fitting: 0.9.50.3 #> R version used for fitting: 4.0.0 -#> Date of fit: Wed May 27 05:54:19 2020 -#> Date of summary: Wed May 27 05:54:19 2020 +#> Date of fit: Wed May 27 07:43:50 2020 +#> Date of summary: Wed May 27 07:43:50 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -642,7 +642,7 @@ Degradation Data. Environments 6(12) 124 #> #> Model predictions using solution type analytical #> -#> Fitted using 421 model solutions performed in 0.126 s +#> Fitted using 421 model solutions performed in 0.125 s #> #> Error model: Constant variance #> @@ -755,8 +755,8 @@ Degradation Data. Environments 6(12) 124 #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00

f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)

#> Warning: Observations with value of zero were removed from the data

summary(f.obs)

#> mkin version used for fitting: 0.9.50.3 #> R version used for fitting: 4.0.0 -#> Date of fit: Wed May 27 05:54:19 2020 -#> Date of summary: Wed May 27 05:54:19 2020 +#> Date of fit: Wed May 27 07:43:51 2020 +#> Date of summary: Wed May 27 07:43:51 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -764,7 +764,7 @@ Degradation Data. Environments 6(12) 124 #> #> Model predictions using solution type analytical #> -#> Fitted using 978 model solutions performed in 0.33 s +#> Fitted using 978 model solutions performed in 0.413 s #> #> Error model: Variance unique to each observed variable #> @@ -892,8 +892,8 @@ Degradation Data. Environments 6(12) 124 #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00

f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)

#> Warning: Observations with value of zero were removed from the data

summary(f.tc)

#> mkin version used for fitting: 0.9.50.3 #> R version used for fitting: 4.0.0 -#> Date of fit: Wed May 27 05:54:20 2020 -#> Date of summary: Wed May 27 05:54:20 2020 +#> Date of fit: Wed May 27 07:43:52 2020 +#> Date of summary: Wed May 27 07:43:52 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index 1b5c1592..3daf16e1 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -75,7 +75,7 @@ datasets specified in its first two arguments." />

@@ -220,8 +220,8 @@ plotting.

time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))

#> Warning: Optimisation did not converge: #> false convergence (8)

time_default

#> user system elapsed -#> 4.516 0.456 1.976

time_1

#> user system elapsed -#> 5.957 0.001 5.961

+#> 4.499 0.456 1.983

time_1

#> user system elapsed +#> 5.771 0.003 5.777

endpoints(fits.0[["SFO_lin", 2]])

#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340479 0.2659521 0.7505687 0.2494313 diff --git a/docs/dev/reference/nlme-1.png b/docs/dev/reference/nlme-1.png index bc04dea8..68ccb43f 100644 Binary files a/docs/dev/reference/nlme-1.png and b/docs/dev/reference/nlme-1.png differ diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html index 8c64fb47..28a9f0a5 100644 --- a/docs/dev/reference/nlme.html +++ b/docs/dev/reference/nlme.html @@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />

@@ -225,28 +225,28 @@ nlme for the case of a single grouping variable ds.

#> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) #> Data: grouped_data #> AIC BIC logLik -#> 252.7798 262.1358 -121.3899 +#> 298.2781 307.7372 -144.1391 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k_parent_sink Residual -#> StdDev: 0.004139378 0.6800778 2.489396 +#> parent_0 log_k_parent_sink Residual +#> StdDev: 0.9374809 0.7098104 3.835429 #> #> Fixed effects: parent_0 + log_k_parent_sink ~ 1 -#> Value Std.Error DF t-value p-value -#> parent_0 101.74884 0.6456057 44 157.60213 0 -#> log_k_parent_sink -3.05575 0.4015812 44 -7.60929 0 +#> Value Std.Error DF t-value p-value +#> parent_0 101.76838 1.1445465 45 88.91589 0 +#> log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0 #> Correlation: #> prnt_0 -#> log_k_parent_sink 0.026 +#> log_k_parent_sink 0.034 #> #> Standardized Within-Group Residuals: #> Min Q1 Med Q3 Max -#> -2.13168782 -0.68780415 0.08282907 0.85913228 2.95298904 +#> -2.61693660 -0.21853517 0.05740766 0.57209378 3.04598387 #> -#> Number of Observations: 48 +#> Number of Observations: 49 #> Number of Groups: 3

plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))

# augPred does not seem to work on fits with more than one state # variable diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index a6716c0f..c7db9c23 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." />

diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index 6a46dad0..a50ca352 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." /> diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html index ad16a81b..da28bff1 100644 --- a/docs/dev/reference/saemix.html +++ b/docs/dev/reference/saemix.html @@ -75,7 +75,7 @@ a list of datasets." /> @@ -234,8 +234,8 @@ variances of the deviations of the parameters from these mean values.

save = FALSE, save.graphs = FALSE, displayProgress = FALSE, nbiter.saemix = c(200, 80)) f_saemix <- saemix(m_saemix, d_saemix, saemix_options)

#> Running main SAEM algorithm -#> [1] "Wed May 27 05:55:50 2020" +#> [1] "Wed May 27 07:45:07 2020" #> .. #> Minimisation finished -#> [1] "Wed May 27 06:01:54 2020"

#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> [1] "Wed May 27 07:51:24 2020"

#> Nonlinear mixed-effects model fit by the SAEM algorithm #> ----------------------------------- #> ---- Data ---- #> ----------------------------------- @@ -333,8 +333,8 @@ variances of the deviations of the parameters from these mean values.

#> res <- unlist(res_list) #> return(res) #> } -#> <bytecode: 0x55555e4213d8> -#> <environment: 0x55555c47cdf0> +#> <bytecode: 0x55555bbf17c0> +#> <environment: 0x55555bbec4e0> #> Nb of parameters: 4 #> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> distribution: diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index d0858eda..b0994d33 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." />

@@ -241,7 +241,7 @@ This is no problem for the internal use in mkinfit< #> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549 # \dontrun{ # Compare to the version without transforming rate parameters -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data #> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: missing value where TRUE/FALSE needed #> Timing stopped at: 0.003 0 0.003 fit.2.s <- summary(fit.2) #> Error in summary(fit.2): object 'fit.2' not found print(fit.2.s$par, 3) #> Error in print(fit.2.s$par, 3): object 'fit.2.s' not found print(fit.2.s$bpar, 3) #> Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found # } +fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data #> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: missing value where TRUE/FALSE needed #> Timing stopped at: 0 0.002 0.002 fit.2.s <- summary(fit.2) #> Error in summary(fit.2): object 'fit.2' not found print(fit.2.s$par, 3) #> Error in print(fit.2.s$par, 3): object 'fit.2.s' not found print(fit.2.s$bpar, 3) #> Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found # } initials <- fit$start$value names(initials) <- rownames(fit$start) diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda index c38cd1ea..cc08f7ad 100644 Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ -- cgit v1.2.1