From 255430279d65bfe92093d48c9a586b062a38303d Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Tue, 22 Jun 2021 15:15:02 +0200
Subject: Update development version of online docs
---
_pkgdown.yml | 1 +
docs/dev/pkgdown.yml | 2 +-
docs/dev/reference/dimethenamid_2018-1.png | Bin 0 -> 264364 bytes
docs/dev/reference/dimethenamid_2018.html | 288 +-
docs/dev/reference/index.html | 6 +
docs/dev/reference/nlmixr.mmkin.html | 9782 ++--------------------------
docs/dev/reference/tffm0.html | 226 +
docs/dev/sitemap.xml | 3 +
8 files changed, 1019 insertions(+), 9289 deletions(-)
create mode 100644 docs/dev/reference/dimethenamid_2018-1.png
create mode 100644 docs/dev/reference/tffm0.html
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 50c0685f..f0a95468 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -87,6 +87,7 @@ reference:
- mkinpredict
- transform_odeparms
- ilr
+ - tffm0
- logLik.mkinfit
- residuals.mkinfit
- nobs.mkinfit
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 0b01e008..b2c50e79 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: 2021-06-11T09:09Z
+last_built: 2021-06-17T12:41Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/dimethenamid_2018-1.png b/docs/dev/reference/dimethenamid_2018-1.png
new file mode 100644
index 00000000..52b8a2be
Binary files /dev/null and b/docs/dev/reference/dimethenamid_2018-1.png differ
diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html
index a06599df..e255765e 100644
--- a/docs/dev/reference/dimethenamid_2018.html
+++ b/docs/dev/reference/dimethenamid_2018.html
@@ -77,7 +77,7 @@ constrained by data protection regulations." />
mkin
- 1.0.3.9000
+ 1.0.5
@@ -203,7 +203,291 @@ specific pieces of information in the comments.
#> Elliot 2 0.75 33.37 23
#> Flaach 0.40 NA 20
#> BBA 2.2 0.40 NA 20
-#> BBA 2.3 0.40 NA 20
+#> BBA 2.3 0.40 NA 20#> With est = 'saem', a different error model is required for each observed variableChanging the error model to 'obs_tc' (Two-component error for each observed variable)
#> function ()
+#> {
+#> ini({
+#> DMTA_0 = 98.7697627680706
+#> eta.DMTA_0 ~ 2.35171765917765
+#> log_k_M23 = -3.92162409637283
+#> eta.log_k_M23 ~ 0.549278519419884
+#> log_k_M27 = -4.33774620773911
+#> eta.log_k_M27 ~ 0.864474956685295
+#> log_k_M31 = -4.24767627688461
+#> eta.log_k_M31 ~ 0.750297149164171
+#> log_k1 = -2.2341008812259
+#> eta.log_k1 ~ 0.902976221565793
+#> log_k2 = -3.7762779983269
+#> eta.log_k2 ~ 1.57684519529298
+#> g_qlogis = 0.450175725479389
+#> eta.g_qlogis ~ 3.0851335687675
+#> f_DMTA_tffm0_1_qlogis = -2.09240906629456
+#> eta.f_DMTA_tffm0_1_qlogis ~ 0.3
+#> f_DMTA_tffm0_2_qlogis = -2.18057573598794
+#> eta.f_DMTA_tffm0_2_qlogis ~ 0.3
+#> f_DMTA_tffm0_3_qlogis = -2.14267187609763
+#> eta.f_DMTA_tffm0_3_qlogis ~ 0.3
+#> sigma_low_DMTA = 0.697933852349996
+#> rsd_high_DMTA = 0.0257724286053519
+#> sigma_low_M23 = 0.697933852349996
+#> rsd_high_M23 = 0.0257724286053519
+#> sigma_low_M27 = 0.697933852349996
+#> rsd_high_M27 = 0.0257724286053519
+#> sigma_low_M31 = 0.697933852349996
+#> rsd_high_M31 = 0.0257724286053519
+#> })
+#> model({
+#> DMTA_0_model = DMTA_0 + eta.DMTA_0
+#> DMTA(0) = DMTA_0_model
+#> k_M23 = exp(log_k_M23 + eta.log_k_M23)
+#> k_M27 = exp(log_k_M27 + eta.log_k_M27)
+#> k_M31 = exp(log_k_M31 + eta.log_k_M31)
+#> k1 = exp(log_k1 + eta.log_k1)
+#> k2 = exp(log_k2 + eta.log_k2)
+#> g = expit(g_qlogis + eta.g_qlogis)
+#> f_DMTA_tffm0_1 = expit(f_DMTA_tffm0_1_qlogis + eta.f_DMTA_tffm0_1_qlogis)
+#> f_DMTA_tffm0_2 = expit(f_DMTA_tffm0_2_qlogis + eta.f_DMTA_tffm0_2_qlogis)
+#> f_DMTA_tffm0_3 = expit(f_DMTA_tffm0_3_qlogis + eta.f_DMTA_tffm0_3_qlogis)
+#> f_DMTA_to_M23 = f_DMTA_tffm0_1
+#> f_DMTA_to_M27 = f_DMTA_tffm0_2 * (1 - f_DMTA_tffm0_1)
+#> f_DMTA_to_M31 = f_DMTA_tffm0_3 * (1 - f_DMTA_tffm0_2) *
+#> (1 - f_DMTA_tffm0_1)
+#> d/dt(DMTA) = -((k1 * g * exp(-k1 * time) + k2 * (1 -
+#> g) * exp(-k2 * time))/(g * exp(-k1 * time) + (1 -
+#> g) * exp(-k2 * time))) * DMTA
+#> d/dt(M23) = +f_DMTA_to_M23 * ((k1 * g * exp(-k1 * time) +
+#> k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) +
+#> (1 - g) * exp(-k2 * time))) * DMTA - k_M23 * M23
+#> d/dt(M27) = +f_DMTA_to_M27 * ((k1 * g * exp(-k1 * time) +
+#> k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) +
+#> (1 - g) * exp(-k2 * time))) * DMTA - k_M27 * M27 +
+#> k_M31 * M31
+#> d/dt(M31) = +f_DMTA_to_M31 * ((k1 * g * exp(-k1 * time) +
+#> k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) +
+#> (1 - g) * exp(-k2 * time))) * DMTA - k_M31 * M31
+#> DMTA ~ add(sigma_low_DMTA) + prop(rsd_high_DMTA)
+#> M23 ~ add(sigma_low_M23) + prop(rsd_high_M23)
+#> M27 ~ add(sigma_low_M27) + prop(rsd_high_M27)
+#> M31 ~ add(sigma_low_M31) + prop(rsd_high_M31)
+#> })
+#> }
+#> <environment: 0x555559c2bd78>
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> → creating full model...
#> → pruning branches (`if`/`else`)...
#> ✔ done
#> → loading into symengine environment...
#> ✔ done
#> → creating full model...
#> → pruning branches (`if`/`else`)...
#> ✔ done
#> → loading into symengine environment...
#> ✔ done
#> → calculate jacobian
#> [====|====|====|====|====|====|====|====|====|====] 0:00:02
+#>
#> → calculate sensitivities
#> [====|====|====|====|====|====|====|====|====|====] 0:00:04
+#>
#> → calculate ∂(f)/∂(η)
#> [====|====|====|====|====|====|====|====|====|====] 0:00:01
+#>
#> → calculate ∂(R²)/∂(η)
#> [====|====|====|====|====|====|====|====|====|====] 0:00:08
+#>
#> → finding duplicate expressions in inner model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:07
+#>
#> → optimizing duplicate expressions in inner model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:07
+#>
#> → finding duplicate expressions in EBE model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
+#>
#> → optimizing duplicate expressions in EBE model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
+#>
#> → compiling inner model...
#>
#> ✔ done
#> → finding duplicate expressions in FD model...
#>
#> → optimizing duplicate expressions in FD model...
#>
#> → compiling EBE model...
#>
#> ✔ done
#> → compiling events FD model...
#>
#> ✔ done
#> Needed Covariates:
#> [1] "CMT"
#> RxODE 1.1.0 using 8 threads (see ?getRxThreads)
+#> no cache: create with `rxCreateCache()`
#> Key: U: Unscaled Parameters; X: Back-transformed parameters; G: Gill difference gradient approximation
+#> F: Forward difference gradient approximation
+#> C: Central difference gradient approximation
+#> M: Mixed forward and central difference gradient approximation
+#> Unscaled parameters for Omegas=chol(solve(omega));
+#> Diagonals are transformed, as specified by foceiControl(diagXform=)
+#> |-----+---------------+-----------+-----------+-----------+-----------|
+#> | #| Objective Fun | DMTA_0 | log_k_M23 | log_k_M27 | log_k_M31 |
+#> |.....................| log_k1 | log_k2 | g_qlogis |f_DMTA_tffm0_1_qlogis |
+#> |.....................|f_DMTA_tffm0_2_qlogis |f_DMTA_tffm0_3_qlogis | sigma_low | rsd_high |
+#> |.....................| o1 | o2 | o3 | o4 |
+#> |.....................| o5 | o6 | o7 | o8 |
+#> |.....................| o9 | o10 |...........|...........|
+#> calculating covariance matrix
+#> done
#> Calculating residuals/tables
#> done
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
#> Warning: last objective function was not at minimum, possible problems in optimization
#> Warning: S matrix non-positive definite
#> Warning: using R matrix to calculate covariance
#> Warning: gradient problems with initial estimate and covariance; see $scaleInfo
#> nlmixr version used for fitting: 2.0.4
+#> mkin version used for pre-fitting: 1.0.5
+#> R version used for fitting: 4.1.0
+#> Date of fit: Thu Jun 17 14:04:58 2021
+#> Date of summary: Thu Jun 17 14:04:58 2021
+#>
+#> Equations:
+#> d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+#> * DMTA
+#> d_M23/dt = + f_DMTA_to_M23 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+#> exp(-k2 * time))) * DMTA - k_M23 * M23
+#> d_M27/dt = + f_DMTA_to_M27 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+#> exp(-k2 * time))) * DMTA - k_M27 * M27 + k_M31 * M31
+#> d_M31/dt = + f_DMTA_to_M31 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+#> exp(-k2 * time))) * DMTA - k_M31 * M31
+#>
+#> Data:
+#> 568 observations of 4 variable(s) grouped in 6 datasets
+#>
+#> Degradation model predictions using RxODE
+#>
+#> Fitted in 242.937 s
+#>
+#> Variance model: Two-component variance function
+#>
+#> Mean of starting values for individual parameters:
+#> DMTA_0 log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1 f_DMTA_ilr_2
+#> 98.7698 -3.9216 -4.3377 -4.2477 0.1380 0.1393
+#> f_DMTA_ilr_3 log_k1 log_k2 g_qlogis
+#> -1.7571 -2.2341 -3.7763 0.4502
+#>
+#> Mean of starting values for error model parameters:
+#> sigma_low rsd_high
+#> 0.69793 0.02577
+#>
+#> Fixed degradation parameter values:
+#> None
+#>
+#> Results:
+#>
+#> Likelihood calculated by focei
+#> AIC BIC logLik
+#> 1936 2031 -945.9
+#>
+#> Optimised parameters:
+#> est. lower upper
+#> DMTA_0 98.7698 98.7356 98.8039
+#> log_k_M23 -3.9216 -3.9235 -3.9197
+#> log_k_M27 -4.3377 -4.3398 -4.3357
+#> log_k_M31 -4.2477 -4.2497 -4.2457
+#> log_k1 -2.2341 -2.2353 -2.2329
+#> log_k2 -3.7763 -3.7781 -3.7744
+#> g_qlogis 0.4502 0.4496 0.4507
+#> f_DMTA_tffm0_1_qlogis -2.0924 -2.0936 -2.0912
+#> f_DMTA_tffm0_2_qlogis -2.1806 -2.1818 -2.1794
+#> f_DMTA_tffm0_3_qlogis -2.1427 -2.1439 -2.1415
+#>
+#> Correlation:
+#> DMTA_0 l__M23 l__M27 l__M31 log_k1 log_k2 g_qlgs
+#> log_k_M23 0
+#> log_k_M27 0 0
+#> log_k_M31 0 0 0
+#> log_k1 0 0 0 0
+#> log_k2 0 0 0 0 0
+#> g_qlogis 0 0 0 0 0 0
+#> f_DMTA_tffm0_1_qlogis 0 0 0 0 0 0 0
+#> f_DMTA_tffm0_2_qlogis 0 0 0 0 0 0 0
+#> f_DMTA_tffm0_3_qlogis 0 0 0 0 0 0 0
+#> f_DMTA_0_1 f_DMTA_0_2
+#> log_k_M23
+#> log_k_M27
+#> log_k_M31
+#> log_k1
+#> log_k2
+#> g_qlogis
+#> f_DMTA_tffm0_1_qlogis
+#> f_DMTA_tffm0_2_qlogis 0
+#> f_DMTA_tffm0_3_qlogis 0 0
+#>
+#> Random effects (omega):
+#> eta.DMTA_0 eta.log_k_M23 eta.log_k_M27 eta.log_k_M31
+#> eta.DMTA_0 2.352 0.0000 0.0000 0.0000
+#> eta.log_k_M23 0.000 0.5493 0.0000 0.0000
+#> eta.log_k_M27 0.000 0.0000 0.8645 0.0000
+#> eta.log_k_M31 0.000 0.0000 0.0000 0.7503
+#> eta.log_k1 0.000 0.0000 0.0000 0.0000
+#> eta.log_k2 0.000 0.0000 0.0000 0.0000
+#> eta.g_qlogis 0.000 0.0000 0.0000 0.0000
+#> eta.f_DMTA_tffm0_1_qlogis 0.000 0.0000 0.0000 0.0000
+#> eta.f_DMTA_tffm0_2_qlogis 0.000 0.0000 0.0000 0.0000
+#> eta.f_DMTA_tffm0_3_qlogis 0.000 0.0000 0.0000 0.0000
+#> eta.log_k1 eta.log_k2 eta.g_qlogis
+#> eta.DMTA_0 0.000 0.000 0.000
+#> eta.log_k_M23 0.000 0.000 0.000
+#> eta.log_k_M27 0.000 0.000 0.000
+#> eta.log_k_M31 0.000 0.000 0.000
+#> eta.log_k1 0.903 0.000 0.000
+#> eta.log_k2 0.000 1.577 0.000
+#> eta.g_qlogis 0.000 0.000 3.085
+#> eta.f_DMTA_tffm0_1_qlogis 0.000 0.000 0.000
+#> eta.f_DMTA_tffm0_2_qlogis 0.000 0.000 0.000
+#> eta.f_DMTA_tffm0_3_qlogis 0.000 0.000 0.000
+#> eta.f_DMTA_tffm0_1_qlogis eta.f_DMTA_tffm0_2_qlogis
+#> eta.DMTA_0 0.0 0.0
+#> eta.log_k_M23 0.0 0.0
+#> eta.log_k_M27 0.0 0.0
+#> eta.log_k_M31 0.0 0.0
+#> eta.log_k1 0.0 0.0
+#> eta.log_k2 0.0 0.0
+#> eta.g_qlogis 0.0 0.0
+#> eta.f_DMTA_tffm0_1_qlogis 0.3 0.0
+#> eta.f_DMTA_tffm0_2_qlogis 0.0 0.3
+#> eta.f_DMTA_tffm0_3_qlogis 0.0 0.0
+#> eta.f_DMTA_tffm0_3_qlogis
+#> eta.DMTA_0 0.0
+#> eta.log_k_M23 0.0
+#> eta.log_k_M27 0.0
+#> eta.log_k_M31 0.0
+#> eta.log_k1 0.0
+#> eta.log_k2 0.0
+#> eta.g_qlogis 0.0
+#> eta.f_DMTA_tffm0_1_qlogis 0.0
+#> eta.f_DMTA_tffm0_2_qlogis 0.0
+#> eta.f_DMTA_tffm0_3_qlogis 0.3
+#>
+#> Variance model:
+#> sigma_low rsd_high
+#> 0.69793 0.02577
+#>
+#> Backtransformed parameters:
+#> est. lower upper
+#> DMTA_0 98.76976 98.73563 98.80390
+#> k_M23 0.01981 0.01977 0.01985
+#> k_M27 0.01307 0.01304 0.01309
+#> k_M31 0.01430 0.01427 0.01433
+#> f_DMTA_to_M23 0.10984 NA NA
+#> f_DMTA_to_M27 0.09036 NA NA
+#> f_DMTA_to_M31 0.08399 NA NA
+#> k1 0.10709 0.10696 0.10722
+#> k2 0.02291 0.02287 0.02295
+#> g 0.61068 0.61055 0.61081
+#>
+#> Resulting formation fractions:
+#> ff
+#> DMTA_M23 0.10984
+#> DMTA_M27 0.09036
+#> DMTA_M31 0.08399
+#> DMTA_sink 0.71581
+#>
+#> Estimated disappearance times:
+#> DT50 DT90 DT50back DT50_k1 DT50_k2
+#> DMTA 10.66 59.78 18 6.473 30.26
+#> M23 34.99 116.24 NA NA NA
+#> M27 53.05 176.23 NA NA NA
+#> M31 48.48 161.05 NA NA NA
# saem has a problem with this model/data combination, maybe because of the
+# overparameterised error model, to be investigated
+#f_dmta_nlmixr_saem <- nlmixr(f_dmta_mkin_tc, est = "saem",
+# control = saemControl(print = 500))
+#summary(f_dmta_nlmixr_saem)
+#plot(f_dmta_nlmixr_saem)
+# }
+