From b5ee48a86e4b1d4c05aaadb80b44954e2e994ebc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 27 May 2020 07:12:51 +0200 Subject: Add docs generated using released version 0.9.52 --- docs/reference/nlme.mmkin.html | 79 ++++++++++++++++++++---------------------- 1 file changed, 38 insertions(+), 41 deletions(-) (limited to 'docs/reference/nlme.mmkin.html') diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 2ada9501..c0fb499d 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> mkin - 0.9.50.3 + 0.9.50.2 @@ -111,9 +111,6 @@ have been obtained by fitting the same model to a list of datasets." />
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -
  • @@ -184,7 +181,7 @@ have been obtained by fitting the same model to a list of datasets.

    data -

    Ignored, data are taken from the mmkin model

    +

    Should the data be printed?

    fixed @@ -274,19 +271,19 @@ with additional elements

    #> Log-likelihood: -307.5269 #> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> parent_0 log_k_parent_sink -#> 85.541149 -3.229596 +#> 85.540979 -3.229602 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k_parent_sink Residual -#> StdDev: 1.30857 1.288591 6.304906 +#> StdDev: 1.308245 1.288586 6.304923 #> #> Number of Observations: 90 #> Number of Groups: 5
    endpoints(f_nlme)
    #> $distimes #> DT50 DT90 -#> parent 17.51545 58.18505 +#> parent 17.51556 58.18543 #>
    # \dontrun{ f_nlme_2 <- nlme(f, start = c(parent_0 = 100, log_k_parent_sink = 0.1)) update(f_nlme_2, random = parent_0 ~ 1)
    #> Nonlinear mixed-effects model fit by maximum likelihood @@ -300,7 +297,7 @@ with additional elements

    #> Random effects: #> Formula: parent_0 ~ 1 | ds #> parent_0 Residual -#> StdDev: 0.002416792 21.63027 +#> StdDev: 0.002416802 21.63027 #> #> Number of Observations: 90 #> Number of Groups: 5
    # Test on some real data @@ -332,88 +329,88 @@ with additional elements

    f_nlme_fomc_sfo <- nlme(f_2["FOMC-SFO", ], control = list(pnlsMaxIter = 100, tolerance = 1e-4), verbose = TRUE)
    #> #> **Iteration 1 -#> LME step: Loglik: -394.1603, nlminb iterations: 3 +#> LME step: Loglik: -394.1603, nlminb iterations: 2 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.2079793 0.8563830 1.7454105 1.0917354 1.2756825 +#> -0.2079863 0.8563823 1.7454253 1.0917707 1.2756955 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.8803 -#> fixed effects: 94.17379 -5.473193 -0.6970236 -0.2025091 2.103883 +#> PNLS step: RSS = 643.8814 +#> fixed effects: 94.17379 -5.473189 -0.6970234 -0.202509 2.103883 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 0.7960134 0.1447728 +#> 0.7959873 0.1447512 #> #> **Iteration 2 #> LME step: Loglik: -396.3824, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -1.712404e-01 -2.432655e-05 1.842120e+00 1.073975e+00 1.322925e+00 +#> -1.712406e-01 -2.278541e-05 1.842120e+00 1.073975e+00 1.322924e+00 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.8035 -#> fixed effects: 94.17385 -5.473487 -0.6970404 -0.2025137 2.103871 +#> PNLS step: RSS = 643.8025 +#> fixed effects: 94.17385 -5.473491 -0.6970406 -0.2025139 2.103871 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): -#> fixed reStruct -#> 5.382757e-05 1.236667e-03 +#> fixed reStruct +#> 5.51758e-05 1.26861e-03 #> #> **Iteration 3 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.1712499044 -0.0001499831 1.8420971364 1.0739799123 1.3229167796 +#> -0.1712500923 -0.0001515734 1.8420972550 1.0739796967 1.3229177241 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.7948 -#> fixed effects: 94.17386 -5.473521 -0.6970422 -0.2025144 2.10387 +#> PNLS step: RSS = 643.7941 +#> fixed effects: 94.17386 -5.473523 -0.6970424 -0.2025146 2.103869 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 6.072817e-06 1.400857e-04 +#> 5.792621e-06 1.335434e-04 #> #> **Iteration 4 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.1712529502 -0.0001641277 1.8420957542 1.0739797181 1.3229173076 +#> -0.1712517206 -0.0001651603 1.8420950864 1.0739800294 1.3229173529 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.7936 -#> fixed effects: 94.17386 -5.473526 -0.6970426 -0.2025146 2.103869 +#> PNLS step: RSS = 643.7949 +#> fixed effects: 94.17386 -5.473521 -0.6970423 -0.2025145 2.10387 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 1.027451e-06 2.275704e-05
    f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ], +#> 4.025781e-07 9.628656e-06
    f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ], control = list(pnlsMaxIter = 120, tolerance = 5e-4), verbose = TRUE)
    #> #> **Iteration 1 -#> LME step: Loglik: -404.9582, nlminb iterations: 1 +#> LME step: Loglik: -404.9583, nlminb iterations: 1 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.4114355 0.9798697 1.6990037 0.7293315 0.3354323 1.7113046 +#> -0.4114357 0.9798641 1.6990035 0.7293314 0.3354323 1.7113047 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3644 -#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.05532828 +#> PNLS step: RSS = 630.3642 +#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.0553284 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 0.7885368 0.5822683 +#> 0.7879730 0.5822574 #> #> **Iteration 2 #> LME step: Loglik: -407.7755, nlminb iterations: 11 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371224133 0.003056179 1.789939402 0.724671158 0.301602977 1.754200729 +#> -0.371224105 0.003056163 1.789939431 0.724671132 0.301602942 1.754200482 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3633 -#> fixed effects: 93.82269 -5.455992 -0.6788958 -1.862196 -4.199671 0.05532831 +#> PNLS step: RSS = 630.364 +#> fixed effects: 93.82269 -5.455991 -0.6788958 -1.862196 -4.199671 0.05532834 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 4.789774e-07 2.200661e-05
    plot(f_2["FOMC-SFO", 3:4])
    plot(f_nlme_fomc_sfo, 3:4)
    +#> 9.814652e-07 1.059239e-05
    plot(f_2["FOMC-SFO", 3:4])
    plot(f_nlme_fomc_sfo, 3:4)
    plot(f_2["DFOP-SFO", 3:4])
    plot(f_nlme_dfop_sfo, 3:4)
    anova(f_nlme_dfop_sfo, f_nlme_fomc_sfo, f_nlme_sfo_sfo)
    #> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273 -#> f_nlme_fomc_sfo 2 11 818.5149 853.0087 -398.2575 1 vs 2 21.33975 <.0001 -#> f_nlme_sfo_sfo 3 9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716 <.0001
    anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo) # if we ignore FOMC
    #> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273 +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 +#> f_nlme_fomc_sfo 2 11 818.5151 853.0089 -398.2576 1 vs 2 21.33957 <.0001 +#> f_nlme_sfo_sfo 3 9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66697 <.0001
    anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo) # if we ignore FOMC
    #> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 #> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001
    endpoints(f_nlme_sfo_sfo)
    #> $ff #> parent_sink parent_A1 A1_sink @@ -430,7 +427,7 @@ with additional elements

    #> $distimes #> DT50 DT90 DT50_k1 DT50_k2 #> parent 11.07091 104.6320 4.462384 46.20825 -#> A1 162.30536 539.1667 NA NA +#> A1 162.30518 539.1661 NA NA #>
    # }
    -- cgit v1.2.1