From 9ac853c7ceece333099021974025d07e75be2b33 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 12 May 2020 08:07:07 +0200 Subject: Documentation improvements, rebuild static docs --- docs/reference/nlme.mmkin.html | 152 +++++++++++++++++++---------------------- 1 file changed, 71 insertions(+), 81 deletions(-) (limited to 'docs/reference/nlme.mmkin.html') diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 33cc9164..4e5a86cb 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -57,7 +60,7 @@ have been obtained by fitting the same model to a list of datasets." /> - +
@@ -115,7 +118,12 @@ have been obtained by fitting the same model to a list of datasets." />
@@ -130,7 +138,7 @@ have been obtained by fitting the same model to a list of datasets." />

Create an nlme model for an mmkin row object

- + Source: R/nlme.mmkin.R
@@ -243,7 +251,7 @@ parameters taken from the mmkin object are used

Value

Upon success, a fitted nlme.mmkin object, which is an nlme object - with additional elements

+with additional elements

See also

nlme_function

@@ -309,142 +317,124 @@ parameters taken from the mmkin object are used

"FOMC-SFO" = m_fomc_sfo, "DFOP-SFO" = m_dfop_sfo), ds_2, quiet = TRUE) - plot(f_2["SFO-SFO", 3:4]) # Separate fits for datasets 3 and 4
+ plot(f_2["SFO-SFO", 3:4]) # Separate fits for datasets 3 and 4
f_nlme_sfo_sfo <- nlme(f_2["SFO-SFO", ]) # plot(f_nlme_sfo_sfo) # not feasible with pkgdown figures - plot(f_nlme_sfo_sfo, 3:4) # Global mixed model: Fits for datasets 3 and 4
+ plot(f_nlme_sfo_sfo, 3:4) # Global mixed model: Fits for datasets 3 and 4
# With formation fractions f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ]) - plot(f_nlme_sfo_sfo_ff, 3:4) # chi2 different due to different df attribution
+ plot(f_nlme_sfo_sfo_ff, 3:4) # chi2 different due to different df attribution
# For more parameters, we need to increase pnlsMaxIter and the tolerance # to get convergence 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: 2 +#> LME step: Loglik: -394.1603, nlminb iterations: 3 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.2079984 0.8563873 1.7454146 1.0917723 1.2756924 +#> -0.2079793 0.8563830 1.7454105 1.0917354 1.2756825 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.8786 -#> fixed effects: 94.17379 -5.473199 -0.6970239 -0.2025094 2.103883 +#> PNLS step: RSS = 643.8803 +#> fixed effects: 94.17379 -5.473193 -0.6970236 -0.2025091 2.103883 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 0.7865373 0.1448077 +#> 0.7960134 0.1447728 #> #> **Iteration 2 #> LME step: Loglik: -396.3824, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -1.712408e-01 -2.680989e-05 1.842119e+00 1.073975e+00 1.322924e+00 +#> -1.712404e-01 -2.432655e-05 1.842120e+00 1.073975e+00 1.322925e+00 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.8022 -#> fixed effects: 94.17385 -5.473491 -0.6970405 -0.202514 2.103871 +#> PNLS step: RSS = 643.8035 +#> fixed effects: 94.17385 -5.473487 -0.6970404 -0.2025137 2.103871 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 5.341904e-05 1.227073e-03 +#> 5.382757e-05 1.236667e-03 #> #> **Iteration 3 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.1712484347 -0.0001513555 1.8420964843 1.0739800649 1.3229176990 +#> -0.1712499044 -0.0001499831 1.8420971364 1.0739799123 1.3229167796 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.7947 -#> fixed effects: 94.17386 -5.473522 -0.6970423 -0.2025142 2.10387 +#> PNLS step: RSS = 643.7948 +#> fixed effects: 94.17386 -5.473521 -0.6970422 -0.2025144 2.10387 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 5.568186e-06 1.276609e-04 +#> 6.072817e-06 1.400857e-04 #> #> **Iteration 4 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 -#> -0.171251200 -0.000164506 1.842095097 1.073980200 1.322916184 +#> ds1 ds2 ds3 ds4 ds5 +#> -0.1712529502 -0.0001641277 1.8420957542 1.0739797181 1.3229173076 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.7934 +#> PNLS step: RSS = 643.7936 #> fixed effects: 94.17386 -5.473526 -0.6970426 -0.2025146 2.103869 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 2.332100e-06 1.979007e-05
f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ], +#> 1.027451e-06 2.275704e-05
f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ], control = list(pnlsMaxIter = 120, tolerance = 5e-4), verbose = TRUE)
#> #> **Iteration 1 -#> LME step: Loglik: -404.9591, nlminb iterations: 1 +#> LME step: Loglik: -404.9582, nlminb iterations: 1 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.4114594 0.9798456 1.6990016 0.7293119 0.3353829 1.7112922 +#> -0.4114355 0.9798697 1.6990037 0.7293315 0.3354323 1.7113046 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.391 -#> fixed effects: 93.82265 -5.455841 -0.6788837 -1.862191 -4.199654 0.05531046 +#> PNLS step: RSS = 630.3644 +#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.05532828 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 0.7872619 0.5811683 +#> 0.7885368 0.5822683 #> #> **Iteration 2 #> LME step: Loglik: -407.7755, nlminb iterations: 11 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371222832 0.003084754 1.789952290 0.724634064 0.301559136 1.754244638 -#> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.359 -#> fixed effects: 93.82269 -5.456014 -0.6788967 -1.862202 -4.199678 0.05534118 -#> iterations: 120 -#> Convergence crit. (must all become <= tolerance = 0.0005): -#> fixed reStruct -#> 0.0005550885 0.0007749418 -#> -#> **Iteration 3 -#> LME step: Loglik: -407.7756, nlminb iterations: 11 -#> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371217033 0.003064156 1.789935045 0.724683005 0.301622307 1.754234135 +#> -0.371224133 0.003056179 1.789939402 0.724671158 0.301602977 1.754200729 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.358 -#> fixed effects: 93.82269 -5.456017 -0.6788969 -1.862197 -4.199677 0.05532978 +#> PNLS step: RSS = 630.3633 +#> fixed effects: 93.82269 -5.455992 -0.6788958 -1.862196 -4.199671 0.05532831 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 2.059533e-04 4.860085e-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)
+#> 4.789774e-07 2.200661e-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 13 843.8541 884.6194 -408.9270 -#> f_nlme_fomc_sfo 2 11 818.5149 853.0087 -398.2575 1 vs 2 21.33913 <.0001 -#> f_nlme_sfo_sfo 3 9 1085.1821 1113.4042 -533.5910 2 vs 3 270.66712 <.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 13 843.8541 884.6194 -408.927 -#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4042 -533.591 1 vs 2 249.328 <.0001
+#> 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_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 -#> 0.5912435 0.4087565 1.0000000 +#> 0.5912432 0.4087568 1.0000000 #> #> $distimes -#> DT50 DT90 -#> parent 19.13517 63.56565 -#> A1 66.02149 219.31865 +#> DT50 DT90 +#> parent 19.13518 63.5657 +#> A1 66.02155 219.3189 #>
endpoints(f_nlme_dfop_sfo)
#> $ff -#> parent_A1 parent_sink A1_sink -#> 0.2768571 0.7231429 1.0000000 +#> parent_A1 parent_sink +#> 0.2768574 0.7231426 #> #> $distimes -#> DT50 DT90 DT50_k1 DT50_k2 -#> parent 11.07092 104.6325 4.462389 46.2085 -#> A1 162.30937 539.1801 NA NA +#> DT50 DT90 DT50_k1 DT50_k2 +#> parent 11.07091 104.6320 4.462384 46.20825 +#> A1 162.30536 539.1667 NA NA #>
# }
- @@ -455,7 +445,7 @@ parameters taken from the mmkin object are used

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

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