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Diffstat (limited to 'docs/dev/reference/nlme.mmkin.html')
| -rw-r--r-- | docs/dev/reference/nlme.mmkin.html | 97 |
1 files changed, 48 insertions, 49 deletions
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index c7db9c23..16df54af 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -262,45 +262,44 @@ with additional elements</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>)) -<span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>) -<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>) +<span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0195</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.011</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>) <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f</span><span class='kw'>[[</span><span class='fl'>1</span>]])</div><div class='output co'>#> $distimes #> DT50 DT90 #> parent 11.96183 39.73634 #> </div><div class='input'><span class='no'>f_nlme</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>) <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood -#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink) +#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent) #> Data: "Not shown" #> Log-likelihood: -307.5269 -#> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) -#> parent_0 log_k_parent_sink -#> 85.540979 -3.229602 +#> Fixed: list(parent_0 ~ 1, log_k_parent ~ 1) +#> parent_0 log_k_parent +#> 85.541149 -3.229596 #> #> Random effects: -#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) +#> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k_parent_sink Residual -#> StdDev: 1.308245 1.288586 6.304923 +#> parent_0 log_k_parent Residual +#> StdDev: 1.30857 1.288591 6.304906 #> #> Number of Observations: 90 #> Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#> $distimes #> DT50 DT90 -#> parent 17.51556 58.18543 +#> parent 17.51545 58.18505 #> </div><div class='input'><span class='co'># \dontrun{</span> <span class='no'>f_nlme_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)) <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood -#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink) +#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent) #> Data: "Not shown" #> Log-likelihood: -404.3729 -#> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) -#> parent_0 log_k_parent_sink -#> 75.933480 -3.555983 +#> Fixed: list(parent_0 ~ 1, log_k_parent ~ 1) +#> parent_0 log_k_parent +#> 75.933480 -3.555983 #> #> Random effects: #> Formula: parent_0 ~ 1 | ds #> parent_0 Residual -#> StdDev: 0.002416802 21.63027 +#> StdDev: 0.002416792 21.63027 #> #> Number of Observations: 90 #> Number of Groups: 5 </div><div class='input'> <span class='co'># Test on some real data</span> @@ -332,88 +331,88 @@ with additional elements</p> <span class='no'>f_nlme_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ], <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> #> **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 -#> -0.2079863 0.8563823 1.7454253 1.0917707 1.2756955 +#> -0.2079793 0.8563830 1.7454105 1.0917354 1.2756825 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.8814 -#> fixed effects: 94.17379 -5.473189 -0.6970234 -0.202509 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 -#> 0.7959873 0.1447512 +#> 0.7960134 0.1447728 #> #> **Iteration 2 #> LME step: Loglik: -396.3824, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -1.712406e-01 -2.278541e-05 1.842120e+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 = 643.8025 -#> fixed effects: 94.17385 -5.473491 -0.6970406 -0.2025139 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 -#> 5.51758e-05 1.26861e-03 +#> fixed reStruct +#> 5.382757e-05 1.236667e-03 #> #> **Iteration 3 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.1712500923 -0.0001515734 1.8420972550 1.0739796967 1.3229177241 +#> -0.1712499044 -0.0001499831 1.8420971364 1.0739799123 1.3229167796 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.7941 -#> fixed effects: 94.17386 -5.473523 -0.6970424 -0.2025146 2.103869 +#> 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 -#> 5.792621e-06 1.335434e-04 +#> 6.072817e-06 1.400857e-04 #> #> **Iteration 4 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.1712517206 -0.0001651603 1.8420950864 1.0739800294 1.3229173529 +#> -0.1712529502 -0.0001641277 1.8420957542 1.0739797181 1.3229173076 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.7949 -#> fixed effects: 94.17386 -5.473521 -0.6970423 -0.2025145 2.10387 +#> 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 -#> 4.025781e-07 9.628656e-06 </div><div class='input'> <span class='no'>f_nlme_dfop_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ], +#> 1.027451e-06 2.275704e-05 </div><div class='input'> <span class='no'>f_nlme_dfop_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ], <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>120</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>5e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> #> **Iteration 1 -#> LME step: Loglik: -404.9583, nlminb iterations: 1 +#> LME step: Loglik: -404.9582, nlminb iterations: 1 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.4114357 0.9798641 1.6990035 0.7293314 0.3354323 1.7113047 +#> -0.4114355 0.9798697 1.6990037 0.7293315 0.3354323 1.7113046 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3642 -#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.0553284 +#> 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 -#> 0.7879730 0.5822574 +#> 0.7885368 0.5822683 #> #> **Iteration 2 #> LME step: Loglik: -407.7755, nlminb iterations: 11 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371224105 0.003056163 1.789939431 0.724671132 0.301602942 1.754200482 +#> -0.371224133 0.003056179 1.789939402 0.724671158 0.301602977 1.754200729 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.364 -#> fixed effects: 93.82269 -5.455991 -0.6788958 -1.862196 -4.199671 0.05532834 +#> 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 -#> 9.814652e-07 1.059239e-05 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> +#> 4.789774e-07 2.200661e-05 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> 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</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 +#> 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</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#> 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</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> $ff #> parent_sink parent_A1 A1_sink @@ -428,9 +427,9 @@ with additional elements</p> #> 0.2768574 0.7231426 #> #> $distimes -#> DT50 DT90 DT50_k1 DT50_k2 -#> parent 11.07091 104.6320 4.462384 46.20825 -#> A1 162.30518 539.1661 NA NA +#> DT50 DT90 DT50back DT50_k1 DT50_k2 +#> parent 11.07091 104.6320 31.49738 4.462384 46.20825 +#> A1 162.30536 539.1667 NA NA NA #> </div><div class='input'># } </div></pre> </div> |