From ce73c044b949154e3bc3e715b9b79e1360b3f794 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 1 Nov 2019 15:34:28 +0100 Subject: Make the 'quadratic' the default for 'confint' Also the documentation was improved here and there --- docs/reference/update.mkinfit.html | 350 +------------------------------------ 1 file changed, 6 insertions(+), 344 deletions(-) (limited to 'docs/reference/update.mkinfit.html') diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index b9f6f9a9..bb93a61e 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -72,7 +72,7 @@ override these starting values." /> mkin - 0.9.49.6 + 0.9.49.8 @@ -167,349 +167,11 @@ remove arguments given in the original call

Examples

# \dontrun{
-fit <- mkinfit("DFOP", subset(FOCUS_2006_D, value != 0), quiet = TRUE)
-update(fit, error_model = "tc")
#> $par
-#>     parent_0       log_k1       log_k2        g_ilr    sigma_low     rsd_high 
-#> 100.85489822   8.84468217  -2.29693632 -14.95263998   0.00375222   0.06763435 
-#> 
-#> $objective
-#> [1] 19.40656
-#> 
-#> $convergence
-#> [1] 0
-#> 
-#> $iterations
-#> [1] 120
-#> 
-#> $evaluations
-#> function gradient 
-#>      144      847 
-#> 
-#> $message
-#> [1] "relative convergence (4)"
-#> 
-#> $logLik
-#> [1] -19.40656
-#> 
-#> $d_3_message
-#>                                                            threestep 
-#> "Three-step fitting yielded a higher likelihood than direct fitting" 
-#> 
-#> $hessian
-#>                parent_0        log_k1        log_k2         g_ilr     sigma_low
-#> parent_0   3.662473e-01 -2.914408e-16 -7.241561e+01 -3.021629e-08  1.923504e+01
-#> log_k1    -2.914408e-16  0.000000e+00 -2.215935e-13 -7.291307e-25  3.416474e-15
-#> log_k2    -7.241561e+01 -2.215935e-13  3.127457e+04  6.766544e-06 -1.495826e+04
-#> g_ilr     -3.021629e-08 -7.291307e-25  6.766544e-06  3.122099e-09 -1.797429e-06
-#> sigma_low  1.923504e+01  3.416474e-15 -1.495826e+04 -1.797429e-06  7.759299e+04
-#> rsd_high   3.902119e+00 -1.801019e-16 -1.685343e+02 -3.750713e-07  3.984179e+03
-#>                rsd_high
-#> parent_0   3.902119e+00
-#> log_k1    -1.801019e-16
-#> log_k2    -1.685343e+02
-#> g_ilr     -3.750713e-07
-#> sigma_low  3.984179e+03
-#> rsd_high   7.188991e+03
-#> 
-#> $hessian_notrans
-#>                parent_0            k1            k2             g     sigma_low
-#> parent_0   3.662473e-01 -3.714445e-19 -7.201669e+02 -3.261485e+01  1.923504e+01
-#> k1        -3.714445e-19  0.000000e+00 -4.258512e-15  7.218123e-21  4.355854e-18
-#> k2        -7.201669e+02 -4.258512e-15  3.092510e+06  7.263235e+04 -1.456870e+05
-#> g         -3.261485e+01  7.218123e-21  7.263235e+04  3.291750e+03 -1.939948e+03
-#> sigma_low  1.923504e+01  4.355854e-18 -1.456870e+05 -1.939948e+03  7.759299e+04
-#> rsd_high   3.902119e+00 -2.259812e-19 -1.779680e+03 -4.048658e+02  3.984179e+03
-#>                rsd_high
-#> parent_0   3.902119e+00
-#> k1        -2.259812e-19
-#> k2        -1.779680e+03
-#> g         -4.048658e+02
-#> sigma_low  3.984179e+03
-#> rsd_high   7.188991e+03
-#> 
-#> $call
-#> mkinfit(mkinmod = "DFOP", observed = subset(FOCUS_2006_D, value != 
-#>     0), parms.ini = c(k1 = 0.699298911979803, k2 = 0.0899931270871125, 
-#> g = 0.0923391681138686), state.ini = c(parent = 101.948852047129), 
-#>     quiet = TRUE, error_model = "tc")
-#> 
-#> $error_model_algorithm
-#> [1] "d_3"
-#> 
-#> $solution_type
-#> [1] "analytical"
-#> 
-#> $transform_rates
-#> [1] TRUE
-#> 
-#> $transform_fractions
-#> [1] TRUE
-#> 
-#> $reweight.tol
-#> [1] 1e-08
-#> 
-#> $reweight.max.iter
-#> [1] 10
-#> 
-#> $control
-#> $control$eval.max
-#> [1] 300
-#> 
-#> $control$iter.max
-#> [1] 200
-#> 
-#> 
-#> $calls
-#> [1] 3105
-#> 
-#> $time
-#>        User      System verstrichen 
-#>      10.251       0.000      10.257 
-#> 
-#> $mkinmod
-#> <mkinmod> model generated with
-#> Use of formation fractions $use_of_ff: min 
-#> Specification $spec:
-#> $parent
-#> $type: DFOP; $sink: TRUE
-#> Differential equations:
-#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
-#>            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
-#>            * parent
-#> 
-#> $observed
-#>      name time  value
-#> 1  parent    0  99.46
-#> 2  parent    0 102.04
-#> 3  parent    1  93.50
-#> 4  parent    1  92.50
-#> 5  parent    3  63.23
-#> 6  parent    3  68.99
-#> 7  parent    7  52.32
-#> 8  parent    7  55.13
-#> 9  parent   14  27.27
-#> 10 parent   14  26.64
-#> 11 parent   21  11.50
-#> 12 parent   21  11.64
-#> 13 parent   35   2.85
-#> 14 parent   35   2.91
-#> 15 parent   50   0.69
-#> 16 parent   50   0.63
-#> 17 parent   75   0.05
-#> 18 parent   75   0.06
-#> 
-#> $obs_vars
-#> [1] "parent"
-#> 
-#> $predicted
-#>       name       time        value
-#> 1   parent  0.0000000 100.85489822
-#> 2   parent  0.7575758  93.45650191
-#> 3   parent  1.0000000  91.20560523
-#> 4   parent  1.5151515  86.60082860
-#> 5   parent  2.2727273  80.24806580
-#> 6   parent  3.0000000  74.58828105
-#> 7   parent  3.0303030  74.36132158
-#> 8   parent  3.7878788  68.90641029
-#> 9   parent  4.5454545  63.85165403
-#> 10  parent  5.3030303  59.16769870
-#> 11  parent  6.0606061  54.82734352
-#> 12  parent  6.8181818  50.80538306
-#> 13  parent  7.0000000  49.88485755
-#> 14  parent  7.5757576  47.07846089
-#> 15  parent  8.3333333  43.62493394
-#> 16  parent  9.0909091  40.42474681
-#> 17  parent  9.8484848  37.45931528
-#> 18  parent 10.6060606  34.71141842
-#> 19  parent 11.3636364  32.16509858
-#> 20  parent 12.1212121  29.80556871
-#> 21  parent 12.8787879  27.61912649
-#> 22  parent 13.6363636  25.59307475
-#> 23  parent 14.0000000  24.67405211
-#> 24  parent 14.3939394  23.71564776
-#> 25  parent 15.1515152  21.97594287
-#> 26  parent 15.9090909  20.36385722
-#> 27  parent 16.6666667  18.87002909
-#> 28  parent 17.4242424  17.48578345
-#> 29  parent 18.1818182  16.20308170
-#> 30  parent 18.9393939  15.01447489
-#> 31  parent 19.6969697  13.91306051
-#> 32  parent 20.4545455  12.89244241
-#> 33  parent 21.0000000  12.20428157
-#> 34  parent 21.2121212  11.94669362
-#> 35  parent 21.9696970  11.07032198
-#> 36  parent 22.7272727  10.25823818
-#> 37  parent 23.4848485   9.50572628
-#> 38  parent 24.2424242   8.80841627
-#> 39  parent 25.0000000   8.16225872
-#> 40  parent 25.7575758   7.56350125
-#> 41  parent 26.5151515   7.00866672
-#> 42  parent 27.2727273   6.49453311
-#> 43  parent 28.0303030   6.01811471
-#> 44  parent 28.7878788   5.57664485
-#> 45  parent 29.5454545   5.16755983
-#> 46  parent 30.3030303   4.78848399
-#> 47  parent 31.0606061   4.43721595
-#> 48  parent 31.8181818   4.11171583
-#> 49  parent 32.5757576   3.81009336
-#> 50  parent 33.3333333   3.53059697
-#> 51  parent 34.0909091   3.27160354
-#> 52  parent 34.8484848   3.03160906
-#> 53  parent 35.0000000   2.98576554
-#> 54  parent 35.6060606   2.80921981
-#> 55  parent 36.3636364   2.60314433
-#> 56  parent 37.1212121   2.41218590
-#> 57  parent 37.8787879   2.23523557
-#> 58  parent 38.6363636   2.07126576
-#> 59  parent 39.3939394   1.91932426
-#> 60  parent 40.1515152   1.77852870
-#> 61  parent 40.9090909   1.64806147
-#> 62  parent 41.6666667   1.52716489
-#> 63  parent 42.4242424   1.41513691
-#> 64  parent 43.1818182   1.31132694
-#> 65  parent 43.9393939   1.21513214
-#> 66  parent 44.6969697   1.12599389
-#> 67  parent 45.4545455   1.04339454
-#> 68  parent 46.2121212   0.96685442
-#> 69  parent 46.9696970   0.89592904
-#> 70  parent 47.7272727   0.83020652
-#> 71  parent 48.4848485   0.76930520
-#> 72  parent 49.2424242   0.71287140
-#> 73  parent 50.0000000   0.66057741
-#> 74  parent 50.7575758   0.61211954
-#> 75  parent 51.5151515   0.56721639
-#> 76  parent 52.2727273   0.52560719
-#> 77  parent 53.0303030   0.48705031
-#> 78  parent 53.7878788   0.45132184
-#> 79  parent 54.5454545   0.41821430
-#> 80  parent 55.3030303   0.38753542
-#> 81  parent 56.0606061   0.35910705
-#> 82  parent 56.8181818   0.33276409
-#> 83  parent 57.5757576   0.30835357
-#> 84  parent 58.3333333   0.28573373
-#> 85  parent 59.0909091   0.26477320
-#> 86  parent 59.8484848   0.24535028
-#> 87  parent 60.6060606   0.22735216
-#> 88  parent 61.3636364   0.21067432
-#> 89  parent 62.1212121   0.19521992
-#> 90  parent 62.8787879   0.18089921
-#> 91  parent 63.6363636   0.16762901
-#> 92  parent 64.3939394   0.15533228
-#> 93  parent 65.1515152   0.14393759
-#> 94  parent 65.9090909   0.13337879
-#> 95  parent 66.6666667   0.12359454
-#> 96  parent 67.4242424   0.11452804
-#> 97  parent 68.1818182   0.10612662
-#> 98  parent 68.9393939   0.09834151
-#> 99  parent 69.6969697   0.09112749
-#> 100 parent 70.4545455   0.08444266
-#> 101 parent 71.2121212   0.07824822
-#> 102 parent 71.9696970   0.07250818
-#> 103 parent 72.7272727   0.06718920
-#> 104 parent 73.4848485   0.06226042
-#> 105 parent 74.2424242   0.05769319
-#> 106 parent 75.0000000   0.05346100
-#> 
-#> $rss
-#> function (P) 
-#> cost_function(P, OLS = TRUE, update_data = FALSE)
-#> <bytecode: 0x555558e48258>
-#> <environment: 0x55555caa08e0>
-#> 
-#> $ll
-#> function (P, fixed_degparms = FALSE, fixed_errparms = FALSE) 
-#> {
-#>     -cost_function(P, trans = FALSE, fixed_degparms = fixed_degparms, 
-#>         fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE)
-#> }
-#> <bytecode: 0x555558e47e30>
-#> <environment: 0x55555caa08e0>
-#> 
-#> $start
-#>                  value   type
-#> parent_0  101.94885205  state
-#> k1          0.69929891 deparm
-#> k2          0.08999313 deparm
-#> g           0.09233917 deparm
-#> sigma_low   0.10000000  error
-#> rsd_high    0.10000000  error
-#> 
-#> $start_transformed
-#>                value lower upper
-#> parent_0  101.948852  -Inf   Inf
-#> log_k1     -0.357677  -Inf   Inf
-#> log_k2     -2.408022  -Inf   Inf
-#> g_ilr      -1.616024  -Inf   Inf
-#> sigma_low   0.100000     0   Inf
-#> rsd_high    0.100000     0   Inf
-#> 
-#> $fixed
-#> [1] value type 
-#> <0 Zeilen> (oder row.names mit Länge 0)
-#> 
-#> $data
-#>    time variable observed   predicted     residual
-#> 1     0   parent    99.46 100.8548982  -1.39489822
-#> 2     0   parent   102.04 100.8548982   1.18510178
-#> 3     1   parent    93.50  91.2056052   2.29439477
-#> 4     1   parent    92.50  91.2056052   1.29439477
-#> 5     3   parent    63.23  74.5882810 -11.35828105
-#> 6     3   parent    68.99  74.5882810  -5.59828105
-#> 7     7   parent    52.32  49.8848576   2.43514245
-#> 8     7   parent    55.13  49.8848576   5.24514245
-#> 9    14   parent    27.27  24.6740521   2.59594789
-#> 10   14   parent    26.64  24.6740521   1.96594789
-#> 11   21   parent    11.50  12.2042816  -0.70428157
-#> 12   21   parent    11.64  12.2042816  -0.56428157
-#> 13   35   parent     2.85   2.9857655  -0.13576554
-#> 14   35   parent     2.91   2.9857655  -0.07576554
-#> 15   50   parent     0.69   0.6605774   0.02942259
-#> 16   50   parent     0.63   0.6605774  -0.03057741
-#> 17   75   parent     0.05   0.0534610  -0.00346100
-#> 18   75   parent     0.06   0.0534610   0.00653900
-#> 
-#> $atol
-#> [1] 1e-08
-#> 
-#> $rtol
-#> [1] 1e-10
-#> 
-#> $err_mod
-#> [1] "tc"
-#> 
-#> $bparms.optim
-#>     parent_0           k1           k2            g 
-#> 1.008549e+02 6.937399e+03 1.005665e-01 6.551046e-10 
-#> 
-#> $bparms.fixed
-#> numeric(0)
-#> 
-#> $bparms.ode
-#>           k1           k2            g 
-#> 6.937399e+03 1.005665e-01 6.551046e-10 
-#> 
-#> $bparms.state
-#>   parent 
-#> 100.8549 
-#> 
-#> $errparms
-#>  sigma_low   rsd_high 
-#> 0.00375222 0.06763435 
-#> 
-#> $df.residual
-#> [1] 12
-#> 
-#> $date
-#> [1] "Fri Nov  1 10:10:42 2019"
-#> 
-#> $version
-#> [1] "0.9.49.6"
-#> 
-#> $Rversion
-#> [1] "3.6.1"
-#> 
-#> attr(,"class")
-#> [1] "mkinfit" "modFit" 
# }
+fit <- mkinfit("SFO", subset(FOCUS_2006_D, value != 0), quiet = TRUE)
+parms(fit)
#>      parent_0 k_parent_sink         sigma 
+#>   99.44423886    0.09793574    3.39632469 
plot_err(fit)
fit_2 <- update(fit, error_model = "tc")
+parms(fit_2)
#>      parent_0 k_parent_sink     sigma_low      rsd_high 
+#>  1.008549e+02  1.005665e-01  3.752222e-03  6.763434e-02 
plot_err(fit_2)
# }