From 7091d3738e7e55acb20edb88772b228f6f5b6c98 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Oct 2019 01:55:01 +0100 Subject: Add likelihood ratio test and other methods, fixes The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added. --- docs/reference/update.mkinfit.html | 544 +++++++++++++++++++++++++++++++++++++ 1 file changed, 544 insertions(+) create mode 100644 docs/reference/update.mkinfit.html (limited to 'docs/reference/update.mkinfit.html') diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html new file mode 100644 index 00000000..b4040a1b --- /dev/null +++ b/docs/reference/update.mkinfit.html @@ -0,0 +1,544 @@ + + + + + + + + +Update an mkinfit model with different arguments — update.mkinfit • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Update an mkinfit model with different arguments

+ + +
+ +
+

This function will return an updated mkinfit object. The fitted degradation +model parameters from the old fit are used as starting values for the +updated fit. Values specified as 'parms.ini' and/or 'state.ini' will +override these starting values.

+
+ + 
# S3 method for mkinfit
+update(object, ..., evaluate = TRUE)
+ +

Arguments

+ + + + + + + + + + + + + + +
object

An mkinfit object to be updated

...

Arguments to mkinfit that should replace +the arguments from the original call. Arguments set to NULL will +remove arguments given in the original call

evaluate

Should the call be evaluated or returned as a 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 
+#>      10.314       0.000      10.320 
+#> 
+#> $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: 0x555557c557c8>
+#> <environment: 0x55555bb0e330>
+#> 
+#> $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: 0x555557c55bf0>
+#> <environment: 0x55555bb0e330>
+#> 
+#> $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] "Thu Oct 31 01:49:09 2019"
+#> 
+#> $version
+#> [1] "0.9.49.6"
+#> 
+#> $Rversion
+#> [1] "3.6.1"
+#> 
+#> attr(,"class")
+#> [1] "mkinfit" "modFit" 
# }
+
+
+ +
+ + + +
+ + + + + + + + -- cgit v1.2.1