Likelihood ratio test for mkinfit models

#> 2.5% 97.5% #> parent_0 96.456003650 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 diff --git a/docs/reference/index.html b/docs/reference/index.html index fa424060..8987db96 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -185,45 +185,39 @@ more datasets

parms()

- -

Extract model parameters from mkinfit models

- - - -

confint(<mkinfit>)

summary(<mkinfit>) print(<summary.mkinfit>)

Confidence intervals for parameters of mkinfit objects

Summary method for class "mkinfit"

summary(<mkinfit>) print(<summary.mkinfit>)

parms()

Summary method for class "mkinfit"

Extract model parameters from mkinfit models

logLik(<mkinfit>)

confint(<mkinfit>)

Calculated the log-likelihood of a fitted mkinfit object

Confidence intervals for parameters of mkinfit objects

mkinresplot()

update(<mkinfit>)

Function to plot residuals stored in an mkin object

Update an mkinfit model with different arguments

mkinparplot()

lrtest(<mkinfit>)

Function to plot the confidence intervals obtained using mkinfit

Likelihood ratio test for mkinfit models

mkinerrplot()

mkinerrmin()

Function to plot squared residuals and the error model for an mkin object

Calculate the minimum error to assume in order to pass the variance test

@@ -234,9 +228,9 @@ with mkinfit

mkinerrmin()

CAKE_export()

Calculate the minimum error to assume in order to pass the variance test

Export a list of datasets format to a CAKE study file

@@ -380,7 +374,7 @@ of an mmkin object

Helper functions

Helper functions mainly used internally

@@ -442,9 +436,33 @@ kinetic models fitted with mkinfit

CAKE_export()

logLik(<mkinfit>)

Export a list of datasets format to a CAKE study file

Calculated the log-likelihood of a fitted mkinfit object

+ + + +

residuals(<mkinfit>)

+ +

Extract residuals from an mkinfit model

+ + + +

mkinresplot()

+ +

Function to plot residuals stored in an mkin object

+ + + +

mkinparplot()

+ +

Function to plot the confidence intervals obtained using mkinfit

+ + + +

mkinerrplot()

+ +

Function to plot squared residuals and the error model for an mkin object

@@ -536,7 +554,7 @@ kinetic models fitted with mkinfit

Work with mmkin objects

Datasets and known results

NAFTA guidance

Helper functions

Helper functions mainly used internally

Analytical solutions

Generate synthetic datasets

Deprecated functions

diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index c79146a9..9a54496e 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -36,10 +36,11 @@ - + @@ -136,10 +137,11 @@ deviation predicted by the error model." />

The names of parameters that should not be optimised but -rather kept at the values specified in parms.ini.

#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:34 2019 -#> Date of summary: Fri Oct 25 02:08:34 2019 +#> Date of fit: Thu Oct 31 01:48:56 2019 +#> Date of summary: Thu Oct 31 01:48:56 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -847,7 +849,7 @@ estimators.

#> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.136 s +#> Fitted using 2289 model solutions performed in 9.124 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html new file mode 100644 index 00000000..90cbec1a --- /dev/null +++ b/docs/reference/reexports.html @@ -0,0 +1,180 @@ + + + + + + + + +Objects exported from other packages — reexports • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + +

+ +

+ + +

These objects are imported from other packages. Follow the links +below to see their documentation.

lmtest: lrtest

+ + + + +

+ +

+ + + +

+ + + + + + + + diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html new file mode 100644 index 00000000..7dd25012 --- /dev/null +++ b/docs/reference/residuals.mkinfit.html @@ -0,0 +1,196 @@ + + + + + + + + +Extract residuals from an mkinfit model — residuals.mkinfit • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + +

+ +

+ + +

Extract residuals from an mkinfit model

+ +

# S3 method for mkinfit
+residuals(object, standardized = FALSE, ...)

+ +

Arguments

+ + + + + + + + + + + + + + +

object	An `mkinfit` object
standardized	Should the residuals be standardized by dividing by the +standard deviation obtained from the fitted error model?
...	Not used

+ + +

Examples

f <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)
+residuals(f)
#> [1]  0.09726306 -0.13912135 -0.15351176  0.73388319 -0.08657030 -0.93204730
+#> [7] -0.03269102  1.45347805 -0.88423710
residuals(f, standardized = TRUE)
#> [1]  0.13969820 -0.19981894 -0.22048777  1.05407086 -0.12434027 -1.33869248
+#> [7] -0.04695387  2.08761953 -1.27002305

+ +

+ + + +

+ + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + +

+ +

+ + +

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

Helper functions

Helper functions mainly used internally

Likelihood ratio test for mkinfit models

Arguments

Details

Examples

Contents

Objects exported from other packages

Contents

Extract residuals from an mkinfit model

Arguments

Examples

Contents

Update an mkinfit model with different arguments

Arguments

Examples

Contents

object	An `mkinfit` object
object_2	Optionally, another mkinfit object fitted to the same data.
...	Argument to `mkinfit`, passed to +`update.mkinfit` for creating the alternative fitted object.