From 7c62da1269e8910a210ba1917d4dc62d186d5606 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Oct 2016 09:40:35 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/Extract.mmkin.html | 1199 ----------------------------------------------- 1 file changed, 1199 deletions(-) delete mode 100644 docs/Extract.mmkin.html (limited to 'docs/Extract.mmkin.html') diff --git a/docs/Extract.mmkin.html b/docs/Extract.mmkin.html deleted file mode 100644 index b4686a6c..00000000 --- a/docs/Extract.mmkin.html +++ /dev/null @@ -1,1199 +0,0 @@ - - - - -[.mmkin. mkin 0.9.44.9000 - - - - - - - - - - - - - - - -
-
-
- mkin 0.9.44.9000 -
- -
-
-
-
- - -
-
- -
- -

Subsetting method for mmkin objects

- -
-
-

Usage

- 
# S3 method for mmkin
-[(x, i, j, ..., drop = FALSE)
- -

Arguments

-
-
x
-
An mmkin object
-
i
-
Row index selecting the fits for specific models
-
j
-
Column index selecting the fits to specific datasets
-
...
-
Not used, only there to satisfy the generic method definition
-
drop
-
If FALSE, the method always returns an mmkin object, otherwise either - a list of mkinfit objects or a single mkinfit object.
-
- -
-

Description

- -

Subsetting method for mmkin objects.

- -
- -
-

Value

- -

- An object of class mmkin. -

- -
- -

Examples

- 
  # Only use one core, to pass R CMD check --as-cran
-  fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
-                cores = 1, quiet = TRUE)
-  fits["FOMC", ]

-
      dataset
-model  B       C      
-  FOMC List,42 List,42
-attr(,"class")
-[1] "mmkin"
-

-
  fits[, "B"]

-
      dataset
-model  B      
-  SFO  List,42
-  FOMC List,42
-attr(,"class")
-[1] "mmkin"
-

-
  fits[, "B", drop = TRUE]$FOMC

-
$par
- parent_0 log_alpha  log_beta 
-99.666193  2.549849  5.050586 
-
-$ssr
-[1] 28.58291
-
-$convergence
-[1] 0
-
-$iterations
-[1] 21
-
-$evaluations
-function gradient 
-      25       78 
-
-$counts
-[1] "both X-convergence and relative convergence (5)"
-
-$hessian
-            parent_0   log_alpha    log_beta
-parent_0    4.123033   -95.69983    93.17699
-log_alpha -95.699832  6618.85833 -6352.46648
-log_beta   93.176993 -6352.46648  6101.23483
-
-$residuals
-      parent       parent       parent       parent       parent       parent 
- 1.046192647 -3.322396479  3.655156669 -1.705316770  0.406306255 -0.123734689 
-      parent       parent 
--0.036886982 -0.006240458 
-
-$ms
-[1] 3.572863
-
-$var_ms
-  parent 
-3.572863 
-
-$var_ms_unscaled
-  parent 
-3.572863 
-
-$var_ms_unweighted
-  parent 
-3.572863 
-
-$rank
-[1] 3
-
-$df.residual
-[1] 5
-
-$solution_type
-[1] "analytical"
-
-$transform_rates
-[1] TRUE
-
-$transform_fractions
-[1] TRUE
-
-$method.modFit
-[1] "Port"
-
-$maxit.modFit
-[1] "auto"
-
-$calls
-[1] 111
-
-$time
-   user  system elapsed 
-  0.276   0.000   0.277 
-
-$mkinmod
-<mkinmod> model generated with
-Use of formation fractions $use_of_ff: min 
-Specification $spec:
-$parent
-$type: FOMC; $sink: TRUE
-
-$observed
-    name time value
-1 parent    0 98.62
-2 parent    3 81.43
-3 parent    7 53.18
-4 parent   14 34.89
-5 parent   30 10.09
-6 parent   62  1.50
-7 parent   90  0.33
-8 parent  118  0.08
-
-$obs_vars
-[1] "parent"
-
-$predicted
-      name       time       value
-1   parent   0.000000 99.66619265
-2   parent   1.191919 90.41690342
-3   parent   2.383838 82.08630014
-4   parent   3.000000 78.10760352
-5   parent   3.575758 74.57722848
-6   parent   4.767677 67.80342415
-7   parent   5.959596 61.68822425
-8   parent   7.000000 56.83515667
-9   parent   7.151515 56.16343898
-10  parent   8.343434 51.16836285
-11  parent   9.535354 46.64890734
-12  parent  10.727273 42.55683931
-13  parent  11.919192 38.84911158
-14  parent  13.111111 35.48727414
-15  parent  14.000000 33.18468323
-16  parent  14.303030 32.43695565
-17  parent  15.494949 29.66740651
-18  parent  16.686869 27.15109578
-19  parent  17.878788 24.86335532
-20  parent  19.070707 22.78206538
-21  parent  20.262626 20.88737647
-22  parent  21.454545 19.16146324
-23  parent  22.646465 17.58830644
-24  parent  23.838384 16.15349953
-25  parent  25.030303 14.84407724
-26  parent  26.222222 13.64836315
-27  parent  27.414141 12.55583436
-28  parent  28.606061 11.55700107
-29  parent  29.797980 10.64329940
-30  parent  30.000000 10.49630626
-31  parent  30.989899  9.80699593
-32  parent  32.181818  9.04110261
-33  parent  33.373737  8.33930082
-34  parent  34.565657  7.69587362
-35  parent  35.757576  7.10564515
-36  parent  36.949495  6.56392657
-37  parent  38.141414  6.06646759
-38  parent  39.333333  5.60941311
-39  parent  40.525253  5.18926438
-40  parent  41.717172  4.80284421
-41  parent  42.909091  4.44726569
-42  parent  44.101010  4.11990420
-43  parent  45.292929  3.81837216
-44  parent  46.484848  3.54049644
-45  parent  47.676768  3.28429799
-46  parent  48.868687  3.04797350
-47  parent  50.060606  2.82987892
-48  parent  51.252525  2.62851456
-49  parent  52.444444  2.44251172
-50  parent  53.636364  2.27062056
-51  parent  54.828283  2.11169922
-52  parent  56.020202  1.96470393
-53  parent  57.212121  1.82868009
-54  parent  58.404040  1.70275424
-55  parent  59.595960  1.58612677
-56  parent  60.787879  1.47806529
-57  parent  61.979798  1.37789865
-58  parent  62.000000  1.37626531
-59  parent  63.171717  1.28501157
-60  parent  64.363636  1.19883967
-61  parent  65.555556  1.11886504
-62  parent  66.747475  1.04461220
-63  parent  67.939394  0.97564441
-64  parent  69.131313  0.91156031
-65  parent  70.323232  0.85199096
-66  parent  71.515152  0.79659697
-67  parent  72.707071  0.74506609
-68  parent  73.898990  0.69711084
-69  parent  75.090909  0.65246649
-70  parent  76.282828  0.61088912
-71  parent  77.474747  0.57215389
-72  parent  78.666667  0.53605348
-73  parent  79.858586  0.50239663
-74  parent  81.050505  0.47100683
-75  parent  82.242424  0.44172111
-76  parent  83.434343  0.41438896
-77  parent  84.626263  0.38887128
-78  parent  85.818182  0.36503953
-79  parent  87.010101  0.34277481
-80  parent  88.202020  0.32196716
-81  parent  89.393939  0.30251479
-82  parent  90.000000  0.29311302
-83  parent  90.585859  0.28432347
-84  parent  91.777778  0.26730596
-85  parent  92.969697  0.25138141
-86  parent  94.161616  0.23647487
-87  parent  95.353535  0.22251689
-88  parent  96.545455  0.20944302
-89  parent  97.737374  0.19719349
-90  parent  98.929293  0.18571281
-91  parent 100.121212  0.17494947
-92  parent 101.313131  0.16485560
-93  parent 102.505051  0.15538676
-94  parent 103.696970  0.14650163
-95  parent 104.888889  0.13816179
-96  parent 106.080808  0.13033150
-97  parent 107.272727  0.12297753
-98  parent 108.464646  0.11606895
-99  parent 109.656566  0.10957695
-100 parent 110.848485  0.10347470
-101 parent 112.040404  0.09773723
-102 parent 113.232323  0.09234125
-103 parent 114.424242  0.08726506
-104 parent 115.616162  0.08248842
-105 parent 116.808081  0.07799245
-106 parent 118.000000  0.07375954
-
-$cost
-function (P) 
-{
-    assign("calls", calls + 1, inherits = TRUE)
-    if (trace_parms) 
-        cat(P, "\n")
-    if (length(state.ini.optim) > 0) {
-        odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-        names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-    }
-    else {
-        odeini <- state.ini.fixed
-        names(odeini) <- state.ini.fixed.boxnames
-    }
-    odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], 
-        transparms.fixed)
-    parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, 
-        transform_fractions = transform_fractions)
-    out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, 
-        use_compiled = use_compiled, method.ode = method.ode, 
-        atol = atol, rtol = rtol, ...)
-    assign("out_predicted", out, inherits = TRUE)
-    mC <- modCost(out, observed, y = "value", err = err, weight = weight, 
-        scaleVar = scaleVar)
-    if (mC$model < cost.old) {
-        if (!quiet) 
-            cat("Model cost at call ", calls, ": ", mC$model, 
-                "\n")
-        if (plot) {
-            outtimes_plot = seq(min(observed$time), max(observed$time), 
-                length.out = 100)
-            out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 
-                solution_type = solution_type, use_compiled = use_compiled, 
-                method.ode = method.ode, atol = atol, rtol = rtol, 
-                ...)
-            plot(0, type = "n", xlim = range(observed$time), 
-                ylim = c(0, max(observed$value, na.rm = TRUE)), 
-                xlab = "Time", ylab = "Observed")
-            col_obs <- pch_obs <- 1:length(obs_vars)
-            lty_obs <- rep(1, length(obs_vars))
-            names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars
-            for (obs_var in obs_vars) {
-                points(subset(observed, name == obs_var, c(time, 
-                  value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
-            }
-            matlines(out_plot$time, out_plot[-1], col = col_obs, 
-                lty = lty_obs)
-            legend("topright", inset = c(0.05, 0.05), legend = obs_vars, 
-                col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
-        }
-        assign("cost.old", mC$model, inherits = TRUE)
-    }
-    return(mC)
-}
-<environment: 0x44a0b88>
-
-$cost_notrans
-function (P) 
-{
-    if (length(state.ini.optim) > 0) {
-        odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-        names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-    }
-    else {
-        odeini <- state.ini.fixed
-        names(odeini) <- state.ini.fixed.boxnames
-    }
-    odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], 
-        parms.fixed)
-    out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, 
-        use_compiled = use_compiled, method.ode = method.ode, 
-        atol = atol, rtol = rtol, ...)
-    mC <- modCost(out, observed, y = "value", err = err, weight = weight, 
-        scaleVar = scaleVar)
-    return(mC)
-}
-<environment: 0x44a0b88>
-
-$hessian_notrans
-           parent_0     alpha       beta
-parent_0  4.1230329 -7.473531  0.5968527
-alpha    -7.4735307 40.365690 -3.1777189
-beta      0.5968527 -3.177719  0.2503425
-
-$start
-         value   type
-parent_0 98.62  state
-alpha     1.00 deparm
-beta     10.00 deparm
-
-$start_transformed
-              value lower upper
-parent_0  98.620000  -Inf   Inf
-log_alpha  0.000000  -Inf   Inf
-log_beta   2.302585  -Inf   Inf
-
-$fixed
-[1] value type 
-<0 rows> (or 0-length row.names)
-
-$data
-  time variable observed   predicted     residual
-1    0   parent    98.62 99.66619265 -1.046192647
-2    3   parent    81.43 78.10760352  3.322396479
-3    7   parent    53.18 56.83515667 -3.655156669
-4   14   parent    34.89 33.18468323  1.705316770
-5   30   parent    10.09 10.49630626 -0.406306255
-6   62   parent     1.50  1.37626531  0.123734689
-7   90   parent     0.33  0.29311302  0.036886982
-8  118   parent     0.08  0.07375954  0.006240458
-
-$atol
-[1] 1e-08
-
-$rtol
-[1] 1e-10
-
-$weight.ini
-[1] "none"
-
-$reweight.tol
-[1] 1e-08
-
-$reweight.max.iter
-[1] 10
-
-$bparms.optim
- parent_0     alpha      beta 
- 99.66619  12.80517 156.11390 
-
-$bparms.fixed
-numeric(0)
-
-$bparms.ode
-    alpha      beta 
- 12.80517 156.11390 
-
-$bparms.state
-  parent 
-99.66619 
-
-$date
-[1] "Sat Sep 10 05:52:53 2016"
-
-attr(,"class")
-[1] "mkinfit" "modFit" 
-

-
  fits["SFO", "B"]

-
     dataset
-model B      
-  SFO List,42
-attr(,"class")
-[1] "mmkin"
-

-
  fits[["SFO", "B"]] # This is equivalent to

-
$par
-         parent_0 log_k_parent_sink 
-        99.174072         -2.549028 
-
-$ssr
-[1] 30.65564
-
-$convergence
-[1] 0
-
-$iterations
-[1] 5
-
-$evaluations
-function gradient 
-       8       15 
-
-$counts
-[1] "relative convergence (4)"
-
-$hessian
-                    parent_0 log_k_parent_sink
-parent_0            4.163631         -94.09343
-log_k_parent_sink -94.093431        6311.34610
-
-$residuals
-     parent      parent      parent      parent      parent      parent 
- 0.55407218 -2.98452128  4.20445742 -1.68599939 -0.58185357 -0.72033730 
-     parent      parent 
--0.24260405 -0.07020339 
-
-$ms
-[1] 3.831956
-
-$var_ms
-  parent 
-3.831956 
-
-$var_ms_unscaled
-  parent 
-3.831956 
-
-$var_ms_unweighted
-  parent 
-3.831956 
-
-$rank
-[1] 2
-
-$df.residual
-[1] 6
-
-$solution_type
-[1] "analytical"
-
-$transform_rates
-[1] TRUE
-
-$transform_fractions
-[1] TRUE
-
-$method.modFit
-[1] "Port"
-
-$maxit.modFit
-[1] "auto"
-
-$calls
-[1] 29
-
-$time
-   user  system elapsed 
-  0.108   0.000   0.106 
-
-$mkinmod
-<mkinmod> model generated with
-Use of formation fractions $use_of_ff: min 
-Specification $spec:
-$parent
-$type: SFO; $sink: TRUE
-Coefficient matrix $coefmat available
-
-$observed
-    name time value
-1 parent    0 98.62
-2 parent    3 81.43
-3 parent    7 53.18
-4 parent   14 34.89
-5 parent   30 10.09
-6 parent   62  1.50
-7 parent   90  0.33
-8 parent  118  0.08
-
-$obs_vars
-[1] "parent"
-
-$predicted
-      name       time       value
-1   parent   0.000000 99.17407218
-2   parent   1.191919 90.35253561
-3   parent   2.383838 82.31567498
-4   parent   3.000000 78.44547872
-5   parent   3.575758 74.99369333
-6   parent   4.767677 68.32300215
-7   parent   5.959596 62.24566915
-8   parent   7.000000 57.38445742
-9   parent   7.151515 56.70891509
-10  parent   8.343434 51.66465547
-11  parent   9.535354 47.06908288
-12  parent  10.727273 42.88228661
-13  parent  11.919192 39.06790599
-14  parent  13.111111 35.59281463
-15  parent  14.000000 33.20400061
-16  parent  14.303030 32.42683275
-17  parent  15.494949 29.54246504
-18  parent  16.686869 26.91466193
-19  parent  17.878788 24.52060198
-20  parent  19.070707 22.33949373
-21  parent  20.262626 20.35239512
-22  parent  21.454545 18.54204899
-23  parent  22.646465 16.89273320
-24  parent  23.838384 15.39012410
-25  parent  25.030303 14.02117212
-26  parent  26.222222 12.77398846
-27  parent  27.414141 11.63774182
-28  parent  28.606061 10.60256435
-29  parent  29.797980  9.65946594
-30  parent  30.000000  9.50814643
-31  parent  30.989899  8.80025617
-32  parent  32.181818  8.01747313
-33  parent  33.373737  7.30431867
-34  parent  34.565657  6.65459931
-35  parent  35.757576  6.06267251
-36  parent  36.949495  5.52339762
-37  parent  38.141414  5.03209124
-38  parent  39.333333  4.58448658
-39  parent  40.525253  4.17669637
-40  parent  41.717172  3.80517911
-41  parent  42.909091  3.46670832
-42  parent  44.101010  3.15834451
-43  parent  45.292929  2.87740968
-44  parent  46.484848  2.62146400
-45  parent  47.676768  2.38828471
-46  parent  48.868687  2.17584671
-47  parent  50.060606  1.98230508
-48  parent  51.252525  1.80597899
-49  parent  52.444444  1.64533711
-50  parent  53.636364  1.49898432
-51  parent  54.828283  1.36564963
-52  parent  56.020202  1.24417505
-53  parent  57.212121  1.13350565
-54  parent  58.404040  1.03268029
-55  parent  59.595960  0.94082335
-56  parent  60.787879  0.85713708
-57  parent  61.979798  0.78089471
-58  parent  62.000000  0.77966270
-59  parent  63.171717  0.71143411
-60  parent  64.363636  0.64815202
-61  parent  65.555556  0.59049888
-62  parent  66.747475  0.53797399
-63  parent  67.939394  0.49012119
-64  parent  69.131313  0.44652489
-65  parent  70.323232  0.40680649
-66  parent  71.515152  0.37062104
-67  parent  72.707071  0.33765429
-68  parent  73.898990  0.30761993
-69  parent  75.090909  0.28025713
-70  parent  76.282828  0.25532825
-71  parent  77.474747  0.23261679
-72  parent  78.666667  0.21192552
-73  parent  79.858586  0.19307474
-74  parent  81.050505  0.17590074
-75  parent  82.242424  0.16025436
-76  parent  83.434343  0.14599973
-77  parent  84.626263  0.13301305
-78  parent  85.818182  0.12118154
-79  parent  87.010101  0.11040244
-80  parent  88.202020  0.10058214
-81  parent  89.393939  0.09163535
-82  parent  90.000000  0.08739595
-83  parent  90.585859  0.08348439
-84  parent  91.777778  0.07605845
-85  parent  92.969697  0.06929305
-86  parent  94.161616  0.06312943
-87  parent  95.353535  0.05751406
-88  parent  96.545455  0.05239819
-89  parent  97.737374  0.04773737
-90  parent  98.929293  0.04349113
-91  parent 100.121212  0.03962259
-92  parent 101.313131  0.03609816
-93  parent 102.505051  0.03288723
-94  parent 103.696970  0.02996191
-95  parent 104.888889  0.02729679
-96  parent 106.080808  0.02486874
-97  parent 107.272727  0.02265667
-98  parent 108.464646  0.02064136
-99  parent 109.656566  0.01880531
-100 parent 110.848485  0.01713257
-101 parent 112.040404  0.01560863
-102 parent 113.232323  0.01422024
-103 parent 114.424242  0.01295535
-104 parent 115.616162  0.01180297
-105 parent 116.808081  0.01075310
-106 parent 118.000000  0.00979661
-
-$cost
-function (P) 
-{
-    assign("calls", calls + 1, inherits = TRUE)
-    if (trace_parms) 
-        cat(P, "\n")
-    if (length(state.ini.optim) > 0) {
-        odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-        names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-    }
-    else {
-        odeini <- state.ini.fixed
-        names(odeini) <- state.ini.fixed.boxnames
-    }
-    odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], 
-        transparms.fixed)
-    parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, 
-        transform_fractions = transform_fractions)
-    out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, 
-        use_compiled = use_compiled, method.ode = method.ode, 
-        atol = atol, rtol = rtol, ...)
-    assign("out_predicted", out, inherits = TRUE)
-    mC <- modCost(out, observed, y = "value", err = err, weight = weight, 
-        scaleVar = scaleVar)
-    if (mC$model < cost.old) {
-        if (!quiet) 
-            cat("Model cost at call ", calls, ": ", mC$model, 
-                "\n")
-        if (plot) {
-            outtimes_plot = seq(min(observed$time), max(observed$time), 
-                length.out = 100)
-            out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 
-                solution_type = solution_type, use_compiled = use_compiled, 
-                method.ode = method.ode, atol = atol, rtol = rtol, 
-                ...)
-            plot(0, type = "n", xlim = range(observed$time), 
-                ylim = c(0, max(observed$value, na.rm = TRUE)), 
-                xlab = "Time", ylab = "Observed")
-            col_obs <- pch_obs <- 1:length(obs_vars)
-            lty_obs <- rep(1, length(obs_vars))
-            names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars
-            for (obs_var in obs_vars) {
-                points(subset(observed, name == obs_var, c(time, 
-                  value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
-            }
-            matlines(out_plot$time, out_plot[-1], col = col_obs, 
-                lty = lty_obs)
-            legend("topright", inset = c(0.05, 0.05), legend = obs_vars, 
-                col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
-        }
-        assign("cost.old", mC$model, inherits = TRUE)
-    }
-    return(mC)
-}
-<environment: 0x43a7a48>
-
-$cost_notrans
-function (P) 
-{
-    if (length(state.ini.optim) > 0) {
-        odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-        names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-    }
-    else {
-        odeini <- state.ini.fixed
-        names(odeini) <- state.ini.fixed.boxnames
-    }
-    odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], 
-        parms.fixed)
-    out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, 
-        use_compiled = use_compiled, method.ode = method.ode, 
-        atol = atol, rtol = rtol, ...)
-    mC <- modCost(out, observed, y = "value", err = err, weight = weight, 
-        scaleVar = scaleVar)
-    return(mC)
-}
-<environment: 0x43a7a48>
-
-$hessian_notrans
-                  parent_0 k_parent_sink
-parent_0          4.163631     -1203.894
-k_parent_sink -1203.893702   1033188.753
-
-$start
-              value   type
-parent_0      98.62  state
-k_parent_sink  0.10 deparm
-
-$start_transformed
-                      value lower upper
-parent_0          98.620000  -Inf   Inf
-log_k_parent_sink -2.302585  -Inf   Inf
-
-$fixed
-[1] value type 
-<0 rows> (or 0-length row.names)
-
-$data
-  time variable observed   predicted    residual
-1    0   parent    98.62 99.17407218 -0.55407218
-2    3   parent    81.43 78.44547872  2.98452128
-3    7   parent    53.18 57.38445742 -4.20445742
-4   14   parent    34.89 33.20400061  1.68599939
-5   30   parent    10.09  9.50814643  0.58185357
-6   62   parent     1.50  0.77966270  0.72033730
-7   90   parent     0.33  0.08739595  0.24260405
-8  118   parent     0.08  0.00979661  0.07020339
-
-$atol
-[1] 1e-08
-
-$rtol
-[1] 1e-10
-
-$weight.ini
-[1] "none"
-
-$reweight.tol
-[1] 1e-08
-
-$reweight.max.iter
-[1] 10
-
-$bparms.optim
-     parent_0 k_parent_sink 
-  99.17407218    0.07815759 
-
-$bparms.fixed
-numeric(0)
-
-$bparms.ode
-k_parent_sink 
-   0.07815759 
-
-$bparms.state
-  parent 
-99.17407 
-
-$date
-[1] "Sat Sep 10 05:52:53 2016"
-
-attr(,"class")
-[1] "mkinfit" "modFit" 
-

-
  fits["SFO", "B", drop = TRUE]

-
[[1]]
-$par
-         parent_0 log_k_parent_sink 
-        99.174072         -2.549028 
-
-$ssr
-[1] 30.65564
-
-$convergence
-[1] 0
-
-$iterations
-[1] 5
-
-$evaluations
-function gradient 
-       8       15 
-
-$counts
-[1] "relative convergence (4)"
-
-$hessian
-                    parent_0 log_k_parent_sink
-parent_0            4.163631         -94.09343
-log_k_parent_sink -94.093431        6311.34610
-
-$residuals
-     parent      parent      parent      parent      parent      parent 
- 0.55407218 -2.98452128  4.20445742 -1.68599939 -0.58185357 -0.72033730 
-     parent      parent 
--0.24260405 -0.07020339 
-
-$ms
-[1] 3.831956
-
-$var_ms
-  parent 
-3.831956 
-
-$var_ms_unscaled
-  parent 
-3.831956 
-
-$var_ms_unweighted
-  parent 
-3.831956 
-
-$rank
-[1] 2
-
-$df.residual
-[1] 6
-
-$solution_type
-[1] "analytical"
-
-$transform_rates
-[1] TRUE
-
-$transform_fractions
-[1] TRUE
-
-$method.modFit
-[1] "Port"
-
-$maxit.modFit
-[1] "auto"
-
-$calls
-[1] 29
-
-$time
-   user  system elapsed 
-  0.108   0.000   0.106 
-
-$mkinmod
-<mkinmod> model generated with
-Use of formation fractions $use_of_ff: min 
-Specification $spec:
-$parent
-$type: SFO; $sink: TRUE
-Coefficient matrix $coefmat available
-
-$observed
-    name time value
-1 parent    0 98.62
-2 parent    3 81.43
-3 parent    7 53.18
-4 parent   14 34.89
-5 parent   30 10.09
-6 parent   62  1.50
-7 parent   90  0.33
-8 parent  118  0.08
-
-$obs_vars
-[1] "parent"
-
-$predicted
-      name       time       value
-1   parent   0.000000 99.17407218
-2   parent   1.191919 90.35253561
-3   parent   2.383838 82.31567498
-4   parent   3.000000 78.44547872
-5   parent   3.575758 74.99369333
-6   parent   4.767677 68.32300215
-7   parent   5.959596 62.24566915
-8   parent   7.000000 57.38445742
-9   parent   7.151515 56.70891509
-10  parent   8.343434 51.66465547
-11  parent   9.535354 47.06908288
-12  parent  10.727273 42.88228661
-13  parent  11.919192 39.06790599
-14  parent  13.111111 35.59281463
-15  parent  14.000000 33.20400061
-16  parent  14.303030 32.42683275
-17  parent  15.494949 29.54246504
-18  parent  16.686869 26.91466193
-19  parent  17.878788 24.52060198
-20  parent  19.070707 22.33949373
-21  parent  20.262626 20.35239512
-22  parent  21.454545 18.54204899
-23  parent  22.646465 16.89273320
-24  parent  23.838384 15.39012410
-25  parent  25.030303 14.02117212
-26  parent  26.222222 12.77398846
-27  parent  27.414141 11.63774182
-28  parent  28.606061 10.60256435
-29  parent  29.797980  9.65946594
-30  parent  30.000000  9.50814643
-31  parent  30.989899  8.80025617
-32  parent  32.181818  8.01747313
-33  parent  33.373737  7.30431867
-34  parent  34.565657  6.65459931
-35  parent  35.757576  6.06267251
-36  parent  36.949495  5.52339762
-37  parent  38.141414  5.03209124
-38  parent  39.333333  4.58448658
-39  parent  40.525253  4.17669637
-40  parent  41.717172  3.80517911
-41  parent  42.909091  3.46670832
-42  parent  44.101010  3.15834451
-43  parent  45.292929  2.87740968
-44  parent  46.484848  2.62146400
-45  parent  47.676768  2.38828471
-46  parent  48.868687  2.17584671
-47  parent  50.060606  1.98230508
-48  parent  51.252525  1.80597899
-49  parent  52.444444  1.64533711
-50  parent  53.636364  1.49898432
-51  parent  54.828283  1.36564963
-52  parent  56.020202  1.24417505
-53  parent  57.212121  1.13350565
-54  parent  58.404040  1.03268029
-55  parent  59.595960  0.94082335
-56  parent  60.787879  0.85713708
-57  parent  61.979798  0.78089471
-58  parent  62.000000  0.77966270
-59  parent  63.171717  0.71143411
-60  parent  64.363636  0.64815202
-61  parent  65.555556  0.59049888
-62  parent  66.747475  0.53797399
-63  parent  67.939394  0.49012119
-64  parent  69.131313  0.44652489
-65  parent  70.323232  0.40680649
-66  parent  71.515152  0.37062104
-67  parent  72.707071  0.33765429
-68  parent  73.898990  0.30761993
-69  parent  75.090909  0.28025713
-70  parent  76.282828  0.25532825
-71  parent  77.474747  0.23261679
-72  parent  78.666667  0.21192552
-73  parent  79.858586  0.19307474
-74  parent  81.050505  0.17590074
-75  parent  82.242424  0.16025436
-76  parent  83.434343  0.14599973
-77  parent  84.626263  0.13301305
-78  parent  85.818182  0.12118154
-79  parent  87.010101  0.11040244
-80  parent  88.202020  0.10058214
-81  parent  89.393939  0.09163535
-82  parent  90.000000  0.08739595
-83  parent  90.585859  0.08348439
-84  parent  91.777778  0.07605845
-85  parent  92.969697  0.06929305
-86  parent  94.161616  0.06312943
-87  parent  95.353535  0.05751406
-88  parent  96.545455  0.05239819
-89  parent  97.737374  0.04773737
-90  parent  98.929293  0.04349113
-91  parent 100.121212  0.03962259
-92  parent 101.313131  0.03609816
-93  parent 102.505051  0.03288723
-94  parent 103.696970  0.02996191
-95  parent 104.888889  0.02729679
-96  parent 106.080808  0.02486874
-97  parent 107.272727  0.02265667
-98  parent 108.464646  0.02064136
-99  parent 109.656566  0.01880531
-100 parent 110.848485  0.01713257
-101 parent 112.040404  0.01560863
-102 parent 113.232323  0.01422024
-103 parent 114.424242  0.01295535
-104 parent 115.616162  0.01180297
-105 parent 116.808081  0.01075310
-106 parent 118.000000  0.00979661
-
-$cost
-function (P) 
-{
-    assign("calls", calls + 1, inherits = TRUE)
-    if (trace_parms) 
-        cat(P, "\n")
-    if (length(state.ini.optim) > 0) {
-        odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-        names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-    }
-    else {
-        odeini <- state.ini.fixed
-        names(odeini) <- state.ini.fixed.boxnames
-    }
-    odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], 
-        transparms.fixed)
-    parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, 
-        transform_fractions = transform_fractions)
-    out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, 
-        use_compiled = use_compiled, method.ode = method.ode, 
-        atol = atol, rtol = rtol, ...)
-    assign("out_predicted", out, inherits = TRUE)
-    mC <- modCost(out, observed, y = "value", err = err, weight = weight, 
-        scaleVar = scaleVar)
-    if (mC$model < cost.old) {
-        if (!quiet) 
-            cat("Model cost at call ", calls, ": ", mC$model, 
-                "\n")
-        if (plot) {
-            outtimes_plot = seq(min(observed$time), max(observed$time), 
-                length.out = 100)
-            out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 
-                solution_type = solution_type, use_compiled = use_compiled, 
-                method.ode = method.ode, atol = atol, rtol = rtol, 
-                ...)
-            plot(0, type = "n", xlim = range(observed$time), 
-                ylim = c(0, max(observed$value, na.rm = TRUE)), 
-                xlab = "Time", ylab = "Observed")
-            col_obs <- pch_obs <- 1:length(obs_vars)
-            lty_obs <- rep(1, length(obs_vars))
-            names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars
-            for (obs_var in obs_vars) {
-                points(subset(observed, name == obs_var, c(time, 
-                  value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
-            }
-            matlines(out_plot$time, out_plot[-1], col = col_obs, 
-                lty = lty_obs)
-            legend("topright", inset = c(0.05, 0.05), legend = obs_vars, 
-                col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
-        }
-        assign("cost.old", mC$model, inherits = TRUE)
-    }
-    return(mC)
-}
-<environment: 0x43a7a48>
-
-$cost_notrans
-function (P) 
-{
-    if (length(state.ini.optim) > 0) {
-        odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-        names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-    }
-    else {
-        odeini <- state.ini.fixed
-        names(odeini) <- state.ini.fixed.boxnames
-    }
-    odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], 
-        parms.fixed)
-    out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, 
-        use_compiled = use_compiled, method.ode = method.ode, 
-        atol = atol, rtol = rtol, ...)
-    mC <- modCost(out, observed, y = "value", err = err, weight = weight, 
-        scaleVar = scaleVar)
-    return(mC)
-}
-<environment: 0x43a7a48>
-
-$hessian_notrans
-                  parent_0 k_parent_sink
-parent_0          4.163631     -1203.894
-k_parent_sink -1203.893702   1033188.753
-
-$start
-              value   type
-parent_0      98.62  state
-k_parent_sink  0.10 deparm
-
-$start_transformed
-                      value lower upper
-parent_0          98.620000  -Inf   Inf
-log_k_parent_sink -2.302585  -Inf   Inf
-
-$fixed
-[1] value type 
-<0 rows> (or 0-length row.names)
-
-$data
-  time variable observed   predicted    residual
-1    0   parent    98.62 99.17407218 -0.55407218
-2    3   parent    81.43 78.44547872  2.98452128
-3    7   parent    53.18 57.38445742 -4.20445742
-4   14   parent    34.89 33.20400061  1.68599939
-5   30   parent    10.09  9.50814643  0.58185357
-6   62   parent     1.50  0.77966270  0.72033730
-7   90   parent     0.33  0.08739595  0.24260405
-8  118   parent     0.08  0.00979661  0.07020339
-
-$atol
-[1] 1e-08
-
-$rtol
-[1] 1e-10
-
-$weight.ini
-[1] "none"
-
-$reweight.tol
-[1] 1e-08
-
-$reweight.max.iter
-[1] 10
-
-$bparms.optim
-     parent_0 k_parent_sink 
-  99.17407218    0.07815759 
-
-$bparms.fixed
-numeric(0)
-
-$bparms.ode
-k_parent_sink 
-   0.07815759 
-
-$bparms.state
-  parent 
-99.17407 
-
-$date
-[1] "Sat Sep 10 05:52:53 2016"
-
-attr(,"class")
-[1] "mkinfit" "modFit" 
-
-
-
-
- - - - -

Author

- - Johannes Ranke - - -
-
- - -
- - \ No newline at end of file -- cgit v1.2.1