From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2022 14:54:20 +0100 Subject: Complete update of online docs for v1.2.0 --- docs/reference/index.html | 68 ++++++++++++++++++++++++++++++++++++----------- 1 file changed, 53 insertions(+), 15 deletions(-) (limited to 'docs/reference/index.html') diff --git a/docs/reference/index.html b/docs/reference/index.html index 956648d2..665912f7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ mkin - 1.1.2 + 1.2.0 @@ -44,11 +44,14 @@ Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models
  • - Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method
  • Performance benefit by using compiled model definitions in mkin
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Calculation of time weighted average concentrations with mkin
    • @@ -56,7 +59,10 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -107,11 +113,15 @@ degradation models and one or more error models

    Generic functions introduced by the package

    -

    convergence() print(<convergence.mmkin>)

    +

    parms()

    + +

    Extract model parameters

    + +

    status() print(<status.mmkin>) print(<status.mhmkin>)

    -

    Method to get convergence information

    +

    Method to get status information for fit array objects

    -

    illparms() print(<illparms.mmkin>) print(<illparms.mhmkin>)

    +

    illparms() print(<illparms.mkinfit>) print(<illparms.mmkin>) print(<illparms.saem.mmkin>) print(<illparms.mhmkin>)

    Method to get the names of ill-defined parameters

    @@ -119,6 +129,10 @@ degradation models and one or more error models

    Function to calculate endpoints for further use from kinetic models fitted with mkinfit

    + +

    aw()

    + +

    Calculate Akaike weights for model averaging

    Show results

    Functions working with mkinfit objects

    @@ -131,10 +145,6 @@ with mkinfit

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

    Summary method for class "mkinfit"

    - -

    parms()

    - -

    Extract model parameters from mkinfit models

    confint(<mkinfit>)

    @@ -155,10 +165,6 @@ with mkinfit

    mkinerrmin()

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

    - -

    aw()

    - -

    Calculate Akaike weights for model averaging

    CAKE_export()

    @@ -189,11 +195,15 @@ of an mmkin object

    Create and work with nonlinear hierarchical models

    +

    read_spreadsheet()

    + +

    Read datasets and relevant meta information from a spreadsheet file

    +

    nlme(<mmkin>) print(<nlme.mmkin>) update(<nlme.mmkin>)

    Create an nlme model for an mmkin row object

    -

    saem() print(<saem.mmkin>) saemix_model() saemix_data()

    +

    saem() print(<saem.mmkin>) saemix_model() saemix_data() parms(<saem.mmkin>)

    Fit nonlinear mixed models with SAEM

    @@ -213,6 +223,14 @@ degradation models and one or more error models

    summary(<saem.mmkin>) print(<summary.saem.mmkin>)

    Summary method for class "saem.mmkin"

    + +

    anova(<saem.mmkin>)

    + +

    Anova method for saem.mmkin objects

    + +

    logLik(<saem.mmkin>)

    + +

    logLik method for saem.mmkin objects

    nlme_function() nlme_data()

    @@ -233,6 +251,18 @@ degradation models and one or more error models

    intervals(<saem.mmkin>)

    Confidence intervals for parameters in saem.mmkin objects

    + +

    multistart() print(<multistart>) best() which.best()

    + +

    Perform a hierarchical model fit with multiple starting values

    + +

    llhist()

    + +

    Plot the distribution of log likelihoods from multistart objects

    + +

    parplot()

    + +

    Plot parameter variability of multistart objects

    Datasets and known results

    @@ -322,9 +352,17 @@ degradation models and one or more error models

    +

    tex_listing()

    + +

    Wrap the output of a summary function in tex listing environment

    +

    f_time_norm_focus()

    Normalisation factors for aerobic soil degradation according to FOCUS guidance

    + +

    set_nd_nq() set_nd_nq_focus()

    + +

    Set non-detects and unquantified values in residue series without replicates

    max_twa_parent() max_twa_sfo() max_twa_fomc() max_twa_dfop() max_twa_hs()

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