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diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html new file mode 100644 index 00000000..8536925c --- /dev/null +++ b/inst/web/mkinfit.html @@ -0,0 +1,517 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>mkinfit. mkin 0.9-41</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=" + Johannes Ranke +"> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="#">mkin 0.9-41</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> + </ul> + </div> + </div> + </div> +</div> + + <div class="container"> + <header> + + </header> + + <h1> + Fit a kinetic model to data with one or more state variables +</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><div>mkinfit(mkinmod, observed, parms.ini = "auto", state.ini = "auto", fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], solution_type = c("auto", "analytical", "eigen", "deSolve"), method.ode = "lsoda", use_compiled = "auto", method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"), maxit.modFit = "auto", control.modFit = list(), transform_rates = TRUE, transform_fractions = TRUE, plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, reweight.method = NULL, reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...)</div></pre> + + <h2>Arguments</h2> + <dl> + <dt>mkinmod</dt> + <dd> + A list of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the kinetic model to be + fitted to the data, or one of the shorthand names ("SFO", "FOMC", "DFOP", + "HS", "SFORB"). If a shorthand name is given, a parent only degradation + model is generated for the variable with the highest value in + <code>observed</code>. + </dd> + <dt>observed</dt> + <dd> + The observed data. It has to be in the long format as described in + <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>modFit</a></code>, i.e. the first column called "name" must contain the + name of the observed variable for each data point. The second column must + contain the times of observation, named "time". The third column must be + named "value" and contain the observed values. Optionally, a further column + can contain weights for each data point. If it is not named "err", its name + must be passed as a further argument named <code>err</code> which is then passed + on to <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>modFit</a></code>. + </dd> + <dt>parms.ini</dt> + <dd> + A named vector of initial values for the parameters, including parameters + to be optimised and potentially also fixed parameters as indicated by + <code>fixed_parms</code>. If set to "auto", initial values for rate constants + are set to default values. Using parameter names that are not in the model + gives an error. + + It is possible to only specify a subset of the parameters that the model + needs. You can use the parameter lists "bparms.ode" from a previously + fitted model, which contains the differential equation parameters from this + model. This works nicely if the models are nested. An example is given + below. + </dd> + <dt>state.ini</dt> + <dd> + A named vector of initial values for the state variables of the model. In + case the observed variables are represented by more than one model + variable, the names will differ from the names of the observed variables + (see <code>map</code> component of <code><a href='mkinmod.html'>mkinmod</a></code>). The default is to set + the initial value of the first model variable to the mean of the time zero + values for the variable with the maximum observed value, and all others to 0. + If this variable has no time zero observations, its initial value is set to 100. + </dd> + <dt>fixed_parms</dt> + <dd> + The names of parameters that should not be optimised but rather kept at the + values specified in <code>parms.ini</code>. + </dd> + <dt>fixed_initials</dt> + <dd> + The names of model variables for which the initial state at time 0 should + be excluded from the optimisation. Defaults to all state variables except + for the first one. + </dd> + <dt>solution_type</dt> + <dd> + If set to "eigen", the solution of the system of differential equations is + based on the spectral decomposition of the coefficient matrix in cases that + this is possible. If set to "deSolve", a numerical ode solver from package + <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/deSolve'>deSolve</a></code> is used. If set to "analytical", an analytical + solution of the model is used. This is only implemented for simple + degradation experiments with only one state variable, i.e. with no + metabolites. The default is "auto", which uses "analytical" if possible, + otherwise "eigen" if the model can be expressed using eigenvalues and + eigenvectors, and finally "deSolve" for the remaining models (time + dependence of degradation rates and metabolites). This argument is passed + on to the helper function <code><a href='mkinpredict.html'>mkinpredict</a></code>. + </dd> + <dt>method.ode</dt> + <dd> + The solution method passed via <code><a href='mkinpredict.html'>mkinpredict</a></code> to + <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/ode'>ode</a></code> in case the solution type is "deSolve". The default + "lsoda" is performant, but sometimes fails to converge. + </dd> + <dt>use_compiled</dt> + <dd> + If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code> + model is used, in the calls to <code><a href='mkinpredict.html'>mkinpredict</a></code> even if + a compiled verion is present. + </dd> + <dt>method.modFit</dt> + <dd> + The optimisation method passed to <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>modFit</a></code>. + + In order to optimally deal with problems where local minima occur, the + "Port" algorithm is now used per default as it is less prone to get trapped + in local minima and depends less on starting values for parameters than + the Levenberg Marquardt variant selected by "Marq". However, "Port" needs + more iterations. + + The former default "Marq" is the Levenberg Marquardt algorithm + <code><a href='http://www.inside-r.org/packages/cran/minpack.lm/docs/nls.lm'>nls.lm</a></code> from the package <code>minpack.lm</code> and usually needs + the least number of iterations. + + The "Pseudo" algorithm is not included because it needs finite parameter bounds + which are currently not supported. + + The "Newton" algorithm is not included because its number of iterations + can not be controlled by <code>control.modFit</code> and it does not appear + to provide advantages over the other algorithms. + </dd> + <dt>maxit.modFit</dt> + <dd> + Maximum number of iterations in the optimisation. If not "auto", this will + be passed to the method called by <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>modFit</a></code>, overriding + what may be specified in the next argument <code>control.modFit</code>. + </dd> + <dt>control.modFit</dt> + <dd> + Additional arguments passed to the optimisation method used by + <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>modFit</a></code>. + </dd> + <dt>transform_rates</dt> + <dd> + Boolean specifying if kinetic rate constants should be transformed in the + model specification used in the fitting for better compliance with the + assumption of normal distribution of the estimator. If TRUE, also + alpha and beta parameters of the FOMC model are log-transformed, as well + as k1 and k2 rate constants for the DFOP and HS models and the break point + tb of the HS model. + If FALSE, zero is used as a lower bound for the rates in the optimisation. + </dd> + <dt>transform_fractions</dt> + <dd> + Boolean specifying if formation fractions constants should be transformed in the + model specification used in the fitting for better compliance with the + assumption of normal distribution of the estimator. The default (TRUE) is + to do transformations. If TRUE, the g parameter of the DFOP and HS + models are also transformed, as they can also be seen as compositional + data. The transformation used for these transformations is the + <code><a href='ilr.html'>ilr</a></code> transformation. + </dd> + <dt>plot</dt> + <dd> + Should the observed values and the numerical solutions be plotted at each + stage of the optimisation? + </dd> + <dt>quiet</dt> + <dd> + Suppress printing out the current model cost after each improvement? + </dd> + <dt>err </dt> + <dd>either <code>NULL</code>, or the name of the column with the + <em>error</em> estimates, used to weigh the residuals (see details of + <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modCost'>modCost</a></code>); if <code>NULL</code>, then the residuals are not weighed. + </dd> + <dt>weight</dt> + <dd> + only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of "none", + "std", "mean", see details of <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modCost'>modCost</a></code>. + </dd> + <dt>scaleVar</dt> + <dd> + Will be passed to <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modCost'>modCost</a></code>. Default is not to scale Variables + according to the number of observations. + </dd> + <dt>atol</dt> + <dd> + Absolute error tolerance, passed to <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/ode'>ode</a></code>. Default is 1e-8, + lower than in <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/lsoda'>lsoda</a></code>. + </dd> + <dt>rtol</dt> + <dd> + Absolute error tolerance, passed to <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/ode'>ode</a></code>. Default is 1e-10, + much lower than in <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/lsoda'>lsoda</a></code>. + </dd> + <dt>n.outtimes</dt> + <dd> + The length of the dataseries that is produced by the model prediction + function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy of + the numerical solver if that is used (see <code>solution_type</code> argument. + The default value is 100. + </dd> + <dt>reweight.method</dt> + <dd> + The method used for iteratively reweighting residuals, also known + as iteratively reweighted least squares (IRLS). Default is NULL, + the other method implemented is called "obs", meaning that each + observed variable is assumed to have its own variance, this is + estimated from the fit and used for weighting the residuals + in each iteration until convergence of this estimate up to + <code>reweight.tol</code> or up to the maximum number of iterations + specified by <code>reweight.max.iter</code>. + </dd> + <dt>reweight.tol</dt> + <dd> + Tolerance for convergence criterion for the variance components + in IRLS fits. + </dd> + <dt>reweight.max.iter</dt> + <dd> + Maximum iterations in IRLS fits. + </dd> + <dt>trace_parms</dt> + <dd> + Should a trace of the parameter values be listed? + </dd> + <dt>...</dt> + <dd> + Further arguments that will be passed to <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>modFit</a></code>. + </dd> + </dl> + + <div class="Description"> + <h2>Description</h2> + + <p>This function uses the Flexible Modelling Environment package + <code><a href='http://www.inside-r.org/packages/cran/FME/docs/FME'>FME</a></code> to create a function calculating the model cost, i.e. the + deviation between the kinetic model and the observed data. This model cost is + then minimised using the Port algorithm <code><a href='http://www.inside-r.org/r-doc/stats/nlminb'>nlminb</a></code>, + using the specified initial or fixed parameters and starting values. + Per default, parameters in the kinetic models are internally transformed in order + to better satisfy the assumption of a normal distribution of their estimators. + In each step of the optimsation, the kinetic model is solved using the + function <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the residuals for each + observed variable can optionally be iteratively reweighted until convergence + using the argument <code>reweight.method = "obs"</code>.</p> + + </div> + + <div class="Value"> + <h2>Value</h2> + + <p><dl> + A list with "mkinfit" and "modFit" in the class attribute. + A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>. +</dl></p> + + </div> + + <div class="Note"> + <h2>Note</h2> + + <p>The implementation of iteratively reweighted least squares is inspired by the + work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei + Gao). A similar implemention can also be found in CAKE 2.0, which is the + other GUI derivative of mkin, sponsored by Syngenta.</p> + + </div> + + <div class="Note"> + <h2>Note</h2> + + <p>When using the "IORE" submodel for metabolites, fitting with + "transform_rates = TRUE" (the default) often leads to failures of the + numerical ODE solver. In this situation it may help to switch off the + internal rate transformation.</p> + + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'># Use shorthand notation for parent only degradation +fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) +summary(fit) +</div> +<div class='output'>mkin version: 0.9.41 +R version: 3.2.2 +Date of fit: Mon Nov 9 08:25:21 2015 +Date of summary: Mon Nov 9 08:25:21 2015 + +Equations: +d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent + +Model predictions using solution type analytical + +Fitted with method Port using 64 model solutions performed in 0.18 s + +Weighting: none + +Starting values for parameters to be optimised: + value type +parent_0 85.1 state +alpha 1.0 deparm +beta 10.0 deparm + +Starting values for the transformed parameters actually optimised: + value lower upper +parent_0 85.100000 -Inf Inf +log_alpha 0.000000 -Inf Inf +log_beta 2.302585 -Inf Inf + +Fixed parameter values: +None + +Optimised, transformed parameters with symmetric confidence intervals: + Estimate Std. Error Lower Upper +parent_0 85.87000 2.2460 80.38000 91.3700 +log_alpha 0.05192 0.1605 -0.34080 0.4446 +log_beta 0.65100 0.2801 -0.03452 1.3360 + +Parameter correlation: + parent_0 log_alpha log_beta +parent_0 1.0000 -0.2033 -0.3624 +log_alpha -0.2033 1.0000 0.9547 +log_beta -0.3624 0.9547 1.0000 + +Residual standard error: 2.275 on 6 degrees of freedom + +Backtransformed parameters: +Confidence intervals for internally transformed parameters are asymmetric. +t-test (unrealistically) based on the assumption of normal distribution +for estimators of untransformed parameters. + Estimate t value Pr(>t) Lower Upper +parent_0 85.870 38.230 1.069e-08 80.3800 91.370 +alpha 1.053 6.231 3.953e-04 0.7112 1.560 +beta 1.917 3.570 5.895e-03 0.9661 3.806 + +Chi2 error levels in percent: + err.min n.optim df +All data 6.657 3 6 +parent 6.657 3 6 + +Estimated disappearance times: + DT50 DT90 DT50back +parent 1.785 15.15 4.56 + +Data: + time variable observed predicted residual + 0 parent 85.1 85.875 -0.7749 + 1 parent 57.9 55.191 2.7091 + 3 parent 29.9 31.845 -1.9452 + 7 parent 14.6 17.012 -2.4124 + 14 parent 9.7 9.241 0.4590 + 28 parent 6.6 4.754 1.8460 + 63 parent 4.0 2.102 1.8977 + 91 parent 3.9 1.441 2.4590 + 119 parent 0.6 1.092 -0.4919 +</div> +<div class='input'> +# One parent compound, one metabolite, both single first order. +# Use mkinsub for convenience in model formulation. Pathway to sink included per default. +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO")) +</div> +<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> +<div class='input'># Fit the model to the FOCUS example dataset D using defaults +print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, + solution_type = "eigen", quiet = TRUE))) +</div> +<div class='output'> user system elapsed + 1.176 1.204 0.894 +</div> +<div class='input'>coef(fit) +</div> +<div class='output'> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink + 99.59848 -3.03822 -2.98030 -5.24750 +</div> +<div class='input'>endpoints(fit) +</div> +<div class='output'>$ff +parent_sink parent_m1 m1_sink + 0.485524 0.514476 1.000000 + +$SFORB +logical(0) + +$distimes + DT50 DT90 +parent 7.022929 23.32967 +m1 131.760712 437.69961 + +</div> +<div class='input'>## Not run: +# # deSolve is slower when no C compiler (gcc) was available during model generation +# print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, +# solution_type = "deSolve"))) +# coef(fit.deSolve) +# endpoints(fit.deSolve) +# ## End(Not run) + +# Use stepwise fitting, using optimised parameters from parent only fit, FOMC +## Not run: +# FOMC_SFO <- mkinmod( +# parent = mkinsub("FOMC", "m1"), +# m1 = mkinsub("SFO")) +# # Fit the model to the FOCUS example dataset D using defaults +# fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D) +# # Use starting parameters from parent only FOMC fit +# fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE) +# fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, +# parms.ini = fit.FOMC$bparms.ode, plot=TRUE) +# +# # Use stepwise fitting, using optimised parameters from parent only fit, SFORB +# SFORB_SFO <- mkinmod( +# parent = list(type = "SFORB", to = "m1", sink = TRUE), +# m1 = list(type = "SFO")) +# # Fit the model to the FOCUS example dataset D using defaults +# fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D) +# fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve") +# # Use starting parameters from parent only SFORB fit (not really needed in this case) +# fit.SFORB = mkinfit("SFORB", FOCUS_2006_D) +# fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode) +# ## End(Not run) + +## Not run: +# # Weighted fits, including IRLS +# SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), +# m1 = mkinsub("SFO"), use_of_ff = "max") +# f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D) +# summary(f.noweight) +# f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs") +# summary(f.irls) +# f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean") +# summary(f.w.mean) +# f.w.mean.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", +# reweight.method = "obs") +# summary(f.w.mean.irls) +# ## End(Not run) + +## Not run: +# # Manual weighting +# dw <- FOCUS_2006_D +# errors <- c(parent = 2, m1 = 1) +# dw$err.man <- errors[FOCUS_2006_D$name] +# f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man") +# summary(f.w.man) +# f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", +# reweight.method = "obs") +# summary(f.w.man.irls) +# ## End(Not run) +</div></pre> + </div> + <div class="span4"> + <!-- <ul> + <li>mkinfit</li> + </ul> + <ul> + <li> optimize </li> + </ul> --> + + <h2>See also</h2> + + Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and + <code><a href='mkinparplot.html'>mkinparplot</a></code>. + + Fitting of several models to several datasets in a single call to + <code><a href='mmkin.html'>mmkin</a></code>. + + + <h2>Author</h2> + + Johannes Ranke + + + </div> +</div> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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