diff options
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 26 | ||||
| -rw-r--r-- | docs/reference/add_err.html | 4 | ||||
| -rw-r--r-- | docs/reference/endpoints.html | 4 | ||||
| -rw-r--r-- | docs/reference/ilr.html | 2 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkin_long_to_wide.html | 8 | ||||
| -rw-r--r-- | docs/reference/mkin_wide_to_long.html | 4 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 50 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkinsub.html | 8 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/plot.mkinfit.html | 14 | ||||
| -rw-r--r-- | docs/reference/plot.mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 8 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 26 |
15 files changed, 93 insertions, 93 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 4b6545db..b437fc7d 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -98,7 +98,7 @@ <dt>...</dt> <dd>Not used, only there to satisfy the generic method definition</dd> <dt>drop</dt> - <dd>If FALSE, the method always returns an mmkin object, otherwise either + <dd>If FALSE, the method always returns an mmkin object, otherwise either a list of mkinfit objects or a single mkinfit object.</dd> </dl> @@ -193,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.260 0.000 0.261 +#> 0.268 0.000 0.267 #> #> $mkinmod #> <mkinmod> model generated with @@ -379,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5bbb4a8> +#> <environment: 0x3a2f9e8> #> #> $cost_notrans #> function (P) @@ -401,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5bbb4a8> +#> <environment: 0x3a2f9e8> #> #> $hessian_notrans #> parent_0 alpha beta @@ -467,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Fri Nov 4 17:12:26 2016" +#> [1] "Thu Nov 17 22:56:49 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset @@ -546,7 +546,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.071 +#> 0.116 0.000 0.115 #> #> $mkinmod #> <mkinmod> model generated with @@ -733,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5719c08> +#> <environment: 0x42fb560> #> #> $cost_notrans #> function (P) @@ -755,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5719c08> +#> <environment: 0x42fb560> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -818,7 +818,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 17:12:26 2016" +#> [1] "Thu Nov 17 22:56:48 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] @@ -894,7 +894,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.071 +#> 0.116 0.000 0.115 #> #> $mkinmod #> <mkinmod> model generated with @@ -1081,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5719c08> +#> <environment: 0x42fb560> #> #> $cost_notrans #> function (P) @@ -1103,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5719c08> +#> <environment: 0x42fb560> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1166,7 +1166,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 17:12:26 2016" +#> [1] "Thu Nov 17 22:56:48 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 0a126c5c..8f1e1abb 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -121,7 +121,7 @@ </dd> <dt>seed</dt> <dd> - The seed used for the generation of random numbers. If NA, the seed + The seed used for the generation of random numbers. If NA, the seed is not set. </dd> </dl> @@ -129,7 +129,7 @@ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e. - the components of the list are datasets compatible with + the components of the list are datasets compatible with <code><a href='mkinfit.html'>mkinfit</a></code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 44a8f4c4..990ceadf 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -82,8 +82,8 @@ <p>This function calculates DT50 and DT90 values as well as formation fractions from kinetic models -fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, -the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but +fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, +the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites.</p> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 95fed72e..1e50e216 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -98,7 +98,7 @@ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The result of the forward or backward transformation. The returned components always + <p>The result of the forward or backward transformation. The returned components always sum to 1 for the case of the inverse log-ratio transformation.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 40c21d3c..4314c84e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -122,18 +122,18 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:12:32 2016 -#> Date of summary: Fri Nov 4 17:12:32 2016 +#> Date of fit: Thu Nov 17 22:56:55 2016 +#> Date of summary: Thu Nov 17 22:56:55 2016 #> #> Equations: -#> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 -#> d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol - +#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 +#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - #> k_phenol_anisole * phenol -#> d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole +#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.502 s +#> Fitted with method Port using 246 model solutions performed in 1.457 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index fa131a6d..095468e4 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -81,8 +81,8 @@ </div> - <p>This function takes a dataframe in the long form as required by <code>modCost</code> - and converts it into a dataframe with one independent variable and several + <p>This function takes a dataframe in the long form as required by <code>modCost</code> + and converts it into a dataframe with one independent variable and several dependent variables as columns.</p> @@ -92,8 +92,8 @@ <dl class="dl-horizontal"> <dt>long_data</dt> <dd> - The dataframe must contain one variable called "time" with the time values specified by the - <code>time</code> argument, one column called "name" with the grouping of the observed values, and + The dataframe must contain one variable called "time" with the time values specified by the + <code>time</code> argument, one column called "name" with the grouping of the observed values, and finally one column of observed values called "value". </dd> <dt>time</dt> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 077c0b7d..3b2d46e5 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -81,7 +81,7 @@ </div> - <p>This function simply takes a dataframe with one independent variable and several + <p>This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by <code>modCost</code>.</p> @@ -91,7 +91,7 @@ <dl class="dl-horizontal"> <dt>wide_data</dt> <dd> - The dataframe must contain one variable with the time values specified by the + The dataframe must contain one variable with the time values specified by the <code>time</code> argument and usually more than one column of observed values. </dd> <dt>time</dt> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 32083843..891bc18b 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -82,11 +82,11 @@ <p>This function uses the Flexible Modelling Environment package - <code>FME</code> to create a function calculating the model cost, i.e. the + <code>FME</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>nlminb</code>, + then minimised using the Port algorithm <code>nlminb</code>, using the specified initial or fixed parameters and starting values. - Per default, parameters in the kinetic models are internally transformed in order + 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 @@ -200,13 +200,13 @@ </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> + 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. + a compiled verion is present. </dd> <dt>method.modFit</dt> <dd> - The optimisation method passed to <code>modFit</code>. + The optimisation method passed to <code>modFit</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 @@ -228,20 +228,20 @@ <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>modFit</code>, overriding + be passed to the method called by <code>modFit</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>modFit</code>. + <code>modFit</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 + 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. @@ -250,7 +250,7 @@ <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 + 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 @@ -294,7 +294,7 @@ <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 numerical solver if that is used (see <code>solution_type</code> argument. The default value is 100. </dd> <dt>reweight.method</dt> @@ -302,9 +302,9 @@ 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 + 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 + 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> @@ -323,20 +323,20 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments that will be passed to <code>modFit</code>. + Further arguments that will be passed to <code>modFit</code>. </dd> </dl> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list with "mkinfit" and "modFit" in the class attribute. + <p>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>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> - <p>Fitting of several models to several datasets in a single call to + <p>Fitting of several models to several datasets in a single call to <code><a href='mmkin.html'>mmkin</a></code>.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> @@ -348,7 +348,7 @@ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>When using the "IORE" submodel for metabolites, fitting with + <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> @@ -359,15 +359,15 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:12:35 2016 -#> Date of summary: Fri Nov 4 17:12:35 2016 +#> Date of fit: Thu Nov 17 22:56:57 2016 +#> Date of summary: Thu Nov 17 22:56:57 2016 #> #> Equations: -#> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent +#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.147 s +#> Fitted with method Port using 64 model solutions performed in 0.158 s #> #> Weighting: none #> @@ -436,7 +436,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 1.208 1.256 0.935 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.168 1.260 0.924 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> 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'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -450,7 +450,7 @@ #> m1 131.760712 437.69961 #> </div><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span> -<span class='co'># print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, </span> +<span class='co'># print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,</span> <span class='co'># solution_type = "deSolve")))</span> <span class='co'># coef(fit.deSolve)</span> <span class='co'># endpoints(fit.deSolve)</span> @@ -465,7 +465,7 @@ <span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D)</span> <span class='co'># # Use starting parameters from parent only FOMC fit</span> <span class='co'># fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)</span> -<span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, </span> +<span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D,</span> <span class='co'># parms.ini = fit.FOMC$bparms.ode, plot=TRUE)</span> <span class='co'># </span> <span class='co'># # Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index e8302508..9c78d78a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -128,8 +128,8 @@ </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, even if is present. + If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code> + model is used, even if is present. </dd> <dt>atol</dt> <dd> @@ -144,7 +144,7 @@ <dt>map_output</dt> <dd> Boolean to specify if the output should list values for the observed - variables (default) or for all state variables (if set to FALSE). + variables (default) or for all state variables (if set to FALSE). </dd> <dt>&#8230;</dt> <dd> @@ -275,17 +275,17 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.008 0.016 0.005 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.024 0.004 0.004 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.000 0.016 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.016 0.004 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.036 0.000 0.035 </div></pre> +#> 0.032 0.000 0.035 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 8bb2ce1c..778b9f93 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -81,7 +81,7 @@ </div> - <p>This is a convenience function to set up the lists used as arguments for + <p>This is a convenience function to set up the lists used as arguments for <code><a href='mkinmod.html'>mkinmod</a></code>.</p> @@ -91,17 +91,17 @@ <dl class="dl-horizontal"> <dt>submodel</dt> <dd> - Character vector of length one to specify the submodel type. See + Character vector of length one to specify the submodel type. See <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names. </dd> <dt>to</dt> <dd> - Vector of the names of the state variable to which a transformation + Vector of the names of the state variable to which a transformation shall be included in the model. </dd> <dt>sink</dt> <dd> - Should a pathway to sink be included in the model in addition to the + Should a pathway to sink be included in the model in addition to the pathways to other state variables? </dd> <dt>full_name</dt> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index a21a980b..f7f56164 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -108,12 +108,12 @@ </dd> <dt>cluster</dt> <dd> - A cluster as returned by <code>makeCluster</code> to be used for parallel + A cluster as returned by <code>makeCluster</code> to be used for parallel execution. </dd> <dt>&#8230;</dt> <dd> - Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>. + Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> </dl> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 52db9bc6..362a4eef 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -82,22 +82,22 @@ <p>Solves the differential equations with the optimised and fixed parameters - from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots + from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots the observed data together with the solution of the fitted model.</p> <pre># S3 method for mkinfit plot(x, fit = x, obs_vars = names(fit$mkinmod$map), - xlab = "Time", ylab = "Observed", + xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = "default", - col_obs = 1:length(obs_vars), pch_obs = col_obs, + col_obs = 1:length(obs_vars), pch_obs = col_obs, lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, - lpos = "topright", inset = c(0.05, 0.05), + lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE, errmin_digits = 3, …) plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …)</pre> @@ -105,7 +105,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <dl class="dl-horizontal"> <dt>x</dt> <dd> - Alias for fit introduced for compatibility with the generic S3 method. + Alias for fit introduced for compatibility with the generic S3 method. </dd> <dt>fit</dt> <dd> @@ -113,7 +113,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </dd> <dt>obs_vars</dt> <dd> - A character vector of names of the observed variables for which the + A character vector of names of the observed variables for which the data and the model should be plotted. Defauls to all observed variables in the model. </dd> @@ -157,7 +157,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <dd> Should residuals be shown? If only one plot of the fits is shown, the residual plot is in the lower third of the plot? Otherwise, i.e. if - "sep_obs" is given, the residual plots will be located to the right of + "sep_obs" is given, the residual plots will be located to the right of the plots of the fitted curves. </dd> <dt>maxabs</dt> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index eac31273..f171ab5b 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -82,7 +82,7 @@ <p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the same model - fitted for at least one dataset is shown. When it is a column, the fit of at least one model + fitted for at least one dataset is shown. When it is a column, the fit of at least one model to the same dataset is shown.</p> @@ -136,7 +136,7 @@ <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><img src='plot.mmkin-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='plot.mmkin-4.png' alt='' width='540' height='400' /><div class='input'> - <span class='co'># We can also plot a single fit, if we like the way mmkin works, but then the plot </span> + <span class='co'># We can also plot a single fit, if we like the way mmkin works, but then the plot</span> <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span> <span class='co'># generated by staticdocs, as far as I know).</span> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><img src='plot.mmkin-6.png' alt='' width='540' height='400' /></pre> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 60f7cdf6..8dc57fb7 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -142,15 +142,15 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:12:43 2016 -#> Date of summary: Fri Nov 4 17:12:43 2016 +#> Date of fit: Thu Nov 17 22:57:05 2016 +#> Date of summary: Thu Nov 17 22:57:05 2016 #> #> Equations: -#> d_parent = - k_parent_sink * parent +#> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.084 s +#> Fitted with method Port using 35 model solutions performed in 0.085 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index f455951d..00af0267 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -81,7 +81,7 @@ </div> - <p>The transformations are intended to map parameters that should only take + <p>The transformations are intended to map parameters that should only take on restricted values to the full scale of real numbers. For kinetic rate constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as @@ -112,15 +112,15 @@ <dd> The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of the model variables that are needed for grouping the formation fractions - before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and - the information if the pathway to sink is included in the model. + before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and + the information if the pathway to sink is included in the model. </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 + 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. </dd> @@ -128,8 +128,8 @@ <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. The g parameter of the DFOP and HS models are also + assumption of normal distribution of the estimator. The default (TRUE) is + to do transformations. 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. @@ -149,16 +149,16 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:12:44 2016 -#> Date of summary: Fri Nov 4 17:12:44 2016 +#> Date of fit: Thu Nov 17 22:57:06 2016 +#> Date of summary: Thu Nov 17 22:57:06 2016 #> #> Equations: -#> d_parent = - k_parent_sink * parent - k_parent_m1 * parent -#> d_m1 = + k_parent_m1 * parent - k_m1_sink * m1 +#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.656 s +#> Fitted with method Port using 153 model solutions performed in 0.684 s #> #> Weighting: none #> @@ -224,7 +224,7 @@ #> m1 131.761 437.70</div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span> -<span class='co'># summary(fit.2, data=FALSE) </span> +<span class='co'># summary(fit.2, data=FALSE)</span> <span class='co'>## ---------------------------------------------</span> <span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> |