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Diffstat (limited to 'docs/reference/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 26 |
1 files changed, 13 insertions, 13 deletions
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> |