From 98d684becd9495d370e1bcc8f9c7ca758caa4dd8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2016 22:58:28 +0100 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/reference/Extract.mmkin.html | 26 +++++++++--------- docs/reference/add_err.html | 4 +-- docs/reference/endpoints.html | 4 +-- docs/reference/ilr.html | 2 +- docs/reference/mccall81_245T.html | 12 ++++---- docs/reference/mkin_long_to_wide.html | 8 +++--- docs/reference/mkin_wide_to_long.html | 4 +-- docs/reference/mkinfit.html | 50 +++++++++++++++++----------------- docs/reference/mkinpredict.html | 12 ++++---- docs/reference/mkinsub.html | 8 +++--- docs/reference/mmkin.html | 4 +-- docs/reference/plot.mkinfit.html | 14 +++++----- docs/reference/plot.mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 8 +++--- docs/reference/transform_odeparms.html | 26 +++++++++--------- 15 files changed, 93 insertions(+), 93 deletions(-) (limited to 'docs/reference') 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 @@
...
Not used, only there to satisfy the generic method definition
drop
-
If FALSE, the method always returns an mmkin object, otherwise either +
If FALSE, the method always returns an mmkin object, otherwise either a list of mkinfit objects or a single mkinfit object.
@@ -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"
fits["SFO", "B"]
#> 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"
fits["SFO", "B", drop = TRUE]
#> [[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 @@
seed
- 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.
@@ -129,7 +129,7 @@

Value

A list of datasets compatible with mmkin, i.e. - the components of the list are datasets compatible with + the components of the list are datasets compatible with mkinfit.

References

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 @@

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.

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 @@

Value

-

The result of the forward or backward transformation. The returned components always +

The result of the forward or backward transformation. The returned components always sum to 1 for the case of the inverse log-ratio transformation.

References

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 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> 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 @@
-

This function takes a dataframe in the long form as required by modCost - and converts it into a dataframe with one independent variable and several +

This function takes a dataframe in the long form as required by modCost + and converts it into a dataframe with one independent variable and several dependent variables as columns.

@@ -92,8 +92,8 @@
long_data
- The dataframe must contain one variable called "time" with the time values specified by the - time 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 + time argument, one column called "name" with the grouping of the observed values, and finally one column of observed values called "value".
time
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 @@ -

This function simply takes a dataframe with one independent variable and several +

This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by modCost.

@@ -91,7 +91,7 @@
wide_data
- 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 time argument and usually more than one column of observed values.
time
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 @@

This function uses the Flexible Modelling Environment package - FME to create a function calculating the model cost, i.e. the + FME 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 nlminb, + then minimised using the Port algorithm nlminb, 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 mkinpredict. The variance of the residuals for each @@ -200,13 +200,13 @@

use_compiled
- If set to FALSE, no compiled version of the mkinmod + If set to FALSE, no compiled version of the mkinmod model is used, in the calls to mkinpredict even if - a compiled verion is present. + a compiled verion is present.
method.modFit
- The optimisation method passed to modFit. + The optimisation method passed to modFit. 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 @@
maxit.modFit
Maximum number of iterations in the optimisation. If not "auto", this will - be passed to the method called by modFit, overriding + be passed to the method called by modFit, overriding what may be specified in the next argument control.modFit.
control.modFit
Additional arguments passed to the optimisation method used by - modFit. + modFit.
transform_rates
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 @@
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 @@
The length of the dataseries that is produced by the model prediction function mkinpredict. This impacts the accuracy of - the numerical solver if that is used (see solution_type argument. + the numerical solver if that is used (see solution_type argument. The default value is 100.
reweight.method
@@ -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 reweight.tol or up to the maximum number of iterations specified by reweight.max.iter. @@ -323,20 +323,20 @@
&#8230;
- Further arguments that will be passed to modFit. + Further arguments that will be passed to modFit.

Value

-

A list with "mkinfit" and "modFit" in the class attribute. +

A list with "mkinfit" and "modFit" in the class attribute. A summary can be obtained by summary.mkinfit.

See also

Plotting methods plot.mkinfit and mkinparplot.

-

Fitting of several models to several datasets in a single call to +

Fitting of several models to several datasets in a single call to mmkin.

Note

@@ -348,7 +348,7 @@

Note

-

When using the "IORE" submodel for metabolites, fitting with +

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.

@@ -359,15 +359,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> 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 @@ m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# 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)))
#> user system elapsed -#> 1.208 1.256 0.935
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.168 1.260 0.924
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -450,7 +450,7 @@ #> m1 131.760712 437.69961 #>
## Not run: ------------------------------------ # # deSolve is slower when no C compiler (gcc) was available during model generation -# print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, +# print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, # solution_type = "deSolve"))) # coef(fit.deSolve) # endpoints(fit.deSolve) @@ -465,7 +465,7 @@ # fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D) # # Use starting parameters from parent only FOMC fit # fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE) -# fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, +# fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, # parms.ini = fit.FOMC$bparms.ode, plot=TRUE) # # # Use stepwise fitting, using optimised parameters from parent only fit, SFORB 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 @@
use_compiled
- If set to FALSE, no compiled version of the mkinmod - model is used, even if is present. + If set to FALSE, no compiled version of the mkinmod + model is used, even if is present.
atol
@@ -144,7 +144,7 @@
map_output
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).
&#8230;
@@ -275,17 +275,17 @@ c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> user system elapsed -#> 0.008 0.016 0.005
system.time( +#> 0.024 0.004 0.004
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> user system elapsed -#> 0.000 0.016 0.002
system.time( +#> 0.016 0.004 0.003
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE)[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> user system elapsed -#> 0.036 0.000 0.035
+#> 0.032 0.000 0.035 -

This is a convenience function to set up the lists used as arguments for +

This is a convenience function to set up the lists used as arguments for mkinmod.

@@ -91,17 +91,17 @@
submodel
- Character vector of length one to specify the submodel type. See + Character vector of length one to specify the submodel type. See mkinmod for the list of allowed submodel names.
to
- 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.
sink
- 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?
full_name
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 @@
cluster
- A cluster as returned by makeCluster to be used for parallel + A cluster as returned by makeCluster to be used for parallel execution.
&#8230;
- Further arguments that will be passed to mkinfit. + Further arguments that will be passed to mkinfit.
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 @@

Solves the differential equations with the optimised and fixed parameters - from a previous successful call to mkinfit and plots + from a previous successful call to mkinfit and plots the observed data together with the solution of the fitted model.

# 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, …)
@@ -105,7 +105,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …
x
- Alias for fit introduced for compatibility with the generic S3 method. + Alias for fit introduced for compatibility with the generic S3 method.
fit
@@ -113,7 +113,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …
obs_vars
- 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.
@@ -157,7 +157,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …
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.
maxabs
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 @@

When x is a row selected from an mmkin object ([.mmkin), 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.

@@ -136,7 +136,7 @@ fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), cores = 1, quiet = TRUE, method.modFit = "Marq") plot(fits[, "FOCUS C"])
plot(fits["FOMC", ])
- # We can also plot a single fit, if we like the way mmkin works, but then the plot + # We can also plot a single fit, if we like the way mmkin works, but then the plot # height should be smaller than the plot width (this is not possible for the html pages # generated by staticdocs, as far as I know). plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])
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 @@

Examples

  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
#> 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 @@
     

 
     
-    
The transformations are intended to map parameters that should only take 
+    
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 @@
       

     The kinetic model of class mkinmod, containing the names of
     the model variables that are needed for grouping the formation fractions
-    before ilr transformation, the parameter names and 
-    the information if the pathway to sink is included in the model. 
+    before ilr transformation, the parameter names and
+    the information if the pathway to sink is included in the model.
   

       
transform_rates

       

     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.
   

@@ -128,8 +128,8 @@
       

     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 ilr
     transformation.
@@ -149,16 +149,16 @@
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> 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

 ## Not run: ------------------------------------
 # fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)
-# summary(fit.2, data=FALSE) 
+# summary(fit.2, data=FALSE)
 ## ---------------------------------------------
 
 initials <- fit$start$value
-- 
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