From 575fcacaa33076de97f41a79afb37efb97ca82e0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Mar 2020 21:43:10 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/CAKE_export.html | 23 ++++--- docs/reference/add_err-1.png | Bin 89500 -> 89498 bytes docs/reference/add_err.html | 14 ++++- docs/reference/aw.html | 2 +- docs/reference/confint.mkinfit.html | 107 ++++++++++++++------------------ docs/reference/loftest-3.png | Bin 65409 -> 65397 bytes docs/reference/loftest.html | 2 +- docs/reference/lrtest.mkinfit.html | 4 +- docs/reference/mkinds.html | 31 +++++++++- docs/reference/mkinerrplot-1.png | Bin 35440 -> 35440 bytes docs/reference/mkinerrplot.html | 21 +++++-- docs/reference/mkinfit.html | 109 +++++++++++++++++++-------------- docs/reference/mkinmod.html | 13 ++-- docs/reference/mkinpredict.html | 78 +++++++++++++++-------- docs/reference/mkinresplot.html | 20 ++++-- docs/reference/mmkin-2.png | Bin 88000 -> 88002 bytes docs/reference/mmkin-3.png | Bin 85371 -> 85375 bytes docs/reference/mmkin.html | 23 ++++--- docs/reference/plot.mkinfit.html | 57 ++++++++++++----- docs/reference/plot.mmkin.html | 19 ++++-- docs/reference/summary.mkinfit.html | 24 ++++---- docs/reference/transform_odeparms.html | 20 ++++-- 22 files changed, 353 insertions(+), 214 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 47536237..a4161abc 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -70,7 +70,7 @@ specified as well." /> mkin - 0.9.49.6 + 0.9.49.9 @@ -138,12 +138,21 @@ specified as well." /> specified as well.

- 
CAKE_export(ds, map = c(parent = "Parent"), links = NA,
-  filename = "CAKE_export.csf", path = ".", overwrite = FALSE,
-  study = "Codlemone aerobic soil degradation", description = "",
-  time_unit = "days", res_unit = "% AR",
-  comment = "Created using mkin::CAKE_export", date = Sys.Date(),
-  optimiser = "IRLS")
+ 
CAKE_export(
+  ds,
+  map = c(parent = "Parent"),
+  links = NA,
+  filename = "CAKE_export.csf",
+  path = ".",
+  overwrite = FALSE,
+  study = "Codlemone aerobic soil degradation",
+  description = "",
+  time_unit = "days",
+  res_unit = "% AR",
+  comment = "Created using mkin::CAKE_export",
+  date = Sys.Date(),
+  optimiser = "IRLS"
+)

Arguments

diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png index fb369053..3018ff7f 100644 Binary files a/docs/reference/add_err-1.png and b/docs/reference/add_err-1.png differ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 67789694..ab499a19 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -71,7 +71,7 @@ may depend on the predicted value and is specified as a standard deviation." /> mkin - 0.9.49.6 + 0.9.49.9 @@ -140,8 +140,16 @@ degradation model using mkinpredict. may depend on the predicted value and is specified as a standard deviation.

- 
add_err(prediction, sdfunc, secondary = c("M1", "M2"), n = 1000,
-  LOD = 0.1, reps = 2, digits = 1, seed = NA)
+ 
add_err(
+  prediction,
+  sdfunc,
+  secondary = c("M1", "M2"),
+  n = 1000,
+  LOD = 0.1,
+  reps = 2,
+  digits = 1,
+  seed = NA
+)

Arguments

diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 22201229..0b37847c 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -71,7 +71,7 @@ by Burnham and Anderson (2004)." /> mkin - 0.9.49.8 + 0.9.49.9 diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index ea69c3bb..1dd6288b 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -76,7 +76,7 @@ method of Venzon and Moolgavkar (1988)." /> mkin - 0.9.49.8 + 0.9.49.9 @@ -151,10 +151,19 @@ method of Venzon and Moolgavkar (1988).

# S3 method for mkinfit
-confint(object, parm, level = 0.95, alpha = 1 -
-  level, cutoff, method = c("quadratic", "profile"),
-  transformed = TRUE, backtransform = TRUE,
-  cores = round(detectCores()/2), quiet = FALSE, ...)
+confint( + object, + parm, + level=0.95, + alpha=1 - level, + cutoff, + method=c("quadratic", "profile"), + transformed=TRUE, + backtransform=TRUE, + cores=round(detectCores()/2), + quiet=FALSE, + ... +)

Arguments

@@ -253,52 +262,30 @@ On Windows machines, cores > 1 is currently not supported.

SFO_SFO.ff<-mkinmod(parent=mkinsub("SFO", "m1"), m1=mkinsub("SFO"), use_of_ff="max", quiet=TRUE) f_d_1<-mkinfit(SFO_SFO, subset(FOCUS_2006_D, value!=0), quiet=TRUE) -system.time(ci_profile<-confint(f_d_1, method="profile", cores=1, quiet=TRUE))
#> User System verstrichen -#> 51.058 0.000 51.088
# Using more cores does not save much time here, as parent_0 takes up most of the time +system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#> Error in mkinpredict.mkinmod(mkinmod, parms, odeini, outtimes, solution_type = solution_type, use_compiled = use_compiled, method.ode = method.ode, atol = atol, rtol = rtol, ...): Differential equations were not integrated for all output times because +#> NaN values occurred in output from ode()
#> Timing stopped at: 11.39 0 11.4
# Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of # minor interest), we get a nice performance improvement from about 50 # seconds to about 12 seconds if we use at least four cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#> User System verstrichen -#> 0.005 0.004 11.349
ci_profile
#> 2.5% 97.5% -#> parent_0 96.456003650 1.027703e+02 -#> k_parent_sink 0.040762501 5.549764e-02 -#> k_parent_m1 0.046786482 5.500879e-02 -#> k_m1_sink 0.003892605 6.702778e-03 -#> sigma 2.535612399 3.985263e+00
ci_quadratic_transformed <- confint(f_d_1, method = "quadratic") +#> 20.058 0.122 11.784
ci_profile
#> Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden
ci_quadratic_transformed <- confint(f_d_1, method = "quadratic") ci_quadratic_transformed
#> 2.5% 97.5% -#> parent_0 96.403841649 1.027931e+02 +#> parent_0 96.403841641 1.027931e+02 #> k_parent_sink 0.041033378 5.596269e-02 #> k_parent_m1 0.046777902 5.511931e-02 #> k_m1_sink 0.004012217 6.897547e-03 #> sigma 2.396089689 3.854918e+00
ci_quadratic_untransformed <- confint(f_d_1, method = "quadratic", transformed = FALSE) ci_quadratic_untransformed
#> 2.5% 97.5% -#> parent_0 96.403841653 102.79312450 +#> parent_0 96.403841648 102.79312450 #> k_parent_sink 0.040485331 0.05535491 -#> k_parent_m1 0.046611581 0.05494364 +#> k_parent_m1 0.046611582 0.05494364 #> k_m1_sink 0.003835483 0.00668582 #> sigma 2.396089689 3.85491806
# Against the expectation based on Bates and Watts (1988), the confidence # intervals based on the internal parameter transformation are less # congruent with the likelihood based intervals. Note the superiority of the # interval based on the untransformed fit for k_m1_sink -rel_diffs_transformed <- abs((ci_quadratic_transformed - ci_profile)/ci_profile) -rel_diffs_untransformed <- abs((ci_quadratic_untransformed - ci_profile)/ci_profile) -rel_diffs_transformed < rel_diffs_untransformed
#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent_sink TRUE FALSE -#> k_parent_m1 TRUE FALSE -#> k_m1_sink FALSE FALSE -#> sigma FALSE FALSE
signif(rel_diffs_transformed, 3)
#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006650 0.008380 -#> k_parent_m1 0.000183 0.002010 -#> k_m1_sink 0.030700 0.029100 -#> sigma 0.055000 0.032700
signif(rel_diffs_untransformed, 3)
#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006800 0.002570 -#> k_parent_m1 0.003740 0.001180 -#> k_m1_sink 0.014700 0.002530 -#> sigma 0.055000 0.032700
+rel_diffs_transformed <- abs((ci_quadratic_transformed - ci_profile)/ci_profile)
#> Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden
rel_diffs_untransformed <- abs((ci_quadratic_untransformed - ci_profile)/ci_profile)
#> Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden
rel_diffs_transformed < rel_diffs_untransformed
#> Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden
signif(rel_diffs_transformed, 3)
#> Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden
signif(rel_diffs_untransformed, 3)
#> Error in eval(expr, envir, enclos): Objekt 'rel_diffs_untransformed' nicht gefunden
# Investigate a case with formation fractions f_d_2 <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), quiet = TRUE) @@ -309,16 +296,16 @@ On Windows machines, cores > 1 is currently not supported.

#> f_parent_to_m1 0.471328495 5.611550e-01 #> sigma 2.535612399 3.985263e+00
ci_quadratic_transformed_ff <- confint(f_d_2, method = "quadratic") ci_quadratic_transformed_ff
#> 2.5% 97.5% -#> parent_0 96.403840123 1.027931e+02 -#> k_parent 0.090823791 1.072543e-01 +#> parent_0 96.403839992 1.027931e+02 +#> k_parent 0.090823790 1.072543e-01 #> k_m1 0.004012216 6.897547e-03 -#> f_parent_to_m1 0.469118710 5.595960e-01 +#> f_parent_to_m1 0.469118711 5.595960e-01 #> sigma 2.396089689 3.854918e+00
ci_quadratic_untransformed_ff <- confint(f_d_2, method = "quadratic", transformed = FALSE) ci_quadratic_untransformed_ff
#> 2.5% 97.5% -#> parent_0 96.403840057 1.027931e+02 -#> k_parent 0.090491932 1.069035e-01 +#> parent_0 96.403839944 1.027931e+02 +#> k_parent 0.090491931 1.069035e-01 #> k_m1 0.003835483 6.685819e-03 -#> f_parent_to_m1 0.469113361 5.598386e-01 +#> f_parent_to_m1 0.469113362 5.598386e-01 #> sigma 2.396089689 3.854918e+00
rel_diffs_transformed_ff <- abs((ci_quadratic_transformed_ff - ci_profile_ff)/ci_profile_ff) rel_diffs_untransformed_ff <- abs((ci_quadratic_untransformed_ff - ci_profile_ff)/ci_profile_ff) # While the confidence interval for the parent rate constant is closer to @@ -330,16 +317,16 @@ On Windows machines, cores > 1 is currently not supported.

#> k_parent TRUE TRUE #> k_m1 FALSE FALSE #> f_parent_to_m1 TRUE FALSE -#> sigma FALSE TRUE
rel_diffs_transformed_ff
#> 2.5% 97.5% -#> parent_0 0.0005408012 0.0002217857 -#> k_parent 0.0009596303 0.0009003981 -#> k_m1 0.0307277425 0.0290579163 -#> f_parent_to_m1 0.0046884178 0.0027782643 +#> sigma FALSE FALSE
rel_diffs_transformed_ff
#> 2.5% 97.5% +#> parent_0 0.0005408026 0.0002217846 +#> k_parent 0.0009596414 0.0009003877 +#> k_m1 0.0307277403 0.0290579212 +#> f_parent_to_m1 0.0046884168 0.0027782604 #> sigma 0.0550252516 0.0327066836
rel_diffs_untransformed_ff
#> 2.5% 97.5% -#> parent_0 0.0005408019 0.0002217863 -#> k_parent 0.0046099989 0.0023730118 -#> k_m1 0.0146746451 0.0025300990 -#> f_parent_to_m1 0.0046997668 0.0023460293 +#> parent_0 0.0005408031 0.0002217851 +#> k_parent 0.0046100089 0.0023730230 +#> k_m1 0.0146746442 0.0025300972 +#> f_parent_to_m1 0.0046997642 0.0023460268 #> sigma 0.0550252516 0.0327066836
# The profiling for the following fit does not finish in a reasonable time, # therefore we use the quadratic approximation @@ -351,17 +338,17 @@ On Windows machines, cores > 1 is currently not supported.

f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc", error_model_algorithm = "direct", quiet = TRUE) confint(f_tc_2, method = "quadratic")
#> 2.5% 97.5% -#> parent_0 94.596183241 106.19937044 -#> k_M1 0.037605436 0.04490758 -#> k_M2 0.008568746 0.01087675 -#> f_parent_to_M1 0.021464277 0.62023879 -#> f_parent_to_M2 0.015166876 0.37975352 -#> k1 0.273897622 0.33388081 -#> k2 0.018614564 0.02250380 -#> g 0.671943572 0.73583247 -#> sigma_low 0.251284138 0.83992136 -#> rsd_high 0.040410998 0.07661999
confint(f_tc_2, "parent_0", method = "quadratic")
#> 2.5% 97.5% -#> parent_0 94.59618 106.1994
# } +#> parent_0 94.596218141 106.19934683 +#> k_M1 0.037605440 0.04490756 +#> k_M2 0.008568747 0.01087674 +#> f_parent_to_M1 0.021466788 0.62023878 +#> f_parent_to_M2 0.015168650 0.37975352 +#> k1 0.273897581 0.33388066 +#> k2 0.018614556 0.02250379 +#> g 0.671943831 0.73583255 +#> sigma_low 0.251283700 0.83992071 +#> rsd_high 0.040411017 0.07662005
confint(f_tc_2, "parent_0", method = "quadratic")
#> 2.5% 97.5% +#> parent_0 94.59622 106.1993
# }
diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 70157db9..6861b747 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -73,7 +73,7 @@ and can be expressed by fixing the parameters of the other." /> mkin - 0.9.49.8 + 0.9.49.9 @@ -205,7 +205,7 @@ lower number of fitted parameters (null hypothesis).

#lrtest(dfop_fit, error_model = "tc")#lrtest(dfop_fit, fixed_parms = c(k2 = 0)) -# However, this equivalent syntax works for static help pages +# However, this equivalent syntax also works for static help pageslrtest(dfop_fit, update(dfop_fit, error_model="tc"))
#> Likelihood ratio test #> #> Model 1: DFOP with error model tc diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 386c00d7..c1cdcf99 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -69,7 +69,7 @@ mkin - 0.9.49.6 + 0.9.49.9
@@ -136,7 +136,6 @@

A dataset class for mkin

- 
mkinds

Format

@@ -164,6 +163,33 @@ value in order to be compatible with mkinfit

+

Methods

+ + +

Public methods

+ + +

+

Method new()

+ +

Usage

+

mkinds$new(title = "", data, time_unit = NA, unit = NA)

+ +

+

Method clone()

+

The objects of this class are cloneable with this method.

Usage

+

mkinds$clone(deep = FALSE)

+ +

Arguments

+

+
deep

Whether to make a deep clone.

+ +

+ +

Examples


@@ -174,6 +200,7 @@ value in order to be compatible with mkinfit

     
 
diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png
index 476edc49..46a80308 100644
Binary files a/docs/reference/mkinerrplot-1.png and b/docs/reference/mkinerrplot-1.png differ
diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html
index 079a6708..47f48b72 100644
--- a/docs/reference/mkinerrplot.html
+++ b/docs/reference/mkinerrplot.html
@@ -73,7 +73,7 @@ using the argument show_errplot = TRUE." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.9
       
     

 
@@ -144,11 +144,20 @@ and this error model plot can be obtained with show_errplot = TRUE.

     
 
-    
mkinerrplot(object, obs_vars = names(object$mkinmod$map), xlim = c(0,
-  1.1 * max(object$data$predicted)), xlab = "Predicted",
-  ylab = "Squared residual", maxy = "auto", legend = TRUE,
-  lpos = "topright", col_obs = "auto", pch_obs = "auto",
-  frame = TRUE, ...)

+    
mkinerrplot(
+  object,
+  obs_vars = names(object$mkinmod$map),
+  xlim = c(0, 1.1 * max(object$data$predicted)),
+  xlab = "Predicted",
+  ylab = "Squared residual",
+  maxy = "auto",
+  legend = TRUE,
+  lpos = "topright",
+  col_obs = "auto",
+  pch_obs = "auto",
+  frame = TRUE,
+  ...
+)

 
     
Arguments
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7ee73f15..ffc8d52b 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -75,7 +75,7 @@ likelihood function." /> mkin - 0.9.49.6 + 0.9.49.9 @@ -148,18 +148,33 @@ degradation model parameters, as both of them are arguments of the likelihood function.

- 
mkinfit(mkinmod, observed, parms.ini = "auto", state.ini = "auto",
-  err.ini = "auto", fixed_parms = NULL,
-  fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE,
+    
mkinfit(
+  mkinmod,
+  observed,
+  parms.ini = "auto",
+  state.ini = "auto",
+  err.ini = "auto",
+  fixed_parms = NULL,
+  fixed_initials = names(mkinmod$diffs)[-1],
+  from_max_mean = FALSE,
   solution_type = c("auto", "analytical", "eigen", "deSolve"),
-  method.ode = "lsoda", use_compiled = "auto",
+  method.ode = "lsoda",
+  use_compiled = "auto",
   control = list(eval.max = 300, iter.max = 200),
-  transform_rates = TRUE, transform_fractions = TRUE, quiet = FALSE,
-  atol = 1e-08, rtol = 1e-10, n.outtimes = 100,
+  transform_rates = TRUE,
+  transform_fractions = TRUE,
+  quiet = FALSE,
+  atol = 1e-08,
+  rtol = 1e-10,
+  n.outtimes = 100,
   error_model = c("const", "obs", "tc"),
-  error_model_algorithm = c("auto", "d_3", "direct", "twostep",
-  "threestep", "fourstep", "IRLS", "OLS"), reweight.tol = 1e-08,
-  reweight.max.iter = 10, trace_parms = FALSE, ...)

+  error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep",
+    "IRLS", "OLS"),
+  reweight.tol = 1e-08,
+  reweight.max.iter = 10,
+  trace_parms = FALSE,
+  ...
+)

Arguments

@@ -400,17 +415,17 @@ estimators.


 # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:08:21 2019 
-#> Date of summary: Fri Nov  1 10:08:21 2019 
+summary(fit)
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:41:20 2020 
+#> Date of summary: Mon Mar 30 21:41:20 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.456 s
+#> Fitted using 222 model solutions performed in 0.463 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -440,10 +455,10 @@ estimators.

 #> 
 #> Parameter correlation:
 #>             parent_0  log_alpha   log_beta     sigma
-#> parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.770e-08
-#> log_alpha -1.565e-01  1.000e+00  9.564e-01 9.974e-08
-#> log_beta  -3.142e-01  9.564e-01  1.000e+00 8.468e-08
-#> sigma      4.770e-08  9.974e-08  8.468e-08 1.000e+00
+#> parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.758e-08
+#> log_alpha -1.565e-01  1.000e+00  9.564e-01 1.007e-07
+#> log_beta  -3.142e-01  9.564e-01  1.000e+00 8.568e-08
+#> sigma      4.758e-08  1.007e-07  8.568e-08 1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
@@ -482,7 +497,7 @@ estimators.

   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)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.488       0.000       1.491 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.526       0.000       1.530 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -533,9 +548,9 @@ estimators.

 #> Sum of squared residuals at call 82: 373.1711
 #> Sum of squared residuals at call 84: 373.1711
 #> Sum of squared residuals at call 87: 372.6445
-#> Sum of squared residuals at call 88: 372.1615
-#> Sum of squared residuals at call 90: 372.1615
-#> Sum of squared residuals at call 91: 372.1615
+#> Sum of squared residuals at call 88: 372.1614
+#> Sum of squared residuals at call 90: 372.1614
+#> Sum of squared residuals at call 91: 372.1614
 #> Sum of squared residuals at call 94: 371.6464
 #> Sum of squared residuals at call 99: 371.4299
 #> Sum of squared residuals at call 101: 371.4299
@@ -555,7 +570,7 @@ estimators.

 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.058       0.000       1.059 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.083       0.000       1.084 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -589,10 +604,10 @@ estimators.

 # \dontrun{
 # Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:08:36 2019 
-#> Date of summary: Fri Nov  1 10:08:36 2019 
+                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:41:36 2020 
+#> Date of summary: Mon Mar 30 21:41:36 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -600,7 +615,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.083 s
+#> Fitted using 422 model solutions performed in 1.144 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -634,11 +649,11 @@ estimators.

 #> 
 #> Parameter correlation:
 #>                  parent_0 log_k_parent   log_k_m1 f_parent_ilr_1      sigma
-#> parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -2.265e-07
-#> log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01  3.785e-07
-#> log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.386e-07
-#> f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00 -3.641e-08
-#> sigma          -2.265e-07    3.785e-07 -1.386e-07     -3.641e-08  1.000e+00
+#> parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -2.443e-07
+#> log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01  3.181e-07
+#> log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.369e-07
+#> f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00 -2.287e-08
+#> sigma          -2.443e-07    3.181e-07 -1.369e-07     -2.287e-08  1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
@@ -706,10 +721,10 @@ estimators.

 #>   100       m1    31.04  31.98163 -9.416e-01
 #>   100       m1    33.13  31.98163  1.148e+00
 #>   120       m1    25.15  28.78984 -3.640e+00
-#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:08:39 2019 
-#> Date of summary: Fri Nov  1 10:08:39 2019 
+#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:41:39 2020 
+#> Date of summary: Mon Mar 30 21:41:39 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -717,7 +732,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 978 model solutions performed in 2.553 s
+#> Fitted using 979 model solutions performed in 2.576 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -838,10 +853,10 @@ estimators.

 #>   100       m1    31.04  31.98773 -9.477e-01
 #>   100       m1    33.13  31.98773  1.142e+00
 #>   120       m1    25.15  28.80429 -3.654e+00
-#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:08:48 2019 
-#> Date of summary: Fri Nov  1 10:08:48 2019 
+#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:41:50 2020 
+#> Date of summary: Mon Mar 30 21:41:50 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -849,12 +864,12 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.253 s
+#> Fitted using 2552 model solutions performed in 10.593 s
 #> 
 #> Error model: Two-component variance function 
 #> 
 #> Error model algorithm: d_3 
-#> Direct fitting and three-step fitting yield approximately the same likelihood 
+#> Three-step fitting yielded a higher likelihood than direct fitting 
 #> 
 #> Starting values for parameters to be optimised:
 #>                   value   type
@@ -960,8 +975,8 @@ estimators.

 #>    50       m1    40.01  41.34199  -1.331985
 #>    75       m1    40.09  36.61471   3.475295
 #>    75       m1    33.85  36.61471  -2.764705
-#>   100       m1    31.04  32.20082  -1.160823
-#>   100       m1    33.13  32.20082   0.929177
+#>   100       m1    31.04  32.20082  -1.160824
+#>   100       m1    33.13  32.20082   0.929176
 #>   120       m1    25.15  29.04130  -3.891304
 #>   120       m1    33.31  29.04130   4.268696
# }
 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 317ffe5f..b25f2da3 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -72,7 +72,7 @@ list of lists can be given in the speclist argument." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.9
       
     

 
@@ -142,8 +142,13 @@ to other observed compartments. Instead of specifying several expressions, a
 list of lists can be given in the speclist argument.

     
 
-    
mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE,
-  verbose = FALSE)

+    
mkinmod(
+  ...,
+  use_of_ff = "min",
+  speclist = NULL,
+  quiet = FALSE,
+  verbose = FALSE
+)

 
     
Arguments
@@ -239,7 +244,7 @@ in the FOCUS and NAFTA guidance documents are used.

SFO_SFO<-mkinmod( parent=mkinsub("SFO", "m1"), m1=mkinsub("SFO"), verbose=TRUE)
#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file12cd48616f1.c 2> file12cd48616f1.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file414965c335f6.c 2> file414965c335f6.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 0eca973c..fe5bc975 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -71,7 +71,7 @@ kinetic parameters and initial values for the state variables." /> mkin - 0.9.49.6 + 0.9.49.9
@@ -140,24 +140,49 @@ kinetic model as specified by mkinmod, u kinetic parameters and initial values for the state variables.

- 
mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
-  solution_type = "deSolve", use_compiled = "auto",
-  method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
-  map_output = TRUE, ...)
+    
mkinpredict(
+  x,
+  odeparms,
+  odeini,
+  outtimes = seq(0, 120, by = 0.1),
+  solution_type = "deSolve",
+  use_compiled = "auto",
+  method.ode = "lsoda",
+  atol = 1e-08,
+  rtol = 1e-10,
+  map_output = TRUE,
+  ...
+)
 
 # S3 method for mkinmod
-mkinpredict(x, odeparms = c(k_parent_sink = 0.1),
-  odeini = c(parent = 100), outtimes = seq(0, 120, by = 0.1),
-  solution_type = "deSolve", use_compiled = "auto",
-  method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
-  map_output = TRUE, ...)
+mkinpredict(
+  x,
+  odeparms = c(k_parent_sink = 0.1),
+  odeini = c(parent = 100),
+  outtimes = seq(0, 120, by = 0.1),
+  solution_type = "deSolve",
+  use_compiled = "auto",
+  method.ode = "lsoda",
+  atol = 1e-08,
+  rtol = 1e-10,
+  map_output = TRUE,
+  ...
+)
 
 # S3 method for mkinfit
-mkinpredict(x, odeparms = x$bparms.ode,
-  odeini = x$bparms.state, outtimes = seq(0, 120, by = 0.1),
-  solution_type = "deSolve", use_compiled = "auto",
-  method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
-  map_output = TRUE, ...)

+mkinpredict(
+  x,
+  odeparms = x$bparms.ode,
+  odeini = x$bparms.state,
+  outtimes = seq(0, 120, by = 0.1),
+  solution_type = "deSolve",
+  use_compiled = "auto",
+  method.ode = "lsoda",
+  atol = 1e-08,
+  rtol = 1e-10,
+  map_output = TRUE,
+  ...
+)

Arguments

@@ -350,7 +375,7 @@ solver is used.

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 verstrichen -#> 0.004 0.000 0.003
system.time( +#> 0.003 0.000 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")[201,]))
#> time parent m1 @@ -360,7 +385,7 @@ solver is used.

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 verstrichen -#> 0.021 0.000 0.022
+#> 0.021 0.000 0.021
# \dontrun{ # Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739 @@ -372,10 +397,10 @@ solver is used.

#> Sum of squared residuals at call 9: 279.9294 #> Sum of squared residuals at call 12: 200.3629 #> Sum of squared residuals at call 13: 200.3629 -#> Sum of squared residuals at call 18: 197.9039 -#> Sum of squared residuals at call 23: 197.9039 -#> Sum of squared residuals at call 25: 196.6754 -#> Sum of squared residuals at call 27: 196.6754 +#> Sum of squared residuals at call 18: 197.904 +#> Sum of squared residuals at call 22: 197.904 +#> Sum of squared residuals at call 25: 196.6753 +#> Sum of squared residuals at call 27: 196.6753 #> Sum of squared residuals at call 32: 196.5742 #> Sum of squared residuals at call 33: 196.5742 #> Sum of squared residuals at call 34: 196.5742 @@ -390,14 +415,13 @@ solver is used.

#> Sum of squared residuals at call 58: 196.5334 #> Sum of squared residuals at call 59: 196.5334 #> Sum of squared residuals at call 65: 196.5334 -#> Sum of squared residuals at call 73: 196.5334 #> Negative log-likelihood at call 75: 26.64668
#> Optimisation successfully terminated.
head(mkinpredict(f))
#> time parent m1 #> 1 0.0 82.49216 0.000000 -#> 2 0.1 80.00563 1.179955 -#> 3 0.2 77.59404 2.312580 -#> 4 0.3 75.25515 3.399419 -#> 5 0.4 72.98675 4.441969 -#> 6 0.5 70.78673 5.441679
# } +#> 2 0.1 80.00563 1.179963 +#> 3 0.2 77.59404 2.312596 +#> 4 0.3 75.25515 3.399443 +#> 5 0.4 72.98675 4.442000 +#> 6 0.5 70.78673 5.441717
# }
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 4429798b..698af302 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -72,7 +72,7 @@ argument show_residuals = TRUE." /> mkin - 0.9.49.8 + 0.9.49.9 @@ -142,11 +142,21 @@ the residuals can be obtained using plot.mkinf argument show_residuals = TRUE.

- 
mkinresplot(object, obs_vars = names(object$mkinmod$map), xlim = c(0,
-  1.1 * max(object$data$time)), standardized = FALSE, xlab = "Time",
+    
mkinresplot(
+  object,
+  obs_vars = names(object$mkinmod$map),
+  xlim = c(0, 1.1 * max(object$data$time)),
+  standardized = FALSE,
+  xlab = "Time",
   ylab = ifelse(standardized, "Standardized residual", "Residual"),
-  maxabs = "auto", legend = TRUE, lpos = "topright",
-  col_obs = "auto", pch_obs = "auto", frame = TRUE, ...)

+  maxabs = "auto",
+  legend = TRUE,
+  lpos = "topright",
+  col_obs = "auto",
+  pch_obs = "auto",
+  frame = TRUE,
+  ...
+)

Arguments

diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png index 5e264309..7b1d73d5 100644 Binary files a/docs/reference/mmkin-2.png and b/docs/reference/mmkin-2.png differ diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png index 0a58a86b..4c412abc 100644 Binary files a/docs/reference/mmkin-3.png and b/docs/reference/mmkin-3.png differ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index d1ea7a52..8e1ea54f 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -72,7 +72,7 @@ datasets specified in its first two arguments." /> mkin - 0.9.49.6 + 0.9.49.9 @@ -141,15 +141,20 @@ more datasets datasets specified in its first two arguments.

- 
mmkin(models = c("SFO", "FOMC", "DFOP"), datasets,
-  cores = round(detectCores()/2), cluster = NULL, ...)
+ 
mmkin(
+  models = c("SFO", "FOMC", "DFOP"),
+  datasets,
+  cores = round(detectCores()/2),
+  cluster = NULL,
+  ...
+)

Arguments

- @@ -202,11 +207,11 @@ for parallel execution.

time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.014 0.024 4.895
time_1
#> User System verstrichen -#> 19.047 0.004 19.063
+#> 18.739 0.379 6.198
time_1
#> User System verstrichen +#> 19.910 0.000 19.925
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340481 0.2659519 0.7505684 0.2494316 +#> 0.7340480 0.2659520 0.7505686 0.2494314 #> #> $SFORB #> logical(0) @@ -214,8 +219,8 @@ for parallel execution.

#> $distimes #> DT50 DT90 #> parent 0.8777689 2.915885 -#> M1 2.3257449 7.725957 -#> M2 33.7200958 112.015734 +#> M1 2.3257452 7.725958 +#> M2 33.7200890 112.015711 #>
# plot.mkinfit handles rows or columns of mmkin result objects plot(fits.0[1, ])
plot(fits.0[1, ], obs_var = c("M1", "M2"))
plot(fits.0[, 1])
# Use double brackets to extract a single mkinfit object, which will be plotted diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 8dc21b06..33dc52b7 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -71,7 +71,7 @@ observed data together with the solution of the fitted model." /> mkin - 0.9.49.8 + 0.9.49.9
@@ -141,22 +141,47 @@ 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", xlim = range(fit$data$time),
-  ylim = "default", col_obs = 1:length(obs_vars), pch_obs = col_obs,
-  lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add,
-  show_residuals = FALSE, show_errplot = FALSE, maxabs = "auto",
-  sep_obs = FALSE, rel.height.middle = 0.9, row_layout = FALSE,
-  lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE,
-  errmin_digits = 3, frame = TRUE, ...)
-
-plot_sep(fit, show_errmin = TRUE,
-  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE,
-  "standardized"), ...)
-
-plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs,
+plot(
+  x,
+  fit = x,
+  obs_vars = names(fit$mkinmod$map),
+  xlab = "Time",
+  ylab = "Observed",
+  xlim = range(fit$data$time),
+  ylim = "default",
+  col_obs = 1:length(obs_vars),
+  pch_obs = col_obs,
+  lty_obs = rep(1, length(obs_vars)),
+  add = FALSE,
+  legend = !add,
+  show_residuals = FALSE,
+  show_errplot = FALSE,
+  maxabs = "auto",
+  sep_obs = FALSE,
+  rel.height.middle = 0.9,
+  row_layout = FALSE,
+  lpos = "topright",
+  inset = c(0.05, 0.05),
+  show_errmin = FALSE,
+  errmin_digits = 3,
+  frame = TRUE,
+  ...
+)
+
+plot_sep(
+  fit,
+  show_errmin = TRUE,
+  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"),
+  ...
+)
+
+plot_res(
+  fit,
+  sep_obs = FALSE,
+  show_errmin = sep_obs,
   standardized = ifelse(identical(fit$err_mod, "const"), FALSE, TRUE),
-  ...)
+  ...
+)
 
 plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 18907aa2..9d41b4c1 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -73,7 +73,7 @@ the fit of at least one model to the same dataset is shown." /> mkin - 0.9.49.8 + 0.9.49.9 @@ -144,10 +144,19 @@ the fit of at least one model to the same dataset is shown.

# S3 method for mmkin
-plot(x, main = "auto", legends = 1,
-  resplot = c("time", "errmod"), show_errmin = TRUE,
-  errmin_var = "All data", errmin_digits = 3, cex = 0.7,
-  rel.height.middle = 0.9, ymax = "auto", ...)
+plot( + x, + main = "auto", + legends = 1, + resplot = c("time", "errmod"), + show_errmin = TRUE, + errmin_var = "All data", + errmin_digits = 3, + cex = 0.7, + rel.height.middle = 0.9, + ymax = "auto", + ... +)

Arguments

models

Either a character vector of shorthand names like +

Either a character vector of shorthand names like c("SFO", "FOMC", "DFOP", "HS", "SFORB"), or an optionally named list of mkinmod objects.
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index fb3c43ef..ec79c37d 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -73,7 +73,7 @@ values." /> mkin - 0.9.49.6 + 0.9.49.9 @@ -145,12 +145,10 @@ values.

# S3 method for mkinfit
-summary(object, data = TRUE, distimes = TRUE,
-  alpha = 0.05, ...)
+summary(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
 
 # S3 method for summary.mkinfit
-print(x, digits = max(3, getOption("digits") -
-  3), ...)
+print(x, digits = max(3, getOption("digits") - 3), ...)

Arguments

@@ -223,17 +221,17 @@ distribution

Examples


-  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:10:07 2019 
-#> Date of summary: Fri Nov  1 10:10:07 2019 
+  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:43:00 2020 
+#> Date of summary: Mon Mar 30 21:43:00 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.265 s
+#> Fitted using 131 model solutions performed in 0.306 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -260,9 +258,9 @@ distribution

 #> 
 #> Parameter correlation:
 #>                    parent_0 log_k_parent_sink     sigma
-#> parent_0          1.000e+00         5.428e-01 1.648e-07
-#> log_k_parent_sink 5.428e-01         1.000e+00 2.513e-07
-#> sigma             1.648e-07         2.513e-07 1.000e+00
+#> parent_0          1.000e+00         5.428e-01 1.642e-07
+#> log_k_parent_sink 5.428e-01         1.000e+00 2.507e-07
+#> sigma             1.642e-07         2.507e-07 1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 4d88a03e..2a08228d 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -74,7 +74,7 @@ the ilr transformation is used." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.9
       
     

 
@@ -146,11 +146,19 @@ formations fractions that should always sum up to 1 and can not be negative,
 the ilr transformation is used.

     
 
-    
transform_odeparms(parms, mkinmod, transform_rates = TRUE,
-  transform_fractions = TRUE)
-
-backtransform_odeparms(transparms, mkinmod, transform_rates = TRUE,
-  transform_fractions = TRUE)

+    
transform_odeparms(
+  parms,
+  mkinmod,
+  transform_rates = TRUE,
+  transform_fractions = TRUE
+)
+
+backtransform_odeparms(
+  transparms,
+  mkinmod,
+  transform_rates = TRUE,
+  transform_fractions = TRUE
+)

 
     
Arguments
-- cgit v1.2.1