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 From 64a476750ff57f4c612620bd58cc4ac42812e185 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 31 Mar 2020 09:52:19 +0200 Subject: Use inline documentation for R6 class mkinds --- docs/reference/mkinds.html | 64 +++++++++++++++++++++++++--------------- docs/reference/print.mkinds.html | 6 ++-- 2 files changed, 44 insertions(+), 26 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index c1cdcf99..ef6fb35c 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -36,7 +36,10 @@ - + @@ -133,36 +136,36 @@
-

A dataset class for mkin

+

At the moment this dataset class is hardly used in mkin. For example, +mkinfit does not take mkinds datasets as argument, but works with dataframes +such as the on contained in the data field of mkinds objects. Some datasets +provided by this package come as mkinds objects nevertheless.

-

Format

+

See also

-

An R6Class generator object.

-

Fields

+

The S3 printing method print.mkinds

+

Public fields

- - - -
-
list("title")

A full title for the dataset

+

+
title

A full title for the dataset

-
list("sampling")

times The sampling times

+
sampling_times

The sampling times

-
list("time_unit")

The time unit

+
time_unit

The time unit

-
list("observed")

Names of the observed compounds

+
observed

Names of the observed variables

-
list("unit")

The unit of the observations

+
unit

The unit of the observations

-
list("replicates")

The number of replicates

+
replicates

The maximum number of replicates per sampling time

-
list("data")

A dataframe with at least the columns name, time and -value in order to be compatible with mkinfit

-
+
data

A data frame with at least the columns name, time +and value in order to be compatible with mkinfit

+

Methods

@@ -174,10 +177,20 @@ value in order to be compatible with mkinfit

Method new()

- -

Usage

+

Create a new mkinds object

Usage

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

+

Arguments

+

+
title

The dataset title

+ +
data

The data

+ +
time_unit

The time unit

+ +
unit

The unit of the observations

+ +

Method clone()

The objects of this class are cloneable with this method.

Usage

@@ -193,13 +206,18 @@ value in order to be compatible with mkinfit

Examples


-mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
+mds <- mkinds$new("FOCUS A", FOCUS_2006_A) +print(mds)
#> <mkinds> with $title: FOCUS A +#> Observed compounds $observed: parent +#> Sampling times $sampling_times: 0, 3, 7, 14, 30, 62, 90, 118 +#> With a maximum of 1 replicates
+
@@ -133,7 +133,7 @@
-

Print mkinds objects.

+

Print mkinds objects

# S3 method for mkinds
-- 
cgit v1.2.1


From 47ba9ea512b82fb8b31da8ec5558f3c0952d86d4 Mon Sep 17 00:00:00 2001
From: Johannes Ranke 
Date: Thu, 2 Apr 2020 10:58:34 +0200
Subject: Compiled models article, reduce distractions

- Added a section with platform specific notes on getting compiled
models to work to the compiled models article
- Don't return empty SFORB parameter list from endpoints() if there is no
SFORB model
- Avoid warnings when using standardized = TRUE in plot.mmkin()
---
 docs/reference/endpoints.html  | 5 +----
 docs/reference/plot.mmkin.html | 7 +++++++
 2 files changed, 8 insertions(+), 4 deletions(-)

(limited to 'docs/reference')

diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index e81bdbb5..f201294d 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -75,7 +75,7 @@ advantage that the SFORB model can also be used for metabolites." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.9
       
     
 
@@ -171,9 +171,6 @@ advantage that the SFORB model can also be used for metabolites.

   endpoints(fit)
#> $ff
 #> logical(0)
 #> 
-#> $SFORB
-#> logical(0)
-#> 
 #> $distimes
 #>            DT50    DT90 DT50back
 #> parent 1.785233 15.1479 4.559973
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 9d41b4c1..be60f228 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -149,6 +149,7 @@ the fit of at least one model to the same dataset is shown.

   main = "auto",
   legends = 1,
   resplot = c("time", "errmod"),
+  standardized = FALSE,
   show_errmin = TRUE,
   errmin_var = "All data",
   errmin_digits = 3,
@@ -179,6 +180,12 @@ column.
+ + + + -- cgit v1.2.1

Should the residuals plotted against time, using mkinresplot, or as squared residuals against predicted values, with the error model, using mkinerrplot.

standardized

Should the residuals be standardized? This option +is passed to mkinresplot, it only takes effect if +`resplot = "time"`.
show_errmin