From 6e5630a0df7e857697ff2ce4730a5f7f45b67377 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 26 Oct 2019 22:52:53 +0200 Subject: Fix checks and tests Static documentation rebuilt by pkgdown --- docs/reference/confint.mkinfit.html | 252 ++++++++++++++++++++++++++++++++++++ docs/reference/index.html | 24 +++- docs/reference/parms.html | 200 ++++++++++++++++++++++++++++ 3 files changed, 470 insertions(+), 6 deletions(-) create mode 100644 docs/reference/confint.mkinfit.html create mode 100644 docs/reference/parms.html (limited to 'docs/reference') diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html new file mode 100644 index 00000000..64ea0d4c --- /dev/null +++ b/docs/reference/confint.mkinfit.html @@ -0,0 +1,252 @@ + + + + + + + + +Confidence intervals for parameters of mkinfit objects — confint.mkinfit • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Confidence intervals for parameters of mkinfit objects

+ + +
+ +
+

Confidence intervals for parameters of mkinfit objects

+
+ + 
# S3 method for mkinfit
+confint(object, parm, level = 0.95, alpha = 1 -
+  level, method = c("profile", "quadratic"), transformed = TRUE,
+  backtransform = TRUE, distribution = c("student_t", "normal"),
+  quiet = FALSE, ...)
+ +

Arguments

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
object

An mkinfit object

parm

A vector of names of the parameters which are to be given +confidence intervals. If missing, all parameters are considered.

level

The confidence level required

alpha

The allowed error probability, overrides 'level' if specified.

method

The 'profile' method searches the parameter space for the +cutoff of the confidence intervals by means of a likelihood ratio test. +The 'quadratic' method approximates the likelihood function at the +optimised parameters using the second term of the Taylor expansion, using +a second derivative (hessian) contained in the object.

transformed

If the quadratic approximation is used, should it be +applied to the likelihood based on the transformed parameters?

backtransform

If we approximate the likelihood in terms of the +transformed parameters, should we backtransform the parameters with +their confidence intervals?

distribution

For the quadratic approximation, should we use +the student t distribution or assume normal distribution for +the parameter estimate

quiet

Should we suppress messages?

...

Not used

+ +

Value

+ +

A matrix with columns giving lower and upper confidence limits for + each parameter.

+

References

+ +

Pawitan Y (2013) In all likelihood - Statistical modelling and + inference using likelihood. Clarendon Press, Oxford.

+ +

Examples

+ 
f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
+confint(f, method = "quadratic")
#>                     2.5%      97.5%
+#> parent_0      71.8242430 93.1600766
+#> k_parent_sink  0.2109541  0.4440528
+#> sigma          1.9778868  7.3681380
# \dontrun{
+  confint(f, method = "profile")
#> Profiling the likelihood
#>                     2.5%      97.5%
+#> parent_0      71.3471007 93.9447024
+#> k_parent_sink  0.2030765  0.4491067
+#> sigma          2.9810656  8.8633278
# }
+
+
+ +
+ + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.4.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 328f5aca..fa424060 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -184,12 +184,30 @@ more datasets

Plot the observed data and the fitted model of an mkinfit object

+ +

parms()

+ +

Extract model parameters from mkinfit models

+ + + +

confint(<mkinfit>)

+ +

Confidence intervals for parameters of mkinfit objects

+ +

summary(<mkinfit>) print(<summary.mkinfit>)

Summary method for class "mkinfit"

+ +

logLik(<mkinfit>)

+ +

Calculated the log-likelihood of a fitted mkinfit object

+ +

mkinresplot()

@@ -219,12 +237,6 @@ with mkinfit

mkinerrmin()

Calculate the minimum error to assume in order to pass the variance test

- - - -

logLik(<mkinfit>)

- -

Calculated the log-likelihood of a fitted mkinfit object

diff --git a/docs/reference/parms.html b/docs/reference/parms.html new file mode 100644 index 00000000..8ab26240 --- /dev/null +++ b/docs/reference/parms.html @@ -0,0 +1,200 @@ + + + + + + + + +Extract model parameters from mkinfit models — parms • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Extract model parameters from mkinfit models

+ + +
+ +
+

This function always returns degradation model parameters as well as error +model parameters, in order to avoid working with a fitted model without +considering the error structure that was assumed for the fit.

+
+ + 
parms(object, ...)
+
+# S3 method for mkinfit
+parms(object, transformed = FALSE, ...)
+ +

Arguments

+ + + + + + + + + + + + + + +
object

A fitted model object

...

Not used

transformed

Should the parameters be returned +as used internally during the optimisation?

+ +

Value

+ +

A numeric vector of fitted model parameters

+ +
+ +
+ + + +
+ + + + + + + + -- cgit v1.2.1