From aed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Wed, 31 Jan 2024 13:16:17 +0100 Subject: Reorganise data generation - Use inst/data_generation for R code generating data as in some of my other packages - data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff contents were not changed - Remove ChangeLog, the history is in the git logs - Update docs and some links contained therein - use \doi{} markup - Move logs to log directory --- docs/reference/one_box.html | 236 +++++++++++++++++--------------------------- 1 file changed, 88 insertions(+), 148 deletions(-) (limited to 'docs/reference/one_box.html') diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index cf58a58..62875b3 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -1,64 +1,12 @@ - - - - - - - -Create a time series of decline data — one_box • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Create a time series of decline data — one_box • pfm - - - - + + -
-
- -
- -
+

Create a time series of decline data

@@ -109,99 +43,105 @@

Create a time series of decline data

- 
one_box(x, ini, ..., t_end = 100, res = 0.01)
-
-# S3 method for numeric
-one_box(x, ini = 1, ..., t_end = 100, res = 0.01)
-
-# S3 method for character
-one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01)
-
-# S3 method for mkinfit
-one_box(x, ini = "model", ..., t_end = 100, res = 0.01)
+
+ 
one_box(x, ini, ..., t_end = 100, res = 0.01)
+
+# S3 method for numeric
+one_box(x, ini = 1, ..., t_end = 100, res = 0.01)
+
+# S3 method for character
+one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01)
+
+# S3 method for mkinfit
+one_box(x, ini = "model", ..., t_end = 100, res = 0.01)
+
-

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - -
x

When numeric, this is the half-life to be used for an exponential +

+

Arguments

+
x
+

When numeric, this is the half-life to be used for an exponential decline. When a character string specifying a parent decline model is given e.g. FOMC, parms must contain the corresponding parameters. -If x is an mkinfit object, the decline is calculated from this -object.

ini

The initial amount. If x is an mkinfit object, and +If x is an mkinfit object, the decline is calculated from this +object.

+ + +
ini
+

The initial amount. If x is an mkinfit object, and ini is 'model', the fitted initial concentrations are used. Otherwise, ini must be numeric. If it has length one, it is used for the parent and initial values of metabolites are zero, otherwise, it must give values for -all observed variables.

...

Further arguments passed to methods

t_end

End of the time series

res

Resolution of the time series

parms

A named numeric vector containing the model parameters

- -

Value

- -

An object of class one_box, inheriting from ts.

- -

Examples

- 
# Only use a half-life
-pred_0 <- one_box(10)
-plot(pred_0)

-# Use a fitted mkinfit model
-require(mkin)
-fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-pred_1 <- one_box(fit)
-plot(pred_1)

-# Use a model with more than one observed variable
-m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
pred_2 <- one_box(fit_2, ini = "model")
-plot(pred_2)
-
- +
+

Value

+ + +

An object of class one_box, inheriting from ts.

+
+ +
+

Examples

+ 
# Only use a half-life
+pred_0 <- one_box(10)
+plot(pred_0)
+
+
+# Use a fitted mkinfit model
+require(mkin)
+fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+pred_1 <- one_box(fit)
+plot(pred_1)
+
+
+# Use a model with more than one observed variable
+m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
+#> Temporary DLL for differentials generated and loaded
+fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
+#> Warning: Observations with value of zero were removed from the data
+pred_2 <- one_box(fit_2, ini = "model")
+plot(pred_2)
+
+
+
+
-
- - + + -- cgit v1.2.1