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diff --git a/docs/reference/one_box.md b/docs/reference/one_box.md new file mode 100644 index 0000000..89ccecf --- /dev/null +++ b/docs/reference/one_box.md @@ -0,0 +1,115 @@ +# Create a time series of decline data + +Create a time series of decline data + +## Usage + +``` r +one_box(x, ini, ..., t_end = 100, res = 0.01) + +# S3 method for class 'numeric' +one_box(x, ini = 1, ..., t_end = 100, res = 0.01) + +# S3 method for class 'character' +one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01) + +# S3 method for class 'mkinmod' +one_box( + x, + ini = c(1, rep(0, length(x$diffs) - 1)), + odeparms, + solution_type = "deSolve", + ..., + t_end = 100, + res = 0.01 +) + +# S3 method for class '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 + 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](https://pkgdown.jrwb.de/mkin/reference/mkinfit.html) object, + the decline is calculated from this object. + +- ini: + + The initial amount. If x is an + [mkinfit](https://pkgdown.jrwb.de/mkin/reference/mkinfit.html) 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 + +- odeparms: + + Will be passed to + [mkinpredict](https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html) + +- solution_type: + + Will be passed to + [mkinpredict](https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html) + +## Value + +An object of class `one_box`, inheriting from +[ts](https://rdrr.io/r/stats/ts.html). + +## Examples + +``` r +# Only use a half-life +pred_0 <- one_box(10) +plot(pred_0) + + +# Use a custom mkin model +require(mkin) +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", to = "m1"), + m1 = mkinsub("SFO")) +#> Temporary DLL for differentials generated and loaded +c_0 = c(parent = 100, m1 = 0) +deg_parms = c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01) +pred_sfo_sfo <- one_box(SFO_SFO, odeparms = deg_parms, ini = c_0) +plot(pred_sfo_sfo) + + +# Use a fitted mkin model +fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) +pred_1 <- one_box(fit) +plot(pred_1) + + +# Use a fitted model with a metabolite +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) +``` |
