diff options
| -rw-r--r-- | NAMESPACE | 1 | ||||
| -rw-r--r-- | R/twa.R | 40 | ||||
| -rw-r--r-- | docs/reference/index.html | 2 | ||||
| -rw-r--r-- | docs/reference/one_box.html | 5 | ||||
| -rw-r--r-- | docs/reference/plot.one_box-2.png | bin | 11641 -> 5828 bytes | |||
| -rw-r--r-- | docs/reference/plot.one_box-4.png | bin | 0 -> 10603 bytes | |||
| -rw-r--r-- | docs/reference/plot.one_box.html | 8 | ||||
| -rw-r--r-- | man/one_box.Rd | 5 | ||||
| -rw-r--r-- | man/plot.one_box.Rd | 12 |
9 files changed, 63 insertions, 10 deletions
@@ -3,6 +3,7 @@ S3method(GUS,chent) S3method(GUS,numeric) S3method(max_twa,one_box) +S3method(one_box,character) S3method(one_box,mkinfit) S3method(one_box,numeric) S3method(plot,TOXSWA_cwa) @@ -66,6 +66,34 @@ one_box.numeric <- function(x, } #' @rdname one_box +#' @param parms A named numeric vector containing the model parameters +#' @export +one_box.character <- function(x, parms, + t_end = 100, res = 0.01, ...) +{ + parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE") + if (length(x) == 1 & x %in% parent_models_available) { + m <- mkinmod(parent = mkinsub(x)) + } else { + stop("If you specify the decline model using a character string, ", + "x has to be one of\n ", + paste(parent_models_available, collapse = ", ")) + } + + if (!setequal(names(parms), m$par)) { + stop("Please supply the parameters\n", + paste(m$par, collapse = ", ")) + } + + t_out <- seq(0, t_end, by = res) + pred <- mkinpredict(m, odeparms = parms, odeini = c(parent = 1), + outtimes = t_out, solution_type = "analytical")[-1] + result <- ts(pred, 0, t_end, frequency = 1/res) + class(result) <- c("one_box", "ts") + return(result) +} + +#' @rdname one_box #' @importFrom mkin mkinpredict #' @export one_box.mkinfit <- function(x, t_end = 100, res = 0.01, ...) { @@ -99,9 +127,15 @@ one_box.mkinfit <- function(x, t_end = 100, res = 0.01, ...) { #' @seealso \code{\link{sawtooth}} #' @export #' @examples -#' fomc_fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) -#' fomc_pred <- one_box(fomc_fit) -#' plot(sawtooth(fomc_pred, 3, 7), max_twa = 21) +#' dfop_pred <- one_box("DFOP", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7)) +#' plot(dfop_pred) +#' plot(sawtooth(dfop_pred, 3, 7), max_twa = 21) +#' +#' # Use a fitted mkinfit model +#' m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) +#' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) +#' pred_2_saw <- sawtooth(pred_2, 2, 7) +#' plot(pred_2_saw, max_twa = 21, max_twa_var = "m1") plot.one_box <- function(x, xlim = range(time(x)), ylim = c(0, max(x)), xlab = "Time", ylab = "Fraction of initial", diff --git a/docs/reference/index.html b/docs/reference/index.html index e458048..8f57cd2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -82,7 +82,7 @@ <p><a href="one_box.html">Create a time series of decline data</a></p> <ul> - <li><code><a href="one_box.html">one_box</a></code></li><li><code><a href="one_box.html">one_box.numeric</a></code></li><li><code><a href="one_box.html">one_box.mkinfit</a></code></li> + <li><code><a href="one_box.html">one_box</a></code></li><li><code><a href="one_box.html">one_box.numeric</a></code></li><li><code><a href="one_box.html">one_box.character</a></code></li><li><code><a href="one_box.html">one_box.mkinfit</a></code></li> </ul> <p><a href="plot.one_box.html">Plot time series of decline data</a></p> diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index 791528a..c8f8ad3 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -79,6 +79,9 @@ This does not create objects of type <code>ts</code>.</p> <span class='co'># S3 method for numeric</span> <span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>) +<span class='co'># S3 method for character</span> +<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>parms</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>) + <span class='co'># S3 method for mkinfit</span> <span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>)</pre> @@ -93,6 +96,8 @@ decline. If x is an mkinfit object, the decline is calculated from this object</ <dd>Resolution of the time series</dd> <dt>...</dt> <dd>Further arguments passed to methods</dd> + <dt>parms</dt> + <dd>A named numeric vector containing the model parameters</dd> </dl> diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png Binary files differindex 1941d44..1145f68 100644 --- a/docs/reference/plot.one_box-2.png +++ b/docs/reference/plot.one_box-2.png diff --git a/docs/reference/plot.one_box-4.png b/docs/reference/plot.one_box-4.png Binary files differnew file mode 100644 index 0000000..9664c14 --- /dev/null +++ b/docs/reference/plot.one_box-4.png diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index 235fb80..ec784c5 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -106,9 +106,11 @@ be shown if max_twa is not NULL.</dd> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>fomc_fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>fomc_pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fomc_fit</span>) -<span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>fomc_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><img src='plot.one_box-2.png' alt='' width='540' height='400' /></pre> + <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>)) +<span class='fu'>plot</span>(<span class='no'>dfop_pred</span>)</div><img src='plot.one_box-2.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><img src='plot.one_box-4.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># Use a fitted mkinfit model</span> +<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)</div><div class='output co'>#> <span class='error'>Error in as.matrix(x): Objekt 'pred_2' nicht gefunden</span></div><div class='input'><span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='output co'>#> <span class='error'>Error in plot(pred_2_saw, max_twa = 21, max_twa_var = "m1"): Objekt 'pred_2_saw' nicht gefunden</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/man/one_box.Rd b/man/one_box.Rd index 0085f3f..dc524a8 100644 --- a/man/one_box.Rd +++ b/man/one_box.Rd @@ -3,6 +3,7 @@ \name{one_box} \alias{one_box} \alias{one_box.numeric} +\alias{one_box.character} \alias{one_box.mkinfit} \title{Create a time series of decline data} \usage{ @@ -10,6 +11,8 @@ one_box(x, t_end = 100, res = 0.01, ...) \method{one_box}{numeric}(x, t_end = 100, res = 0.01, ...) +\method{one_box}{character}(x, parms, t_end = 100, res = 0.01, ...) + \method{one_box}{mkinfit}(x, t_end = 100, res = 0.01, ...) } \arguments{ @@ -21,6 +24,8 @@ decline. If x is an mkinfit object, the decline is calculated from this object} \item{res}{Resolution of the time series} \item{...}{Further arguments passed to methods} + +\item{parms}{A named numeric vector containing the model parameters} } \description{ The time series starts with the amount specified for the first application. diff --git a/man/plot.one_box.Rd b/man/plot.one_box.Rd index 6245b4c..e2c9a42 100644 --- a/man/plot.one_box.Rd +++ b/man/plot.one_box.Rd @@ -31,9 +31,15 @@ be shown if max_twa is not NULL.} Plot time series of decline data } \examples{ -fomc_fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) -fomc_pred <- one_box(fomc_fit) -plot(sawtooth(fomc_pred, 3, 7), max_twa = 21) +dfop_pred <- one_box("DFOP", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7)) +plot(dfop_pred) +plot(sawtooth(dfop_pred, 3, 7), max_twa = 21) + +# Use a fitted mkinfit model +m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) +fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) +pred_2_saw <- sawtooth(pred_2, 2, 7) +plot(pred_2_saw, max_twa = 21, max_twa_var = "m1") } \seealso{ \code{\link{sawtooth}} |
