Corrections in the documentation

4 files changed, 60 insertions, 23 deletions

diff --git a/ChangeLog b/ChangeLog
index bcb7553..0a73e39 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,15 @@
+commit 46883a0c3a3c00127a563a7befa0af440573baaa
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-01-19 11:22:08 +0100
+
+    Correct default y axis label for plot.one_box
+
+commit 3947731a5a8c3598271b26f5201dea4bcb13ef6d
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-01-19 10:47:09 +0100
+
+    Fix one_box for ini = 1, use in sawtooth examples
+
 commit dd30f0d0ff1d8d0cc46aaef6e0917c51fe798f52
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2017-01-19 10:36:19 +0100
diff --git a/R/twa.R b/R/twa.R
index 7fa6241..75aaf85 100644
--- a/R/twa.R
+++ b/R/twa.R
@@ -18,15 +18,20 @@
 
 #' Create a time series of decline data
 #'
-#' The time series starts with the amount specified for the first application.
-#' This does not create objects of type \code{\link{ts}}.
-#'
 #' @param x When numeric, this is the half-life to be used for an exponential
-#' decline. If x is an mkinfit object, the decline is calculated from this object
-#' @param ini The initial amount for each compound
+#'   decline. When a character string specifying a parent decline model is given
+#'   e.g. \code{FOMC}, \code{parms} must contain the corresponding paramters.
+#'   If x is an \code{\link{mkinfit}} object, the decline is calculated from this
+#'   object.  
+#' @param ini The initial amount for the parent compound. If x is an 
+#'   \code{\link{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.
 #' @param t_end End of the time series
 #' @param res Resolution of the time series
 #' @param ... Further arguments passed to methods
+#' @return An object of class \code{one_box}, inheriting from \code{\link{ts}}.
 #' @importFrom stats filter frequency time ts
 #' @export
 #' @examples
@@ -59,7 +64,7 @@ one_box.numeric <- function(x, ini = 1, ...,
   half_life = x
   k = log(2)/half_life
   t_out <- seq(0, t_end, by = res)
-  raw <- matrix(exp( - k * t_out), ncol = 1)
+  raw <- matrix(ini * exp( - k * t_out), ncol = 1)
   dimnames(raw) <- list(NULL, "parent")
   result <- ts(raw, 0, t_end, frequency = 1/res)
   class(result) <- c("one_box", "ts")
@@ -87,7 +92,7 @@ one_box.character <- function(x, ini = 1, parms, ...,
   }
 
   t_out <- seq(0, t_end, by = res)
-  pred <- mkinpredict(m, odeparms = parms, odeini = c(parent = 1),
+  pred <- mkinpredict(m, odeparms = parms, odeini = c(parent = ini),
                       outtimes = t_out, solution_type = "analytical")[-1]
   result <- ts(pred, 0, t_end, frequency = 1/res)
   class(result) <- c("one_box", "ts")
@@ -97,13 +102,14 @@ one_box.character <- function(x, ini = 1, parms, ...,
 #' @rdname one_box
 #' @importFrom mkin mkinpredict
 #' @export
-one_box.mkinfit <- function(x, ini = c("model", 1), ..., t_end = 100, res = 0.01) {
+one_box.mkinfit <- function(x, ini = "model", ..., t_end = 100, res = 0.01) {
   fit <- x
   if (ini[1] == "model") {
     odeini = x$bparms.state
   } else {
-    if (ini[1] != 1) stop ("Argument ini can only be 'model' or 1")
-    odeini <- c(1, rep(0, length(fit$mkinmod$spec) - 1))
+    if (!is.numeric(ini[1])) stop ("Argument ini can only be 'model' or numeric")
+    if (length(ini) == 1) odeini <- c(ini[1], rep(0, length(fit$mkinmod$spec) - 1))
+    else odeini = ini
     names(odeini) <- names(fit$mkinmod$spec)
   }
 
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 853f892..4e60143 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -70,8 +70,7 @@
     </div>
 
     
-    <p>The time series starts with the amount specified for the first application.
-This does not create objects of type <code>ts</code>.</p>
+    <p>Create a time series of decline data</p>
     
 
     <pre><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>ini</span>, <span class='no'>...</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>)
@@ -84,16 +83,22 @@ This does not create objects of type <code>ts</code>.</p>
   <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
 
 <span class='co'># S3 method for mkinfit</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"model"</span>, <span class='fl'>1</span>), <span class='no'>...</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>)</pre>
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</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>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <dl class="dl-horizontal">
       <dt>x</dt>
       <dd>When numeric, this is the half-life to be used for an exponential
-decline. If x is an mkinfit object, the decline is calculated from this object</dd>
+decline. When a character string specifying a parent decline model is given
+e.g. <code>FOMC</code>, <code>parms</code> must contain the corresponding paramters.
+If x is an <code>mkinfit</code> object, the decline is calculated from this
+object.</dd>
       <dt>ini</dt>
-      <dd>The initial amount for each compound</dd>
+      <dd>The initial amount for the parent compound. If x is an 
+<code>mkinfit</code> object, and ini is &#39;model&#39;, 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.</dd>
       <dt>...</dt>
       <dd>Further arguments passed to methods</dd>
       <dt>t_end</dt>
@@ -104,6 +109,10 @@ decline. If x is an mkinfit object, the decline is calculated from this object</
       <dd>A named numeric vector containing the model parameters</dd>
     </dl>
     
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>An object of class <code>one_box</code>, inheriting from <code>ts</code>.</p>
+    
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># Only use a half-life</span>
@@ -123,7 +132,9 @@ decline. If x is an mkinfit object, the decline is calculated from this object</
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
-            
+      
+      <li><a href="#value">Value</a></li>
+      
       <li><a href="#examples">Examples</a></li>
     </ul>
 
diff --git a/man/one_box.Rd b/man/one_box.Rd
index 1bdc791..134b206 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -14,14 +14,20 @@ one_box(x, ini, ..., t_end = 100, res = 0.01)
 \method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100,
   res = 0.01)
 
-\method{one_box}{mkinfit}(x, ini = c("model", 1), ..., t_end = 100,
-  res = 0.01)
+\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, res = 0.01)
 }
 \arguments{
 \item{x}{When numeric, this is the half-life to be used for an exponential
-decline. If x is an mkinfit object, the decline is calculated from this object}
+decline. When a character string specifying a parent decline model is given
+e.g. \code{FOMC}, \code{parms} must contain the corresponding paramters.
+If x is an \code{\link{mkinfit}} object, the decline is calculated from this
+object.}
 
-\item{ini}{The initial amount for each compound}
+\item{ini}{The initial amount for the parent compound. If x is an 
+\code{\link{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.}
 
 \item{...}{Further arguments passed to methods}
 
@@ -31,9 +37,11 @@ decline. If x is an mkinfit object, the decline is calculated from this object}
 
 \item{parms}{A named numeric vector containing the model parameters}
 }
+\value{
+An object of class \code{one_box}, inheriting from \code{\link{ts}}.
+}
 \description{
-The time series starts with the amount specified for the first application.
-This does not create objects of type \code{\link{ts}}.
+Create a time series of decline data
 }
 \examples{
 # Only use a half-life