aboutsummaryrefslogtreecommitdiff
path: root/inst/web/mkinfit.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2016-03-23 17:03:09 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2016-03-23 18:00:06 +0100
commit7875935fdfc3c55e0ef328b3c3a4512a30011df1 (patch)
treecb0c1596d34d4db08271890ac922f026a53206cf /inst/web/mkinfit.html
parentc9667fbfd5a8c9601ac0c977776b12fe7d9b19dd (diff)
Added 'from_max_mean' to 'mkinfit'.
- Now it is easier to do decline kinetics from the maximum occurrence - Static documentation rebuilt by staticdocs::build_site() - Fixed an URL in the README, thanks to the win-builder check with R-devel
Diffstat (limited to 'inst/web/mkinfit.html')
-rw-r--r--inst/web/mkinfit.html26
1 files changed, 17 insertions, 9 deletions
diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html
index 3c48dcc0..75d8be8b 100644
--- a/inst/web/mkinfit.html
+++ b/inst/web/mkinfit.html
@@ -2,7 +2,7 @@
<html lang="en">
<head>
<meta charset="utf-8">
-<title>mkinfit. mkin 0.9.41.9000</title>
+<title>mkinfit. mkin 0.9.42</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="
Johannes Ranke
@@ -34,7 +34,7 @@
<div class="navbar">
<div class="navbar-inner">
<div class="container">
- <a class="brand" href="#">mkin 0.9.41.9000</a>
+ <a class="brand" href="#">mkin 0.9.42</a>
<div class="nav">
<ul class="nav">
<li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
@@ -56,7 +56,7 @@
<div class="row">
<div class="span8">
<h2>Usage</h2>
- <pre><div>mkinfit(mkinmod, observed, parms.ini&nbsp;=&nbsp;"auto", state.ini&nbsp;=&nbsp;"auto", fixed_parms&nbsp;=&nbsp;NULL, fixed_initials&nbsp;=&nbsp;names(mkinmod$diffs)[-1], solution_type&nbsp;=&nbsp;c("auto", "analytical", "eigen", "deSolve"), method.ode&nbsp;=&nbsp;"lsoda", use_compiled&nbsp;=&nbsp;"auto", method.modFit&nbsp;=&nbsp;c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"), maxit.modFit&nbsp;=&nbsp;"auto", control.modFit&nbsp;=&nbsp;list(), transform_rates&nbsp;=&nbsp;TRUE, transform_fractions&nbsp;=&nbsp;TRUE, plot&nbsp;=&nbsp;FALSE, quiet&nbsp;=&nbsp;FALSE, err&nbsp;=&nbsp;NULL, weight&nbsp;=&nbsp;"none", scaleVar&nbsp;=&nbsp;FALSE, atol&nbsp;=&nbsp;1e-8, rtol&nbsp;=&nbsp;1e-10, n.outtimes&nbsp;=&nbsp;100, reweight.method&nbsp;=&nbsp;NULL, reweight.tol&nbsp;=&nbsp;1e-8, reweight.max.iter&nbsp;=&nbsp;10, trace_parms&nbsp;=&nbsp;FALSE, ...)</div></pre>
+ <pre><div>mkinfit(mkinmod, observed, parms.ini&nbsp;=&nbsp;"auto", state.ini&nbsp;=&nbsp;"auto", fixed_parms&nbsp;=&nbsp;NULL, fixed_initials&nbsp;=&nbsp;names(mkinmod$diffs)[-1], from_max_mean&nbsp;=&nbsp;FALSE, solution_type&nbsp;=&nbsp;c("auto", "analytical", "eigen", "deSolve"), method.ode&nbsp;=&nbsp;"lsoda", use_compiled&nbsp;=&nbsp;"auto", method.modFit&nbsp;=&nbsp;c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"), maxit.modFit&nbsp;=&nbsp;"auto", control.modFit&nbsp;=&nbsp;list(), transform_rates&nbsp;=&nbsp;TRUE, transform_fractions&nbsp;=&nbsp;TRUE, plot&nbsp;=&nbsp;FALSE, quiet&nbsp;=&nbsp;FALSE, err&nbsp;=&nbsp;NULL, weight&nbsp;=&nbsp;"none", scaleVar&nbsp;=&nbsp;FALSE, atol&nbsp;=&nbsp;1e-8, rtol&nbsp;=&nbsp;1e-10, n.outtimes&nbsp;=&nbsp;100, reweight.method&nbsp;=&nbsp;NULL, reweight.tol&nbsp;=&nbsp;1e-8, reweight.max.iter&nbsp;=&nbsp;10, trace_parms&nbsp;=&nbsp;FALSE, ...)</div></pre>
<h2>Arguments</h2>
<dl>
@@ -114,6 +114,14 @@
be excluded from the optimisation. Defaults to all state variables except
for the first one.
</dd>
+ <dt>from_max_mean</dt>
+ <dd>
+ If this is set to TRUE, and the model has only one observed variable, then
+ data before the time of the maximum observed value (after averaging for each
+ sampling time) are discarded, and this time is subtracted from all
+ remaining time values, so the time of the maximum observed mean value is
+ the new time zero.
+ </dd>
<dt>solution_type</dt>
<dd>
If set to "eigen", the solution of the system of differential equations is
@@ -315,17 +323,17 @@
fit &lt;- mkinfit(&quot;FOMC&quot;, FOCUS_2006_C, quiet = TRUE)
summary(fit)
</div>
-<div class='output'>mkin version: 0.9.41.9000
-R version: 3.2.2
-Date of fit: Wed Dec 9 10:16:57 2015
-Date of summary: Wed Dec 9 10:16:57 2015
+<div class='output'>mkin version: 0.9.42
+R version: 3.2.4
+Date of fit: Wed Mar 23 16:59:43 2016
+Date of summary: Wed Mar 23 16:59:43 2016
Equations:
d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
Model predictions using solution type analytical
-Fitted with method Port using 64 model solutions performed in 0.189 s
+Fitted with method Port using 64 model solutions performed in 0.195 s
Weighting: none
@@ -401,7 +409,7 @@ print(system.time(fit &lt;- mkinfit(SFO_SFO, FOCUS_2006_D,
solution_type = &quot;eigen&quot;, quiet = TRUE)))
</div>
<div class='output'> user system elapsed
- 1.184 1.180 0.891
+ 1.200 1.272 0.936
</div>
<div class='input'>coef(fit)
</div>

Contact - Imprint