diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-03-23 17:03:09 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-03-23 18:00:06 +0100 |
| commit | 7875935fdfc3c55e0ef328b3c3a4512a30011df1 (patch) | |
| tree | cb0c1596d34d4db08271890ac922f026a53206cf /inst/web/mkinfit.html | |
| parent | c9667fbfd5a8c9601ac0c977776b12fe7d9b19dd (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.html | 26 |
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 = "auto", state.ini = "auto", fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], solution_type = c("auto", "analytical", "eigen", "deSolve"), method.ode = "lsoda", use_compiled = "auto", method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"), maxit.modFit = "auto", control.modFit = list(), transform_rates = TRUE, transform_fractions = TRUE, plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, reweight.method = NULL, reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...)</div></pre> + <pre><div>mkinfit(mkinmod, observed, parms.ini = "auto", state.ini = "auto", fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE, solution_type = c("auto", "analytical", "eigen", "deSolve"), method.ode = "lsoda", use_compiled = "auto", method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"), maxit.modFit = "auto", control.modFit = list(), transform_rates = TRUE, transform_fractions = TRUE, plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, reweight.method = NULL, reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = 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 <- mkinfit("FOMC", 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 <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", 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> |