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

1 files changed, 14 insertions, 1 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index 4a5be20a..929c73f0 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2015 Johannes Ranke

+# Copyright (C) 2010-2016 Johannes Ranke

 # Portions of this code are copyright (C) 2013 Eurofins Regulatory AG

 # Contact: jranke@uni-bremen.de

 # The summary function is an adapted and extended version of summary.modFit

@@ -26,6 +26,7 @@ mkinfit <- function(mkinmod, observed,
   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",

@@ -79,6 +80,18 @@ mkinfit <- function(mkinmod, observed,
   # Subset observed data with names of observed data in the model

   observed <- subset(observed, name %in% obs_vars)

 

+  # Obtain data for decline from maximum mean value if requested

+  if (from_max_mean) {

+    # This is only used for simple decline models

+    if (length(obs_vars) > 1) 

+      stop("Decline from maximum is only implemented for models with a single observed variable")

+

+    means <- aggregate(value ~ time, data = observed, mean, na.rm=TRUE)

+    t_of_max <- means[which.max(means$value), "time"]

+    observed <- subset(observed, time >= t_of_max)

+    observed$time <- observed$time - t_of_max

+  }

+

   # Define starting values for parameters where not specified by the user

   if (parms.ini[[1]] == "auto") parms.ini = vector()