From 850aa313ba60c7b784d96cfdc8d4c22f2beb661a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 18 Sep 2018 15:15:55 +0200 Subject: Make mkinpredict generic and write a method for fits --- man/mkinpredict.Rd | 42 ++++++++++++++++++++++++++---------------- 1 file changed, 26 insertions(+), 16 deletions(-) (limited to 'man') diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd index 524abbb5..24b918dc 100644 --- a/man/mkinpredict.Rd +++ b/man/mkinpredict.Rd @@ -1,5 +1,7 @@ \name{mkinpredict} \alias{mkinpredict} +\alias{mkinpredict.mkinmod} +\alias{mkinpredict.mkinfit} \title{ Produce predictions from a kinetic model using specific parameters } @@ -9,13 +11,15 @@ kinetic parameters and initial values for the state variables. } \usage{ - mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", - use_compiled = "auto", method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, - map_output = TRUE, ...) + mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1), + solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda", + atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...) } \arguments{ - \item{mkinmod}{ - A kinetic model as produced by \code{\link{mkinmod}}. + \item{x}{ + A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic + fit as fitted by \code{\link{mkinfit}}. In the latter case, the fitted + parameters are used for the prediction. } \item{odeparms}{ A numeric vector specifying the parameters used in the kinetic model, which @@ -69,35 +73,35 @@ Johannes Ranke } \examples{ - SFO <- mkinmod(degradinol = list(type = "SFO")) + SFO <- mkinmod(degradinol = mkinsub("SFO")) # Compare solution types mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - solution_type = "analytical") + solution_type = "analytical") mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - solution_type = "deSolve") + solution_type = "deSolve") mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - solution_type = "deSolve", use_compiled = FALSE) + solution_type = "deSolve", use_compiled = FALSE) mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - solution_type = "eigen") + solution_type = "eigen") # Compare integration methods to analytical solution mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - solution_type = "analytical")[21,] + solution_type = "analytical")[21,] mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - method = "lsoda")[21,] + method = "lsoda")[21,] mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - method = "ode45")[21,] + method = "ode45")[21,] mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - method = "rk4")[21,] + method = "rk4")[21,] # rk4 is not as precise here # The number of output times used to make a lot of difference until the # default for atol was adjusted mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), - seq(0, 20, by = 0.1))[201,] + seq(0, 20, by = 0.1))[201,] mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), - seq(0, 20, by = 0.01))[2001,] + seq(0, 20, by = 0.01))[2001,] # Check compiled model versions - they are faster than the eigenvalue based solutions! SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"), @@ -114,5 +118,11 @@ print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE)[201,])) + + \dontrun{ + # Predict from a fitted model + f <- mkinfit(SFO_SFO, FOCUS_2006_C) + head(mkinpredict(f)) + } } \keyword{ manip } -- cgit v1.2.1