Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## ----install packages, echo=FALSE, warning=FALSE, results='hide',message=FALSE----
###*****************************
seedNo=14159
set.seed(seedNo)
###*****************************
###*****************************
require("sicegar")
require("dplyr")
require("ggplot2")
###*****************************
## ----generate data for double - sigmoidal-------------------------------------
time <- seq(3, 24, 0.5)
noise_parameter <- 0.2
intensity_noise <- runif(n = length(time), min = 0, max = 1) * noise_parameter
intensity <- doublesigmoidalFitFormula(time,
finalAsymptoteIntensityRatio = .3,
maximum = 4,
slope1Param = 1,
midPoint1Param = 7,
slope2Param = 1,
midPointDistanceParam = 8)
intensity <- intensity + intensity_noise
dataInput <- data.frame(time, intensity)
head(dataInput) # the generated input data
## ----normalize_data-----------------------------------------------------------
normalizedInput <- normalizeData(dataInput = dataInput,
dataInputName = "doubleSigmoidalSample")
head(normalizedInput$timeIntensityData) # the normalized time and intensity data
## ----normalized_data_output---------------------------------------------------
normalizedInput$dataScalingParameters # scaling parameters
normalizedInput$dataInputName # data input name
## ----time normalization, eval=FALSE-------------------------------------------
# timeRange <- time
# timeNormalized <- time/timeRange # normalized time values
## ----intensity normalization, eval=FALSE--------------------------------------
# intensityMin <- min(intensity)
# intensityMax <- max(intensity)
# intensityRange <- intensityMax - intensityMin
#
# intensityNormalized <- (intensity-intensityMin)/intensityRange # normalized intensity values
## -----------------------------------------------------------------------------
# Do the sigmoidal fit
sigmoidalModel <- multipleFitFunction(dataInput=normalizedInput,
model="sigmoidal")
# Do the double-sigmoidal fit
doubleSigmoidalModel <- multipleFitFunction(dataInput=normalizedInput,
model="doublesigmoidal")
## ----parameter vectors--------------------------------------------------------
t(sigmoidalModel)
t(doubleSigmoidalModel)
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