multipleFitFunction: multiple fit function.

In wilkelab/sicegar: Analysis of Single-Cell Viral Growth Curves

Description

Calls the fitting algorithms to fit the data multiple times with starting from different randomly generated initial parameters in each run. Multiple attempts at fitting the data are necessary to avoid local minima.

Usage

multipleFitFunction(
  dataInput,
  dataInputName = NA,
  model,
  n_runs_min = 20,
  n_runs_max = 500,
  showDetails = FALSE,
  ...
)

Arguments

dataInput	A data frame or a list contatining the dataframe. The data frame should be composed of at least two columns. One represents time, and the other represents intensity. The data should be normalized with the normalize data function sicegar::normalizeData() before imported into this function.
dataInputName	Name of data set (Default is 'NA').
model	Type of fit model that will be used. Can be "sigmoidal", or "double_sigmoidal".
n_runs_min	This number indicates the lower limit of the successful fitting attempts. It should be smaller than the upper limit of the fitting attempts (n_runs_max). Default is 20.
n_runs_max	This number indicates the upper limit of the fitting attempts. Default is 500.
showDetails	Logical if TRUE prints details of intermediate steps of individual fits (Default is FALSE).
...	All other arguments that model functions ("sigmoidalFitFunction" and, "doublesigmoidalFitFunction") may need.

Value

Returns the parameters related with the model fitted for the input data.

Examples

# Example 1 (sigmoidal function with normalization)
time <- seq(3, 24, 0.5)

#simulate intensity data and add noise
noise_parameter <- 2.5
intensity_noise <- stats::runif(n = length(time), min = 0, max = 1) * noise_parameter
intensity <- sigmoidalFitFormula(time, maximum = 4, slopeParam = 1, midPoint = 8)
intensity <- intensity + intensity_noise

dataInput <- data.frame(intensity = intensity, time = time)
normalizedInput <- normalizeData(dataInput, dataInputName = "sample001")
parameterVector <- multipleFitFunction(dataInput = normalizedInput,
                                      model = "sigmoidal",
                                      n_runs_min = 20,
                                      n_runs_max = 500)

#Check the results
if(parameterVector$isThisaFit){
  intensityTheoretical <- sigmoidalFitFormula(time,
                            maximum = parameterVector$maximum_Estimate,
                            slopeParam = parameterVector$slopeParam_Estimate,
                            midPoint = parameterVector$midPoint_Estimate)

 comparisonData <- cbind(dataInput, intensityTheoretical)

 print(parameterVector$residual_Sum_of_Squares)

 require(ggplot2)
 ggplot(comparisonData)+
   geom_point(aes(x = time, y = intensity)) +
   geom_line(aes(x = time, y = intensityTheoretical), color = "orange") +
   expand_limits(x = 0, y = 0)
}



if(!parameterVector$isThisaFit){
  print(parameterVector)
}

# Example 2 (doublesigmoidal function with normalization)
time <- seq(3, 24, 0.1)

#simulate intensity data with noise
noise_parameter <- 0.2
intensity_noise <- stats::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(intensity = intensity, time = time)
normalizedInput <- normalizeData(dataInput)
parameterVector <- multipleFitFunction(dataInput = normalizedInput,
                           dataInputName="sample001",
                           model = "doublesigmoidal",
                           n_runs_min = 20,
                           n_runs_max = 500,
                           showDetails = FALSE)


#Check the results
if(parameterVector$isThisaFit){
 intensityTheoretical <-
       doublesigmoidalFitFormula(
               time,
               finalAsymptoteIntensityRatio = parameterVector$finalAsymptoteIntensityRatio_Estimate,
               maximum = parameterVector$maximum_Estimate,
               slope1Param = parameterVector$slope1Param_Estimate,
               midPoint1Param = parameterVector$midPoint1Param_Estimate,
               slope2Param = parameterVector$slope2Param_Estimate,
               midPointDistanceParam = parameterVector$midPointDistanceParam_Estimate)

 comparisonData <- cbind(dataInput, intensityTheoretical)

 require(ggplot2)
 ggplot(comparisonData) +
   geom_point(aes(x = time, y = intensity)) +
   geom_line(aes(x = time, y = intensityTheoretical), color = "orange") +
   expand_limits(x = 0, y = 0)
 }

if(!parameterVector$isThisaFit){
  print(parameterVector)
  }

wilkelab/sicegar documentation built on May 8, 2021, 11:08 p.m.