Nothing
R/pguNormDist.R
In pguIMP: 'pguIMP'
#' @title pgu.normDist
#'
#' @description
#' Compares the distribution of a single attribute's values to normal distribution
#' by using several statistic tests.
#'
#' @details
#' The distribution of a single value is tested for normality by
#' Shapiro-Wilk test, Kolmogorov-Smirnov test, Anderson-Darling test.
#' The expectation value and standard deviation of a normal distribution
#' representing the data are determined by maximizing the log Likelihood
#' with respect to the expectation value and standard deviation.
#' This object is used by the shiny based gui and is not for use in individual R-scripts!
#'
#' @format [R6::R6Class] object.
#'
#' @importFrom bbmle AIC AICc logLik mle2 residuals
#' @importFrom dplyr mutate
#' @importFrom ggplot2 aes aes_string element_rect geom_col geom_histogram geom_line geom_point
#' @importFrom ggplot2 geom_smooth ggplot ggplot_build ggtitle stat_qq stat_qq_line
#' @importFrom ggplot2 theme theme_linedraw xlab ylab
#' @importFrom magrittr %>%
#' @importFrom nortest ad.test lillie.test
#' @importFrom purrr discard
#' @importFrom R6 R6Class
#' @importFrom stats BIC ks.test na.omit optim shapiro.test
#' @importFrom tibble tibble
#'
#' @include dLogLikelihood.R
#' @include sLogLikelihood.R
#' @include normalDistribution.R
#'
#' @author Sebastian Malkusch, \email{malkusch@@med.uni-frankfurt.de}
#'
#' @export
#'
pgu.normDist <- R6::R6Class("pgu.normDist",
####################
# instance variables
####################
private = list(
.featureName = "character",
.rawData = "tbl_df",
.histogram = "tbl_df",
.expMu = "numeric",
.expSigma = "numeric",
.dataPoints = "numeric",
.logLikelihood = "numeric",
.degOfFreedom = "numeric",
.n = "integer",
.bic = "numeric",
.aic = "numeric",
.aicc = "numeric",
.rmse = "numeric",
# Test results
.fitSuccess = "logical",
.testNames = "character",
.testParameterNames = "character",
.alpha = "numeric",
# Shapiro Wilk test
.w.shapiro = "numeric",
.p.shapiro = "numeric",
# Kolmogorow Smirnow test
.d.kolmogorow = "numeric",
.p.kolmogorow = "numeric",
# Anderson Darling test
.a.anderson = "numeric",
.p.anderson = "numeric"
),
##################
# accessor methods
##################
active = list(
#' @field featureName
#' Returns the instance variable featureName.
#' (character)
featureName = function(){
return(private$.featureName)
},
#' @field rawData
#' Returns the instance variable rawData.
#' (tibble::tibble)
rawData = function(){
return(private$.rawData)
},
#' @field setRawData
#' Sets the instance variable rawData.
#' (tibble::tibble)
setRawData = function(data = "tbl_df"){
self$resetNormDist(data)
},
#' @field histogram
#' Returns the instance variable histogram.
#' (tibble::tibble)
histogram = function(){
return(private$.histogram)
},
#' @field expMu
#' Returns the instance variable expMu.
#' (numeric)
expMu = function(){
return(private$.expMu)
},
#' @field expSigma
#' Returns the instance variable expSigma.
#' (numeric)
expSigma = function(){
return(private$.expSigma)
},
#' @field dataPoints
#' Returns the instance variable dataPoints.
#' (numeric)
dataPoints = function(){
return(private$.dataPoints)
},
#' @field logLikelihood
#' Returns the instance variable logLikelihood.
#' (numeric)
logLikelihood = function(){
return(private$.logLikelihood)
},
#' @field degOfFreedom
#' Returns the instance variable degOfFreedom.
#' (numeric)
degOfFreedom = function(){
return(private$.degOfFreedom)
},
#' @field n
#' Returns the instance variable n.
#' (integer)
n = function(){
return(private$.n)
},
#' @field bic
#' Returns the instance variable bic.
#' (numeric)
bic = function(){
return(private$.bic)
},
#' @field aic
#' Returns the instance variable aic.
#' (numeric)
aic = function(){
return(private$.aic)
},
#' @field aicc
#' Returns the instance variable aicc.
#' (numeric)
aicc = function(){
return(private$.aicc)
},
#' @field rmse
#' Returns the instance variable rmse.
#' (numeric)
rmse = function(){
return(private$.rmse)
},
#' @field fitSuccess
#' Returns the instance variable fitSuccess.
#' (logical)
fitSuccess = function(){
return(private$.fitSuccess)
},
#' @field testNames
#' Returns the instance variable testNames.
#' (character)
testNames = function(){
return(private$.testNames)
},
#' @field testParameterNames
#' Returns the instance variable testParameterNames.
#' (character)
testParameterNames = function(){
return(private$.testParameterNames)
},
#' @field alpha
#' Returns the instance variable alpha.
#' (numeric)
alpha = function(){
return(private$.alpha)
},
#' @field w.shapiro
#' Returns the instance variable w.shapiro.
#' (numeric)
w.shapiro = function(){
return(private$.w.shapiro)
},
#' @field p.shapiro
#' Returns the instance variable p.shapiro.
#' (numeric)
p.shapiro = function(){
return(private$.p.shapiro)
},
#' @field d.kolmogorow
#' Returns the instance variable d.kolmogorow.
#' (numeric)
d.kolmogorow = function(){
return(private$.d.kolmogorow)
},
#' @field p.kolmogorow
#' Returns the instance variable p.kolmogorow.
#' (numeric)
p.kolmogorow = function(){
return(private$.p.kolmogorow)
},
#' @field a.anderson
#' Returns the instance variable a.anderson.
#' (numeric)
a.anderson = function(){
return(private$.a.anderson)
},
#' @field p.anderson
#' Returns the instance variable p.anderson.
#' (numeric)
p.anderson = function(){
return(private$.p.anderson)
}
),
###################
# memory management
###################
public = list(
#' @description
#' Creates and returns a new `pgu.normDist` object.
#' @param data
#' The data to be analyzed.
#' (tibble::tibble)
#' @return
#' A new `pgu.normDist` object.
#' (pguIMP::pgu.normDist)
initialize = function(data = "tbl_df"){
if(class(data)[1] != "tbl_df"){
data <- tibble::tibble(names <- "none",
values <- c(NA))
}
self$resetNormDist(data)
}, #function
#' @description
#' Clears the heap and
#' indicates that instance of `pgu.normDist` is removed from heap.
finalize = function(){
print("Instance of pgu.normDist removed from heap")
},
##########################
# print instance variables
##########################
#' @description
#' Prints instance variables of a `pgu.normDist` object.
#' @return
#' string
print = function(){
rString <- sprintf("\npgu.normDist:\n%s\n", self$featureName)
cat(rString)
cat(self$fitResult())
cat(self$testResultCompendium())
cat("\n\n")
invisible(self)
}, #function
####################
# public functions #
####################
#' @description
#' Resets instance variables
#' @param data
#' Dataframe to be analyzed.
#' (tibble::tibble)
resetNormDist = function(data = "tbl_df"){
if ((ncol(data) ==1) & (is.numeric(data[[1]]))){
private$.featureName <- colnames(data)
}#if
else{
rString <- sprintf("\nWarning in pgu.normDist: rawData is not numeric\n")
cat(rString)
}#else
colnames(data) <- c("x")
private$.rawData <- stats::na.omit(data)
private$.testNames <- c("Shapiro-Wilk", "Kolmogorow-Smirnow", "Anderson-Darling")
private$.testParameterNames <- c("W", "D", "A")
names(private$.testParameterNames) <- self$testNames
private$.alpha <- 0.05
private$.dataPoints <- length(self$rawData$x)
private$.expMu <- 0
private$.expSigma <- 0
private$.logLikelihood <- 0
private$.degOfFreedom <- 0
private$.n <- 0
private$.bic <- 0
private$.aic <-0
private$.aicc <- 0
private$.rmse <- 0
private$.fitSuccess <- FALSE
private$.w.shapiro <- 0
private$.p.shapiro <- 0
private$.d.kolmogorow <- 0
private$.p.kolmogorow <- 0
private$.a.anderson <- 0
private$.p.anderson <- 0
}, #function
#' @description
#' Resets instance variables in case of a failed analysis.
resetFail = function(){
private$.expMu <- NA
private$.expSigma <- NA
private$.logLikelihood <- NA
private$.degOfFreedom <- NA
private$.n <- NA
private$.bic <- NA
private$.aic <-NA
private$.aicc <- NA
private$.rmse <- NA
private$.fitSuccess <- FALSE
private$.w.shapiro <- NA
private$.p.shapiro <- NA
private$.d.kolmogorow <- NA
private$.p.kolmogorow <- NA
private$.a.anderson <- NA
private$.p.anderson <- NA
private$.fitSuccess <- FALSE
}, #function
#####################
# fitting functions #
#####################
#' @description
#' Optimizes the logLikelihood between the data and a normal distribution
#' with respect to the expectation value and standard deviation.
#' The quality of the best model ist calculated subsequently.
optimize = function(){
estMu <- mean(self$rawData[["x"]], na.rm=TRUE)
estSigma <- sd(self$rawData[["x"]], na.rm=TRUE)
fit <- NULL
tryCatch({
fit <- stats::optim(par = c(mu = estMu, sigma = estSigma), fn = pguIMP::dLogLikelihood, x = purrr::discard(self$rawData[["x"]], is.na))
private$.fitSuccess <- TRUE
},
error = function(e) {
self$resetFail()
errorMesage <- sprintf("\nError in pgu.normDist during maximum likelihood estimation:\n%s", e)
cat(errorMesage)
private$.fitSuccess <- FALSE
return(NA)
})#tryCatch
if(self$fitSuccess == TRUE){
private$.expMu <- fit$par[1]
private$.expSigma <- fit$par[2]
private$.logLikelihood <- -1 * dLogLikelihood(x=purrr::discard(self$rawData[["x"]], is.na), pars = c(mu =fit$par[1], sigma = fit$par[2]))
private$.degOfFreedom <- 2
private$.n <- length(purrr::discard(self$rawData[["x"]], is.na))
private$.bic <- self$degOfFreedom*log(self$n) - 2*self$logLikelihood
private$.aic <- 2*self$degOfFreedom - 2 *self$logLikelihood
private$.aicc <- self$aic +((2*self$degOfFreedom^2) +(2*self$degOfFreedom))/(self$n-self$degOfFreedom-2)
}#if
# fit<-tryCatch({
# bbmle::mle2(x ~ dLogLikelihood(mu=mu, sigma=sigma), start = list(mu=estMu, sigma=estSigma), data=self$rawData)
# },
# error = function(e) {
# self$resetFail()
# errorMesage <- sprintf("\nError in pgu.normDist during maximum likelihood optimization:\n%s", e)
# cat(errorMesage)
# return(NA)
# })#tryCatch
# if(isS4(fit)){
# private$.rawData["residuals"] <- bbmle::residuals(fit)
# private$.expMu <- fit@coef[1]
# private$.expSigma <- fit@coef[2]
# ll <- bbmle::logLik(fit)
# private$.logLikelihood <- ll[1]
# private$.degOfFreedom <- attr(ll, "df")
# private$.bic <- stats::BIC(fit)
# private$.aic <- bbmle::AIC(fit)
# private$.aicc <- bbmle::AICc(fit)
# private$.fitSuccess <- TRUE
# }#if
}, #function
#' @description
#' Creates a histogram from the instance variable `rawData`.
#' The histogram is stored in the instance variable `histogram`.
createHistogram = function(){
rawHist <- ggplot2::ggplot_build(ggplot2::ggplot(data = self$rawData, mapping = ggplot2::aes_string(x="x"))+
ggplot2::geom_histogram(ggplot2::aes(y=..density..), bins = 30)
)
d <- tibble::tibble(x = rawHist$data[[1]]$x,
y_data =rawHist$data[[1]]$y)
d["y_fit"] <- normalDistribution(x=d["x"], mu=self$expMu, sigma=self$expSigma)
d <- dplyr::mutate(d, res =y_data - y_fit)
private$.rmse <- sqrt(mean(d[["res"]]^2))
private$.histogram <- d
}, #function
#' @description
#' Performes a qq-analysis of the instance variable `rawData`
#' The qq-analysis is stored in the attributes `sample_quantile`
#' and `theoretical_quantile` of the instance variable `rawData`.
normalQQData = function(){
p <- ggplot2::ggplot(data=self$rawData, mapping=ggplot2::aes_string(sample="x"))+
ggplot2::stat_qq()+
ggplot2::stat_qq_line(color="blue")
d <- ggplot2::ggplot_build(p)
private$.rawData["sample_quantile"] <- d$data[[1]]$sample
private$.rawData["theoretical_quantile"] <- d$data[[1]]$theoretical
}, #function
################################
# test functions for normality #
################################
#' @description
#' Performes Shapiro-Wilk's test for normality on the
#' instance variable `rawData`.
#' The test result is stored in the instance variable
#' `w.shapiro`.
#' The p-value of the test is stored in the instance variable
#' `p.shapiro`
test.shapiro = function(){
test <- stats::shapiro.test(self$rawData$x)
private$.w.shapiro <- test$statistic
private$.p.shapiro <- test$p.value
}, #function
#' @description
#' Performes Kolmogorow-Smirnow's test for normality on the
#' instance variable `rawData`.
#' The test result is stored in the instance variable
#' `d.kolmogorow`.
#' The p-value of the test is stored in the instance variable
#' `p.kolmogorow`
test.kolmogorow = function(){
# test <- stats::ks.test(self$rawData$x, "pnorm", mean=self$expMu, sd=self$expSigma)
test <- nortest::lillie.test(self$rawData$x)
private$.d.kolmogorow <- test$statistic
private$.p.kolmogorow <- test$p.value
}, #function
#' @description
#' Performes Anderson-Darling's test for normality on the
#' instance variable `rawData`.
#' The test result is stored in the instance variable
#' `a.anderson`.
#' The p-value of the test is stored in the instance variable
#' `p.anderson`
test.anderson = function(){
test <- nortest::ad.test(self$rawData$x)
private$.a.anderson <- test$statistic
private$.p.anderson <- test$p.value
}, #function
##################
# export results #
##################
#' @description
#' Returns the result of the classes optimize function
#' in form of a formated string.
#' @return
#' String of the results of the fitting routine
#' (character)
fitResult = function(){
s <- sprintf("MLE Fit Result:\nmu = %.5f\nsigma = %.5f\nlogLikelihood = %.5f\nnumber of data points = %i\ndegrees of freedom = %i\nBIC = %.5f\nAIC = %.5f\nAICc = %.5f\nRMSE = %.5f",
self$expMu, self$expSigma, self$logLikelihood, self$dataPoints, self$degOfFreedom, self$bic, self$aic, self$aicc, self$rmse)
return(s)
}, #function
#' @description
#' Returns the result of the classes test functions
#' in form of a formated string.
#' @param testName
#' Defines the test which result shall be returned.
#' Can be of type:`Shapiro-Wilk`, `Kolmogorow-Smirnow`
#' or `Anderson-Darling`.
#' (character)
#' @return
#' String of the results of the testing routine
#' (character)
testResult = function(testName = "Shapiro-Wilk"){
switch (testName,
"Shapiro-Wilk"={
name <- self$testNames[1]
parameter <- self$testParameterNames[1]
s <- self$w.shapiro
p <- self$p.shapiro
}, #Shapiro-Wilk
"Kolmogorow-Smirnow"={
name <- self$testNames[2]
parameter <- self$testParameterNames[2]
s <- self$d.kolmogorow
p <- self$p.kolmogorow
}, #Kolmogorow-Smornow
"Anderson-Darling"={
name <- self$testNames[3]
parameter <- self$testParameterNames[3]
s <- self$a.anderson
p <- self$p.anderson
} #Anderson-Darling
)#switch
s <- sprintf("%s test for normality:\n%s = %.5f\np = %.5f", name, parameter, s, p)
return(s)
}, #function
#' @description
#' Returns the result of the classes test functions
#' `Shapiro-Wilk`, `Kolmogorow-Smirnow` and
#' `Anderson-Darling`
#' in form of a formated string.
#' (character)
#' @return
#' String of the results of the testing routine
#' (character)
testResultCompendium = function(){
s <- "\nStatistical test results:"
for (name in self$testNames) {
s <- paste(s, self$testResult(name), sep="\n")
}
return(s)
}, #function
##################
# plot functions #
##################
#' @description
#' Displays the instance variable `histogram`
#' in form of a bar plot and overlays the corresponding normal distribution.
#' @return
#' A bar plot.
#' (ggplot2::ggplot)
plotHistogram = function(){
p <- ggplot2::ggplot(data=self$histogram, mapping = ggplot2::aes_string(x="x", y="y_data"))+
ggplot2::geom_col()+
ggplot2::geom_line(ggplot2::aes_string(x="x", y="y_fit"), color="blue") +
ggplot2::ggtitle(sprintf("Distribution of %s", self$featureName)) +
ggplot2::ylab("counts") +
ggplot2::xlab("value") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays the residuals between the instance variable
#' `histogram` and the corresponding normal distribution.
#' @return
#' A scatter plot.
#' (ggplot2::ggplot)
plotResiduals = function(){
p <- ggplot2::ggplot(data=self$histogram, mapping=ggplot2::aes_string(x="x", y="res"))+
ggplot2::geom_point()+
ggplot2::geom_smooth(method = 'loess') +
ggplot2::ggtitle("Residuals") +
ggplot2::ylab("residuals") +
ggplot2::xlab("value") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays the distribution of the residuals between the distribution of the instance variable
#' `histogram` in form of a histogram.
#' @return
#' A bar plot.
#' (ggplot2::ggplot)
plotResidualDist = function(){
p <- ggplot2::ggplot(data=self$histogram, mapping=ggplot2::aes_string(x="res"))+
ggplot2::geom_histogram(bins = 30) +
ggplot2::ggtitle("Residual distribution") +
ggplot2::ylab("counts") +
ggplot2::xlab("residual value") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays the distribution of the residuals between the distribution of the instance variable
#' `rawData` in form of a histogram.
#' @return
#' A bar plot.
#' (ggplot2::ggplot)
plotRawResidualDist = function(){
p <- ggplot2::ggplot(data=self$rawData, mapping=ggplot2::aes_string(x="residuals"))+
ggplot2::geom_histogram(bins = 30) +
ggplot2::ggtitle("Residual distribution") +
ggplot2::ylab("counts") +
ggplot2::xlab("residual value") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays the distribution of the instance variable
#' `rawData` in form of a histogram.
#' @return
#' A bar plot.
#' (ggplot2::ggplot)
plotRawDataDist = function(){
p <- ggplot2::ggplot(data=self$rawData, mapping=ggplot2::aes_string(x="x"))+
ggplot2::geom_histogram(bins = 30) +
ggplot2::ggtitle("Feature distribution") +
ggplot2::theme_linedraw() +
ggplot2::ylab("counts") +
ggplot2::xlab("value") +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays a qqplot of the instance variable
#' `rawData`.
#' @return
#' A qq-plot.
#' (ggplot2::ggplot)
normalQQPlot = function(){
p <- ggplot2::ggplot(data=self$rawData, mapping=ggplot2::aes_string(sample="x"))+
ggplot2::stat_qq()+
ggplot2::stat_qq_line(color="blue") +
ggplot2::ggtitle("qq-plot") +
ggplot2::ylab("data") +
ggplot2::xlab("model") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
######################
# compound functions #
######################
#' @description
#' Runs the optimization process and performs all implemented quality controls.
#' Additionally performs hypothesis tests for nromality.
fit = function(){
self$optimize()
if(self$fitSuccess){
self$createHistogram()
self$normalQQData()
self$test.shapiro()
self$test.kolmogorow()
self$test.anderson()
}#if
}#fit
)#public
)#class
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#' @title pgu.normDist
#'
#' @description
#' Compares the distribution of a single attribute's values to normal distribution
#' by using several statistic tests.
#'
#' @details
#' The distribution of a single value is tested for normality by
#' Shapiro-Wilk test, Kolmogorov-Smirnov test, Anderson-Darling test.
#' The expectation value and standard deviation of a normal distribution
#' representing the data are determined by maximizing the log Likelihood
#' with respect to the expectation value and standard deviation.
#' This object is used by the shiny based gui and is not for use in individual R-scripts!
#'
#' @format [R6::R6Class] object.
#'
#' @importFrom bbmle AIC AICc logLik mle2 residuals
#' @importFrom dplyr mutate
#' @importFrom ggplot2 aes aes_string element_rect geom_col geom_histogram geom_line geom_point
#' @importFrom ggplot2 geom_smooth ggplot ggplot_build ggtitle stat_qq stat_qq_line
#' @importFrom ggplot2 theme theme_linedraw xlab ylab
#' @importFrom magrittr %>%
#' @importFrom nortest ad.test lillie.test
#' @importFrom purrr discard
#' @importFrom R6 R6Class
#' @importFrom stats BIC ks.test na.omit optim shapiro.test
#' @importFrom tibble tibble
#'
#' @include dLogLikelihood.R
#' @include sLogLikelihood.R
#' @include normalDistribution.R
#'
#' @author Sebastian Malkusch, \email{malkusch@@med.uni-frankfurt.de}
#'
#' @export
#'
pgu.normDist <- R6::R6Class("pgu.normDist",
####################
# instance variables
####################
private = list(
.featureName = "character",
.rawData = "tbl_df",
.histogram = "tbl_df",
.expMu = "numeric",
.expSigma = "numeric",
.dataPoints = "numeric",
.logLikelihood = "numeric",
.degOfFreedom = "numeric",
.n = "integer",
.bic = "numeric",
.aic = "numeric",
.aicc = "numeric",
.rmse = "numeric",
# Test results
.fitSuccess = "logical",
.testNames = "character",
.testParameterNames = "character",
.alpha = "numeric",
# Shapiro Wilk test
.w.shapiro = "numeric",
.p.shapiro = "numeric",
# Kolmogorow Smirnow test
.d.kolmogorow = "numeric",
.p.kolmogorow = "numeric",
# Anderson Darling test
.a.anderson = "numeric",
.p.anderson = "numeric"
),
##################
# accessor methods
##################
active = list(
#' @field featureName
#' Returns the instance variable featureName.
#' (character)
featureName = function(){
return(private$.featureName)
},
#' @field rawData
#' Returns the instance variable rawData.
#' (tibble::tibble)
rawData = function(){
return(private$.rawData)
},
#' @field setRawData
#' Sets the instance variable rawData.
#' (tibble::tibble)
setRawData = function(data = "tbl_df"){
self$resetNormDist(data)
},
#' @field histogram
#' Returns the instance variable histogram.
#' (tibble::tibble)
histogram = function(){
return(private$.histogram)
},
#' @field expMu
#' Returns the instance variable expMu.
#' (numeric)
expMu = function(){
return(private$.expMu)
},
#' @field expSigma
#' Returns the instance variable expSigma.
#' (numeric)
expSigma = function(){
return(private$.expSigma)
},
#' @field dataPoints
#' Returns the instance variable dataPoints.
#' (numeric)
dataPoints = function(){
return(private$.dataPoints)
},
#' @field logLikelihood
#' Returns the instance variable logLikelihood.
#' (numeric)
logLikelihood = function(){
return(private$.logLikelihood)
},
#' @field degOfFreedom
#' Returns the instance variable degOfFreedom.
#' (numeric)
degOfFreedom = function(){
return(private$.degOfFreedom)
},
#' @field n
#' Returns the instance variable n.
#' (integer)
n = function(){
return(private$.n)
},
#' @field bic
#' Returns the instance variable bic.
#' (numeric)
bic = function(){
return(private$.bic)
},
#' @field aic
#' Returns the instance variable aic.
#' (numeric)
aic = function(){
return(private$.aic)
},
#' @field aicc
#' Returns the instance variable aicc.
#' (numeric)
aicc = function(){
return(private$.aicc)
},
#' @field rmse
#' Returns the instance variable rmse.
#' (numeric)
rmse = function(){
return(private$.rmse)
},
#' @field fitSuccess
#' Returns the instance variable fitSuccess.
#' (logical)
fitSuccess = function(){
return(private$.fitSuccess)
},
#' @field testNames
#' Returns the instance variable testNames.
#' (character)
testNames = function(){
return(private$.testNames)
},
#' @field testParameterNames
#' Returns the instance variable testParameterNames.
#' (character)
testParameterNames = function(){
return(private$.testParameterNames)
},
#' @field alpha
#' Returns the instance variable alpha.
#' (numeric)
alpha = function(){
return(private$.alpha)
},
#' @field w.shapiro
#' Returns the instance variable w.shapiro.
#' (numeric)
w.shapiro = function(){
return(private$.w.shapiro)
},
#' @field p.shapiro
#' Returns the instance variable p.shapiro.
#' (numeric)
p.shapiro = function(){
return(private$.p.shapiro)
},
#' @field d.kolmogorow
#' Returns the instance variable d.kolmogorow.
#' (numeric)
d.kolmogorow = function(){
return(private$.d.kolmogorow)
},
#' @field p.kolmogorow
#' Returns the instance variable p.kolmogorow.
#' (numeric)
p.kolmogorow = function(){
return(private$.p.kolmogorow)
},
#' @field a.anderson
#' Returns the instance variable a.anderson.
#' (numeric)
a.anderson = function(){
return(private$.a.anderson)
},
#' @field p.anderson
#' Returns the instance variable p.anderson.
#' (numeric)
p.anderson = function(){
return(private$.p.anderson)
}
),
###################
# memory management
###################
public = list(
#' @description
#' Creates and returns a new `pgu.normDist` object.
#' @param data
#' The data to be analyzed.
#' (tibble::tibble)
#' @return
#' A new `pgu.normDist` object.
#' (pguIMP::pgu.normDist)
initialize = function(data = "tbl_df"){
if(class(data)[1] != "tbl_df"){
data <- tibble::tibble(names <- "none",
values <- c(NA))
}
self$resetNormDist(data)
}, #function
#' @description
#' Clears the heap and
#' indicates that instance of `pgu.normDist` is removed from heap.
finalize = function(){
print("Instance of pgu.normDist removed from heap")
},
##########################
# print instance variables
##########################
#' @description
#' Prints instance variables of a `pgu.normDist` object.
#' @return
#' string
print = function(){
rString <- sprintf("\npgu.normDist:\n%s\n", self$featureName)
cat(rString)
cat(self$fitResult())
cat(self$testResultCompendium())
cat("\n\n")
invisible(self)
}, #function
####################
# public functions #
####################
#' @description
#' Resets instance variables
#' @param data
#' Dataframe to be analyzed.
#' (tibble::tibble)
resetNormDist = function(data = "tbl_df"){
if ((ncol(data) ==1) & (is.numeric(data[[1]]))){
private$.featureName <- colnames(data)
}#if
else{
rString <- sprintf("\nWarning in pgu.normDist: rawData is not numeric\n")
cat(rString)
}#else
colnames(data) <- c("x")
private$.rawData <- stats::na.omit(data)
private$.testNames <- c("Shapiro-Wilk", "Kolmogorow-Smirnow", "Anderson-Darling")
private$.testParameterNames <- c("W", "D", "A")
names(private$.testParameterNames) <- self$testNames
private$.alpha <- 0.05
private$.dataPoints <- length(self$rawData$x)
private$.expMu <- 0
private$.expSigma <- 0
private$.logLikelihood <- 0
private$.degOfFreedom <- 0
private$.n <- 0
private$.bic <- 0
private$.aic <-0
private$.aicc <- 0
private$.rmse <- 0
private$.fitSuccess <- FALSE
private$.w.shapiro <- 0
private$.p.shapiro <- 0
private$.d.kolmogorow <- 0
private$.p.kolmogorow <- 0
private$.a.anderson <- 0
private$.p.anderson <- 0
}, #function
#' @description
#' Resets instance variables in case of a failed analysis.
resetFail = function(){
private$.expMu <- NA
private$.expSigma <- NA
private$.logLikelihood <- NA
private$.degOfFreedom <- NA
private$.n <- NA
private$.bic <- NA
private$.aic <-NA
private$.aicc <- NA
private$.rmse <- NA
private$.fitSuccess <- FALSE
private$.w.shapiro <- NA
private$.p.shapiro <- NA
private$.d.kolmogorow <- NA
private$.p.kolmogorow <- NA
private$.a.anderson <- NA
private$.p.anderson <- NA
private$.fitSuccess <- FALSE
}, #function
#####################
# fitting functions #
#####################
#' @description
#' Optimizes the logLikelihood between the data and a normal distribution
#' with respect to the expectation value and standard deviation.
#' The quality of the best model ist calculated subsequently.
optimize = function(){
estMu <- mean(self$rawData[["x"]], na.rm=TRUE)
estSigma <- sd(self$rawData[["x"]], na.rm=TRUE)
fit <- NULL
tryCatch({
fit <- stats::optim(par = c(mu = estMu, sigma = estSigma), fn = pguIMP::dLogLikelihood, x = purrr::discard(self$rawData[["x"]], is.na))
private$.fitSuccess <- TRUE
},
error = function(e) {
self$resetFail()
errorMesage <- sprintf("\nError in pgu.normDist during maximum likelihood estimation:\n%s", e)
cat(errorMesage)
private$.fitSuccess <- FALSE
return(NA)
})#tryCatch
if(self$fitSuccess == TRUE){
private$.expMu <- fit$par[1]
private$.expSigma <- fit$par[2]
private$.logLikelihood <- -1 * dLogLikelihood(x=purrr::discard(self$rawData[["x"]], is.na), pars = c(mu =fit$par[1], sigma = fit$par[2]))
private$.degOfFreedom <- 2
private$.n <- length(purrr::discard(self$rawData[["x"]], is.na))
private$.bic <- self$degOfFreedom*log(self$n) - 2*self$logLikelihood
private$.aic <- 2*self$degOfFreedom - 2 *self$logLikelihood
private$.aicc <- self$aic +((2*self$degOfFreedom^2) +(2*self$degOfFreedom))/(self$n-self$degOfFreedom-2)
}#if
# fit<-tryCatch({
# bbmle::mle2(x ~ dLogLikelihood(mu=mu, sigma=sigma), start = list(mu=estMu, sigma=estSigma), data=self$rawData)
# },
# error = function(e) {
# self$resetFail()
# errorMesage <- sprintf("\nError in pgu.normDist during maximum likelihood optimization:\n%s", e)
# cat(errorMesage)
# return(NA)
# })#tryCatch
# if(isS4(fit)){
# private$.rawData["residuals"] <- bbmle::residuals(fit)
# private$.expMu <- fit@coef[1]
# private$.expSigma <- fit@coef[2]
# ll <- bbmle::logLik(fit)
# private$.logLikelihood <- ll[1]
# private$.degOfFreedom <- attr(ll, "df")
# private$.bic <- stats::BIC(fit)
# private$.aic <- bbmle::AIC(fit)
# private$.aicc <- bbmle::AICc(fit)
# private$.fitSuccess <- TRUE
# }#if
}, #function
#' @description
#' Creates a histogram from the instance variable `rawData`.
#' The histogram is stored in the instance variable `histogram`.
createHistogram = function(){
rawHist <- ggplot2::ggplot_build(ggplot2::ggplot(data = self$rawData, mapping = ggplot2::aes_string(x="x"))+
ggplot2::geom_histogram(ggplot2::aes(y=..density..), bins = 30)
)
d <- tibble::tibble(x = rawHist$data[[1]]$x,
y_data =rawHist$data[[1]]$y)
d["y_fit"] <- normalDistribution(x=d["x"], mu=self$expMu, sigma=self$expSigma)
d <- dplyr::mutate(d, res =y_data - y_fit)
private$.rmse <- sqrt(mean(d[["res"]]^2))
private$.histogram <- d
}, #function
#' @description
#' Performes a qq-analysis of the instance variable `rawData`
#' The qq-analysis is stored in the attributes `sample_quantile`
#' and `theoretical_quantile` of the instance variable `rawData`.
normalQQData = function(){
p <- ggplot2::ggplot(data=self$rawData, mapping=ggplot2::aes_string(sample="x"))+
ggplot2::stat_qq()+
ggplot2::stat_qq_line(color="blue")
d <- ggplot2::ggplot_build(p)
private$.rawData["sample_quantile"] <- d$data[[1]]$sample
private$.rawData["theoretical_quantile"] <- d$data[[1]]$theoretical
}, #function
################################
# test functions for normality #
################################
#' @description
#' Performes Shapiro-Wilk's test for normality on the
#' instance variable `rawData`.
#' The test result is stored in the instance variable
#' `w.shapiro`.
#' The p-value of the test is stored in the instance variable
#' `p.shapiro`
test.shapiro = function(){
test <- stats::shapiro.test(self$rawData$x)
private$.w.shapiro <- test$statistic
private$.p.shapiro <- test$p.value
}, #function
#' @description
#' Performes Kolmogorow-Smirnow's test for normality on the
#' instance variable `rawData`.
#' The test result is stored in the instance variable
#' `d.kolmogorow`.
#' The p-value of the test is stored in the instance variable
#' `p.kolmogorow`
test.kolmogorow = function(){
# test <- stats::ks.test(self$rawData$x, "pnorm", mean=self$expMu, sd=self$expSigma)
test <- nortest::lillie.test(self$rawData$x)
private$.d.kolmogorow <- test$statistic
private$.p.kolmogorow <- test$p.value
}, #function
#' @description
#' Performes Anderson-Darling's test for normality on the
#' instance variable `rawData`.
#' The test result is stored in the instance variable
#' `a.anderson`.
#' The p-value of the test is stored in the instance variable
#' `p.anderson`
test.anderson = function(){
test <- nortest::ad.test(self$rawData$x)
private$.a.anderson <- test$statistic
private$.p.anderson <- test$p.value
}, #function
##################
# export results #
##################
#' @description
#' Returns the result of the classes optimize function
#' in form of a formated string.
#' @return
#' String of the results of the fitting routine
#' (character)
fitResult = function(){
s <- sprintf("MLE Fit Result:\nmu = %.5f\nsigma = %.5f\nlogLikelihood = %.5f\nnumber of data points = %i\ndegrees of freedom = %i\nBIC = %.5f\nAIC = %.5f\nAICc = %.5f\nRMSE = %.5f",
self$expMu, self$expSigma, self$logLikelihood, self$dataPoints, self$degOfFreedom, self$bic, self$aic, self$aicc, self$rmse)
return(s)
}, #function
#' @description
#' Returns the result of the classes test functions
#' in form of a formated string.
#' @param testName
#' Defines the test which result shall be returned.
#' Can be of type:`Shapiro-Wilk`, `Kolmogorow-Smirnow`
#' or `Anderson-Darling`.
#' (character)
#' @return
#' String of the results of the testing routine
#' (character)
testResult = function(testName = "Shapiro-Wilk"){
switch (testName,
"Shapiro-Wilk"={
name <- self$testNames[1]
parameter <- self$testParameterNames[1]
s <- self$w.shapiro
p <- self$p.shapiro
}, #Shapiro-Wilk
"Kolmogorow-Smirnow"={
name <- self$testNames[2]
parameter <- self$testParameterNames[2]
s <- self$d.kolmogorow
p <- self$p.kolmogorow
}, #Kolmogorow-Smornow
"Anderson-Darling"={
name <- self$testNames[3]
parameter <- self$testParameterNames[3]
s <- self$a.anderson
p <- self$p.anderson
} #Anderson-Darling
)#switch
s <- sprintf("%s test for normality:\n%s = %.5f\np = %.5f", name, parameter, s, p)
return(s)
}, #function
#' @description
#' Returns the result of the classes test functions
#' `Shapiro-Wilk`, `Kolmogorow-Smirnow` and
#' `Anderson-Darling`
#' in form of a formated string.
#' (character)
#' @return
#' String of the results of the testing routine
#' (character)
testResultCompendium = function(){
s <- "\nStatistical test results:"
for (name in self$testNames) {
s <- paste(s, self$testResult(name), sep="\n")
}
return(s)
}, #function
##################
# plot functions #
##################
#' @description
#' Displays the instance variable `histogram`
#' in form of a bar plot and overlays the corresponding normal distribution.
#' @return
#' A bar plot.
#' (ggplot2::ggplot)
plotHistogram = function(){
p <- ggplot2::ggplot(data=self$histogram, mapping = ggplot2::aes_string(x="x", y="y_data"))+
ggplot2::geom_col()+
ggplot2::geom_line(ggplot2::aes_string(x="x", y="y_fit"), color="blue") +
ggplot2::ggtitle(sprintf("Distribution of %s", self$featureName)) +
ggplot2::ylab("counts") +
ggplot2::xlab("value") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays the residuals between the instance variable
#' `histogram` and the corresponding normal distribution.
#' @return
#' A scatter plot.
#' (ggplot2::ggplot)
plotResiduals = function(){
p <- ggplot2::ggplot(data=self$histogram, mapping=ggplot2::aes_string(x="x", y="res"))+
ggplot2::geom_point()+
ggplot2::geom_smooth(method = 'loess') +
ggplot2::ggtitle("Residuals") +
ggplot2::ylab("residuals") +
ggplot2::xlab("value") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays the distribution of the residuals between the distribution of the instance variable
#' `histogram` in form of a histogram.
#' @return
#' A bar plot.
#' (ggplot2::ggplot)
plotResidualDist = function(){
p <- ggplot2::ggplot(data=self$histogram, mapping=ggplot2::aes_string(x="res"))+
ggplot2::geom_histogram(bins = 30) +
ggplot2::ggtitle("Residual distribution") +
ggplot2::ylab("counts") +
ggplot2::xlab("residual value") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays the distribution of the residuals between the distribution of the instance variable
#' `rawData` in form of a histogram.
#' @return
#' A bar plot.
#' (ggplot2::ggplot)
plotRawResidualDist = function(){
p <- ggplot2::ggplot(data=self$rawData, mapping=ggplot2::aes_string(x="residuals"))+
ggplot2::geom_histogram(bins = 30) +
ggplot2::ggtitle("Residual distribution") +
ggplot2::ylab("counts") +
ggplot2::xlab("residual value") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays the distribution of the instance variable
#' `rawData` in form of a histogram.
#' @return
#' A bar plot.
#' (ggplot2::ggplot)
plotRawDataDist = function(){
p <- ggplot2::ggplot(data=self$rawData, mapping=ggplot2::aes_string(x="x"))+
ggplot2::geom_histogram(bins = 30) +
ggplot2::ggtitle("Feature distribution") +
ggplot2::theme_linedraw() +
ggplot2::ylab("counts") +
ggplot2::xlab("value") +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
#' @description
#' Displays a qqplot of the instance variable
#' `rawData`.
#' @return
#' A qq-plot.
#' (ggplot2::ggplot)
normalQQPlot = function(){
p <- ggplot2::ggplot(data=self$rawData, mapping=ggplot2::aes_string(sample="x"))+
ggplot2::stat_qq()+
ggplot2::stat_qq_line(color="blue") +
ggplot2::ggtitle("qq-plot") +
ggplot2::ylab("data") +
ggplot2::xlab("model") +
ggplot2::theme_linedraw() +
ggplot2::theme(
panel.background = ggplot2::element_rect(fill = "transparent"), # bg of the panel
plot.background = ggplot2::element_rect(fill = "transparent", color = NA), # bg of the plot
legend.background = ggplot2::element_rect(fill = "transparent"),
legend.key = ggplot2::element_rect(fill = "transparent")
)
return(p)
}, #function
######################
# compound functions #
######################
#' @description
#' Runs the optimization process and performs all implemented quality controls.
#' Additionally performs hypothesis tests for nromality.
fit = function(){
self$optimize()
if(self$fitSuccess){
self$createHistogram()
self$normalQQData()
self$test.shapiro()
self$test.kolmogorow()
self$test.anderson()
}#if
}#fit
)#public
)#class
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