R/pguRegressor.R
In SMLMS/pguIMP: 'pguIMP'
#' @title pgu.regressor
#'
#' @description
#' A class that performs pairwise robust regression on the pguIMP data set.
#'
#' @details
#' A class that performs pairwise robust regression on the pguIMP data set.
#' This object is used by the shiny based gui and is not for use in individual R-scripts!
#'
#' @format [R6::R6Class] object.
#'
#' @importFrom dplyr everything mutate select select_if sym
#' @importFrom ggplot2 aes aes_string element_blank geom_boxplot geom_histogram geom_point ggplot
#' @importFrom ggplot2 ggtitle stat_smooth theme
#' @importFrom gridExtra grid.arrange
#' @importFrom magrittr %>%
#' @importFrom R6 R6Class
#' @importFrom robust lmRob
#' @importFrom shiny Progress
#' @importFrom stats as.formula lm
#' @importFrom tibble as_tibble enframe tibble
#'
#' @author Sebastian Malkusch, \email{malkusch@@med.uni-frankfurt.de}
#'
#' @export
#'
pgu.regressor <- R6::R6Class("pgu.regressor",
####################
# instance variables
####################
private = list(
.featureNames = "character",
.intercept = "matrix",
.pIntercept = "matrix",
.slope = "matrix",
.pSlope = "matrix",
.model = "lmRob"
),
##################
# accessor methods
##################
active = list(
#' @field featureNames
#' Returns the instance variable featureNames.
#' (character)
featureNames = function(){
return(private$.featureNames)
},
#' @field setFeatureNames
#' Sets the instance variable featureNames.
#' It further initializes the instance variables:
#' intercept, pIntercept, slope, pSlope.
#' (character)
setFeatureNames = function(names = "character"){
private$.featureNames <- names
private$.intercept <- self$resetMatrix(value = 0)
private$.pIntercept <- self$resetMatrix(value = 1)
private$.slope <- self$resetMatrix(value = 0)
private$.pSlope <- self$resetMatrix(value = 1)
},
#' @field intercept
#' Returns the instance variable intercept.
#' (matrix)
intercept = function(){
return(private$.intercept)
},
#' @field pIntercept
#' Returns instance variable pIntercept.
#' (matrix)
pIntercept = function(){
return(private$.pIntercept)
},
#' @field slope
#' Returns the instance variable slope.
#' (matrix)
slope = function(){
return(private$.slope)
},
#' @field pSlope
#' Returns the instance variable pSlope.
#' (matrix)
pSlope = function(){
return(private$.pSlope)
},
#' @field model
#' Returns the instance variable model.
#' (robust::lmRob)
model = function(){
return(private$.model)
}
),
###################
# memory management
###################
public = list(
#' @description
#' Creates and returns a new `pgu.regressor` object.
#' @param data
#' The data to be modeled.
#' (tibble::tibble)
#' @return
#' A new `pgu.regressor` object.
#' (pguIMP::pgu.regressor)
initialize = function(data = "tbl_df"){
if(class(data)[1] != "tbl_df"){
data <- tibble::tibble(names <- "none",
values <- c(NA))
}
self$resetRegressor(data)
},
#' @description
#' Clears the heap and
#' indicates if instance of `pgu.regressor` is removed from heap.
finalize = function(){
print("Instance of pgu.regressor removed from heap")
},
##########################
# print instance variables
##########################
#' @description
#' Prints instance variables of a `pgu.regressor` object.
#' @return
#' string
print = function(){
rString <- sprintf("\npgu.regressor\n")
cat(rString)
fString <- sprintf("\nfeatureNames:\n")
cat(fString)
print(self$featureNames)
iString <- sprintf("\nintercept matrix:\n")
cat(iString)
print(self$intercept)
sString <- sprintf("\nslope matrix:\n")
cat(sString)
print(self$slope)
pString <- sprintf("\np-Value matrix:\n")
cat(pString)
print(self$pValue)
cat("\n\n")
invisible(self)
},
####################
# public functions #
####################
#' @description
#' Performes pair-wise robust linear regression on the attributes of the data tibble.
#' Progresse is indicated by the progress object passed to the function.
#' @param data
#' Dataframe with at least two numeric attributes.
#' (tibble::tibble)
#' @param progress
#' Keeps track of the analysis progress.
#' (shiny::Progress)
resetRegressor = function(data = "tbl_df", progress = "Progress"){
self$setFeatureNames <- data %>%
dplyr::select_if(is.numeric) %>%
colnames()
self$createRegressionMatrix(data, progress)
},
#' @description
#' Sets the diagonal of a square matrix to NA.
#' @param data
#' The matrix whose diagonal is to be reset.
#' (matrix)
#' @return
#' A matrix with its diagonal reset to NA.
#' (matrix)
resetDiagonal = function(data = "matrix"){
if(nrow(data) == ncol(data)){
for (i in 1:nrow(data)){
data[i,i] <- NA
}
}
else{
print("Warning: Regressor matrix needs to be square")
}
return(data)
},
#' @description
#' Creates a square matrix which dimension corresponds to the length
#' of the instance variable featureNames. The matrix entries are set to a distict `value`.
#' The diagonal is set to NA.
#' @param value
#' The value the matrix entries are set to.
#' (numeric)
#' @return
#' A square matrix.
#' (matrix)
resetMatrix = function(value = "numeric"){
n <- length(self$featureNames)
df <- matrix(data = value,
nrow = n,
ncol = n,
dimnames = list(self$featureNames, self$featureNames))
if(sum(dim(df)) > 0){
self$resetDiagonal(df)
}
return(df)
},
####################
# helper functions #
####################
#' @description
#' Determines the numerical index of the column of an attribute based on the attribute name.
#' @param feature
#' The attribute's name.
#' (character)
#' @return
#' The attributes column index.
#' (numeric)
featureIdx = function(feature = "character"){
idx <- match(c(feature), self$featureNames)
if(is.na(idx)){
rString <- sprintf("\nWarning in pgu.regressor: feature %s is not known\n",
feature)
cat(rString)
}
return(idx)
},
#' @description
#' Checks if the feature is known to the class.
#' @param feature
#' An attribute's name that is to be checked.
#' (character)
#' @return
#' The test result.
#' (logical)
featureIsValid = function(feature = "character"){
idx <- self$featureIdx(feature)
if(is.na(idx)){
return(FALSE)
}
else{
return(TRUE)
}
},
#' @description
#' Checks a if a pair of attributes different and known to the class.
#' @param abscissa
#' An attribute's name that is to be checked.
#' (character)
#' @param ordinate
#' An attribute's name that is to be checked.
#' (character)
#' @return
#' The test result.
#' (logical)
featurePairIsValid = function(abscissa = "character", ordinate = "character"){
val <- TRUE
if(!self$featureIsValid(abscissa)){val <- FALSE}
if(!self$featureIsValid(ordinate)){val <- FALSE}
if(abscissa == ordinate){val <- FALSE}
return(val)
},
######################################
# robust libear regression functions #
######################################
#' @description
#' Creates a robust model of linear regression between two attributes of a dataframe.
#' The model is stored as instance variable.
#' @param data
#' The data to be modeled.
#' (tibble::tibble)
#' @param abscissa
#' An attribute's name that equals a column name in the data.
#' (character)
#' @param ordinate
#' An attribute's name that equals a column name in the data.
#' (character)
createModel = function(data = "tbl_df", abscissa = "character", ordinate = "character"){
if(self$featurePairIsValid(abscissa, ordinate)){
ord <- paste0("`", ordinate, "`")
abs <- paste0("`", abscissa, "`")
private$.model <- paste(ord, abs, sep = "~") %>%
stats::as.formula() %>%
# stats::lm(data, na.action = na.omit)
robust::lmRob(data, na.action = na.omit)
}
},
#' @description
#' Performs the actual robust linear regression routine.
#' Iteratively runs through the attributes known to the class
#' and creates a robust linear regression model for each valid attribute pair.
#' The model results are stored in the instance variables:
#' intercept, pIntercept, slope, pSlope.
#' Here, pX represents the p-value of the respective parameter X.
#' Displays the progress if shiny is loaded.
#' @param data
#' The data to be modeled.
#' (tibble::tibble)
#' @param progress
#' If shiny is loaded, the analysis' progress is stored within this instance of the shiny Progress class.
#' (shiny::Progress)
createRegressionMatrix = function(data = "tbl_df", progress = "Progress"){
for (abscissa in self$featureNames){
for (ordinate in self$featureNames){
if(("shiny" %in% (.packages())) & (class(progress)[1] == "Progress")){
progress$inc(1)
}
abs <- dplyr::sym(abscissa)
ord <- dplyr::sym(ordinate)
if(self$featurePairIsValid(abscissa, ordinate)){
self$createModel(data, abscissa, ordinate)
private$.intercept[[as.name(ord), as.name(abs)]] <- as.numeric(c(summary(self$model)$coefficients[1,1]))
private$.pIntercept[[as.name(ord), as.name(abs)]] <-as.numeric(c(summary(self$model)$coefficients[1,4]))
private$.slope[[as.name(ord), as.name(abs)]] <- as.numeric(c(summary(self$model)$coefficients[2,1]))
private$.pSlope[[as.name(ord), as.name(abs)]] <-as.numeric(c(summary(self$model)$coefficients[2,4]))
}#if
else{
private$.intercept[[as.name(ord), as.name(abs)]] <- NA
private$.pIntercept[[as.name(ord), as.name(abs)]] <-NA
private$.slope[[as.name(ord), as.name(abs)]] <- NA
private$.pSlope[[as.name(ord), as.name(abs)]] <-NA
}#else
}#for
}#for
},#function
###################
# print functions #
###################
#' @description
#' Transforms the results of the modeling procedure for a valid pair of attributes to a dataframe
#' and returns it.
#' @param abscissa
#' The name of the attribute which is assigned to the abscissa.
#' (character)
#' @param ordinate
#' The name of the attribute which is assigned to the ordinate.
#' (character)
#' @return
#' The analyis result as a dataframe.
#' (tibble::tibble)
printModel = function(abscissa = "character", ordinate = "character"){
t <- NULL
if(self$featurePairIsValid(abscissa, ordinate)){
abs <- dplyr::sym(abscissa)
ord <- dplyr::sym(ordinate)
para <- c("abscissa", "ordinate", "intercept", "p.intercept", "slope", "p.slope")
val <- c(abscissa,
ordinate,
sprintf("%.3e", self$intercept[[as.name(ord), as.name(abs)]]),
sprintf("%.3e", self$pIntercept[[as.name(ord), as.name(abs)]]),
sprintf("%.3e", self$slope[[as.name(ord), as.name(abs)]]),
sprintf("%.3e", self$pSlope[[as.name(ord), as.name(abs)]])
)
t <- tibble::tibble(parameter = para,
vlaue = val)
}#if
return(t)
},#function
#' @description
#' Transfroms instance variable intercept to a dataframe and returns it.
#' @return
#' Dataframe of instance variable intercept.
#' (tibble::tibble)
printInterceptTbl = function(){
self$intercept %>%
tibble::as_tibble() %>%
dplyr::mutate(features = self$featureNames) %>%
dplyr::select(features, dplyr::everything()) %>%
return()
},#function
#' @description
#' Transfroms instance variable pIntercept to a dataframe and returns it.
#' @return
#' Dataframe of instance variable pIntercept.
#' (tibble::tibble)
printPInterceptTbl = function(){
self$pIntercept %>%
tibble::as_tibble() %>%
dplyr::mutate(features = self$featureNames) %>%
dplyr::select(features, dplyr::everything()) %>%
return()
},#function
#' @description
#' Transfroms instance variable slope to a dataframe and returns it.
#' @return
#' Dataframe of instance variable slope.
#' (tibble::tibble)
printSlopeTbl = function(){
self$slope %>%
tibble::as_tibble() %>%
dplyr::mutate(features = self$featureNames) %>%
dplyr::select(features, dplyr::everything()) %>%
return()
},#function
#' @description
#' Transfroms instance variable pSlope to a dataframe and returns it.
#' @return
#' Dataframe of instance variable pSlope.
#' (tibble::tibble)
printPSlopeTbl = function(){
self$pSlope %>%
tibble::as_tibble() %>%
dplyr::mutate(features = self$featureNames) %>%
dplyr::select(features, dplyr::everything()) %>%
return()
},#function
##################
# plot functions #
##################
#' @description
#' Creates a scatter plot of the model
#' stored within the instance variable of the class.
#' @return
#' A scatter plot.
#' (ggplot2::ggplot)
plotRegression = function(){
abs <- dplyr::sym(names(self$model$model)[2])
ord <- dplyr::sym(names(self$model$model)[1])
p <- ggplot2::ggplot(data = self$model$model,
ggplot2::aes_string(x=as.name(abs),
y=as.name(ord)),
na.rm = TRUE)+
ggplot2::geom_point()+
ggplot2::stat_smooth(method = "lm") +
ggplot2::ggtitle("Robust Model\nLinear Regression")
return(p)
},#function
#' @description
#' Creates a histogram of the residual distribution of the model
#' stored within the instance variable of the class.
#' @return
#' A histogram plot.
#' (ggplot2::ggplot)
plotResidualDist = function(){
p <- tibble::enframe(self$model$residuals, name=c("index")) %>%
ggplot2::ggplot(mapping=ggplot2::aes_string(x="value"), na.rm=TRUE)+
ggplot2::geom_histogram() +
ggplot2::ggtitle("Residuals\nBar Plot") +
ggplot2::theme(axis.title.y = ggplot2::element_blank())
return(p)
},#function
#' @description
#' Creates a box plot of the residual distribution of the model
#' stored within the instance variable of the class.
#' @return
#' A box plot.
#' (ggplot2::ggplot)
plotResidualBox = function(){
p <- tibble::enframe(self$model$residuals, name=c("index")) %>%
ggplot2::ggplot(mapping=ggplot2::aes_string(y="value"), na.rm=TRUE)+
ggplot2::geom_boxplot()+
ggplot2::ggtitle("Residuals\nBox Plot") +
ggplot2::theme(axis.title.x = ggplot2::element_blank(),
axis.text.x = ggplot2::element_blank(),
axis.ticks.x = ggplot2::element_blank(),
axis.title.y = ggplot2::element_blank())
return(p)
},#function
#' @description
#' Creates a model of robust linear regression.
#' Executes all graphical exploration functions of the class
#' and creates a composite graph based on their results.
#' @param data
#' The data to be modeled.
#' (tibble::tibble)
#' @param abscissa
#' The name of the attribute which is assigned to the abscissa.
#' (character)
#' @param ordinate
#' The name of the attribute which is assigned to the ordinate.
#' (character)
#' @return
#' A composite graph.
#' (gridExtra::grid.arrange)
plotModel = function(data = "tbl_df", abscissa = "character", ordinate = "character"){
p <- NULL
if(self$featurePairIsValid(abscissa, ordinate)){
self$createModel(data, abscissa, ordinate)
p1 <- self$plotRegression()
p2 <- self$plotResidualBox()
p3 <- self$plotResidualDist()
p <- gridExtra::grid.arrange(p1,p2,p3, layout_matrix = rbind(c(1,1,1,2),c(1,1,1,3)))
}
return(p)
}#function
)#public
)#class
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#' @title pgu.regressor
#'
#' @description
#' A class that performs pairwise robust regression on the pguIMP data set.
#'
#' @details
#' A class that performs pairwise robust regression on the pguIMP data set.
#' This object is used by the shiny based gui and is not for use in individual R-scripts!
#'
#' @format [R6::R6Class] object.
#'
#' @importFrom dplyr everything mutate select select_if sym
#' @importFrom ggplot2 aes aes_string element_blank geom_boxplot geom_histogram geom_point ggplot
#' @importFrom ggplot2 ggtitle stat_smooth theme
#' @importFrom gridExtra grid.arrange
#' @importFrom magrittr %>%
#' @importFrom R6 R6Class
#' @importFrom robust lmRob
#' @importFrom shiny Progress
#' @importFrom stats as.formula lm
#' @importFrom tibble as_tibble enframe tibble
#'
#' @author Sebastian Malkusch, \email{malkusch@@med.uni-frankfurt.de}
#'
#' @export
#'
pgu.regressor <- R6::R6Class("pgu.regressor",
####################
# instance variables
####################
private = list(
.featureNames = "character",
.intercept = "matrix",
.pIntercept = "matrix",
.slope = "matrix",
.pSlope = "matrix",
.model = "lmRob"
),
##################
# accessor methods
##################
active = list(
#' @field featureNames
#' Returns the instance variable featureNames.
#' (character)
featureNames = function(){
return(private$.featureNames)
},
#' @field setFeatureNames
#' Sets the instance variable featureNames.
#' It further initializes the instance variables:
#' intercept, pIntercept, slope, pSlope.
#' (character)
setFeatureNames = function(names = "character"){
private$.featureNames <- names
private$.intercept <- self$resetMatrix(value = 0)
private$.pIntercept <- self$resetMatrix(value = 1)
private$.slope <- self$resetMatrix(value = 0)
private$.pSlope <- self$resetMatrix(value = 1)
},
#' @field intercept
#' Returns the instance variable intercept.
#' (matrix)
intercept = function(){
return(private$.intercept)
},
#' @field pIntercept
#' Returns instance variable pIntercept.
#' (matrix)
pIntercept = function(){
return(private$.pIntercept)
},
#' @field slope
#' Returns the instance variable slope.
#' (matrix)
slope = function(){
return(private$.slope)
},
#' @field pSlope
#' Returns the instance variable pSlope.
#' (matrix)
pSlope = function(){
return(private$.pSlope)
},
#' @field model
#' Returns the instance variable model.
#' (robust::lmRob)
model = function(){
return(private$.model)
}
),
###################
# memory management
###################
public = list(
#' @description
#' Creates and returns a new `pgu.regressor` object.
#' @param data
#' The data to be modeled.
#' (tibble::tibble)
#' @return
#' A new `pgu.regressor` object.
#' (pguIMP::pgu.regressor)
initialize = function(data = "tbl_df"){
if(class(data)[1] != "tbl_df"){
data <- tibble::tibble(names <- "none",
values <- c(NA))
}
self$resetRegressor(data)
},
#' @description
#' Clears the heap and
#' indicates if instance of `pgu.regressor` is removed from heap.
finalize = function(){
print("Instance of pgu.regressor removed from heap")
},
##########################
# print instance variables
##########################
#' @description
#' Prints instance variables of a `pgu.regressor` object.
#' @return
#' string
print = function(){
rString <- sprintf("\npgu.regressor\n")
cat(rString)
fString <- sprintf("\nfeatureNames:\n")
cat(fString)
print(self$featureNames)
iString <- sprintf("\nintercept matrix:\n")
cat(iString)
print(self$intercept)
sString <- sprintf("\nslope matrix:\n")
cat(sString)
print(self$slope)
pString <- sprintf("\np-Value matrix:\n")
cat(pString)
print(self$pValue)
cat("\n\n")
invisible(self)
},
####################
# public functions #
####################
#' @description
#' Performes pair-wise robust linear regression on the attributes of the data tibble.
#' Progresse is indicated by the progress object passed to the function.
#' @param data
#' Dataframe with at least two numeric attributes.
#' (tibble::tibble)
#' @param progress
#' Keeps track of the analysis progress.
#' (shiny::Progress)
resetRegressor = function(data = "tbl_df", progress = "Progress"){
self$setFeatureNames <- data %>%
dplyr::select_if(is.numeric) %>%
colnames()
self$createRegressionMatrix(data, progress)
},
#' @description
#' Sets the diagonal of a square matrix to NA.
#' @param data
#' The matrix whose diagonal is to be reset.
#' (matrix)
#' @return
#' A matrix with its diagonal reset to NA.
#' (matrix)
resetDiagonal = function(data = "matrix"){
if(nrow(data) == ncol(data)){
for (i in 1:nrow(data)){
data[i,i] <- NA
}
}
else{
print("Warning: Regressor matrix needs to be square")
}
return(data)
},
#' @description
#' Creates a square matrix which dimension corresponds to the length
#' of the instance variable featureNames. The matrix entries are set to a distict `value`.
#' The diagonal is set to NA.
#' @param value
#' The value the matrix entries are set to.
#' (numeric)
#' @return
#' A square matrix.
#' (matrix)
resetMatrix = function(value = "numeric"){
n <- length(self$featureNames)
df <- matrix(data = value,
nrow = n,
ncol = n,
dimnames = list(self$featureNames, self$featureNames))
if(sum(dim(df)) > 0){
self$resetDiagonal(df)
}
return(df)
},
####################
# helper functions #
####################
#' @description
#' Determines the numerical index of the column of an attribute based on the attribute name.
#' @param feature
#' The attribute's name.
#' (character)
#' @return
#' The attributes column index.
#' (numeric)
featureIdx = function(feature = "character"){
idx <- match(c(feature), self$featureNames)
if(is.na(idx)){
rString <- sprintf("\nWarning in pgu.regressor: feature %s is not known\n",
feature)
cat(rString)
}
return(idx)
},
#' @description
#' Checks if the feature is known to the class.
#' @param feature
#' An attribute's name that is to be checked.
#' (character)
#' @return
#' The test result.
#' (logical)
featureIsValid = function(feature = "character"){
idx <- self$featureIdx(feature)
if(is.na(idx)){
return(FALSE)
}
else{
return(TRUE)
}
},
#' @description
#' Checks a if a pair of attributes different and known to the class.
#' @param abscissa
#' An attribute's name that is to be checked.
#' (character)
#' @param ordinate
#' An attribute's name that is to be checked.
#' (character)
#' @return
#' The test result.
#' (logical)
featurePairIsValid = function(abscissa = "character", ordinate = "character"){
val <- TRUE
if(!self$featureIsValid(abscissa)){val <- FALSE}
if(!self$featureIsValid(ordinate)){val <- FALSE}
if(abscissa == ordinate){val <- FALSE}
return(val)
},
######################################
# robust libear regression functions #
######################################
#' @description
#' Creates a robust model of linear regression between two attributes of a dataframe.
#' The model is stored as instance variable.
#' @param data
#' The data to be modeled.
#' (tibble::tibble)
#' @param abscissa
#' An attribute's name that equals a column name in the data.
#' (character)
#' @param ordinate
#' An attribute's name that equals a column name in the data.
#' (character)
createModel = function(data = "tbl_df", abscissa = "character", ordinate = "character"){
if(self$featurePairIsValid(abscissa, ordinate)){
ord <- paste0("`", ordinate, "`")
abs <- paste0("`", abscissa, "`")
private$.model <- paste(ord, abs, sep = "~") %>%
stats::as.formula() %>%
# stats::lm(data, na.action = na.omit)
robust::lmRob(data, na.action = na.omit)
}
},
#' @description
#' Performs the actual robust linear regression routine.
#' Iteratively runs through the attributes known to the class
#' and creates a robust linear regression model for each valid attribute pair.
#' The model results are stored in the instance variables:
#' intercept, pIntercept, slope, pSlope.
#' Here, pX represents the p-value of the respective parameter X.
#' Displays the progress if shiny is loaded.
#' @param data
#' The data to be modeled.
#' (tibble::tibble)
#' @param progress
#' If shiny is loaded, the analysis' progress is stored within this instance of the shiny Progress class.
#' (shiny::Progress)
createRegressionMatrix = function(data = "tbl_df", progress = "Progress"){
for (abscissa in self$featureNames){
for (ordinate in self$featureNames){
if(("shiny" %in% (.packages())) & (class(progress)[1] == "Progress")){
progress$inc(1)
}
abs <- dplyr::sym(abscissa)
ord <- dplyr::sym(ordinate)
if(self$featurePairIsValid(abscissa, ordinate)){
self$createModel(data, abscissa, ordinate)
private$.intercept[[as.name(ord), as.name(abs)]] <- as.numeric(c(summary(self$model)$coefficients[1,1]))
private$.pIntercept[[as.name(ord), as.name(abs)]] <-as.numeric(c(summary(self$model)$coefficients[1,4]))
private$.slope[[as.name(ord), as.name(abs)]] <- as.numeric(c(summary(self$model)$coefficients[2,1]))
private$.pSlope[[as.name(ord), as.name(abs)]] <-as.numeric(c(summary(self$model)$coefficients[2,4]))
}#if
else{
private$.intercept[[as.name(ord), as.name(abs)]] <- NA
private$.pIntercept[[as.name(ord), as.name(abs)]] <-NA
private$.slope[[as.name(ord), as.name(abs)]] <- NA
private$.pSlope[[as.name(ord), as.name(abs)]] <-NA
}#else
}#for
}#for
},#function
###################
# print functions #
###################
#' @description
#' Transforms the results of the modeling procedure for a valid pair of attributes to a dataframe
#' and returns it.
#' @param abscissa
#' The name of the attribute which is assigned to the abscissa.
#' (character)
#' @param ordinate
#' The name of the attribute which is assigned to the ordinate.
#' (character)
#' @return
#' The analyis result as a dataframe.
#' (tibble::tibble)
printModel = function(abscissa = "character", ordinate = "character"){
t <- NULL
if(self$featurePairIsValid(abscissa, ordinate)){
abs <- dplyr::sym(abscissa)
ord <- dplyr::sym(ordinate)
para <- c("abscissa", "ordinate", "intercept", "p.intercept", "slope", "p.slope")
val <- c(abscissa,
ordinate,
sprintf("%.3e", self$intercept[[as.name(ord), as.name(abs)]]),
sprintf("%.3e", self$pIntercept[[as.name(ord), as.name(abs)]]),
sprintf("%.3e", self$slope[[as.name(ord), as.name(abs)]]),
sprintf("%.3e", self$pSlope[[as.name(ord), as.name(abs)]])
)
t <- tibble::tibble(parameter = para,
vlaue = val)
}#if
return(t)
},#function
#' @description
#' Transfroms instance variable intercept to a dataframe and returns it.
#' @return
#' Dataframe of instance variable intercept.
#' (tibble::tibble)
printInterceptTbl = function(){
self$intercept %>%
tibble::as_tibble() %>%
dplyr::mutate(features = self$featureNames) %>%
dplyr::select(features, dplyr::everything()) %>%
return()
},#function
#' @description
#' Transfroms instance variable pIntercept to a dataframe and returns it.
#' @return
#' Dataframe of instance variable pIntercept.
#' (tibble::tibble)
printPInterceptTbl = function(){
self$pIntercept %>%
tibble::as_tibble() %>%
dplyr::mutate(features = self$featureNames) %>%
dplyr::select(features, dplyr::everything()) %>%
return()
},#function
#' @description
#' Transfroms instance variable slope to a dataframe and returns it.
#' @return
#' Dataframe of instance variable slope.
#' (tibble::tibble)
printSlopeTbl = function(){
self$slope %>%
tibble::as_tibble() %>%
dplyr::mutate(features = self$featureNames) %>%
dplyr::select(features, dplyr::everything()) %>%
return()
},#function
#' @description
#' Transfroms instance variable pSlope to a dataframe and returns it.
#' @return
#' Dataframe of instance variable pSlope.
#' (tibble::tibble)
printPSlopeTbl = function(){
self$pSlope %>%
tibble::as_tibble() %>%
dplyr::mutate(features = self$featureNames) %>%
dplyr::select(features, dplyr::everything()) %>%
return()
},#function
##################
# plot functions #
##################
#' @description
#' Creates a scatter plot of the model
#' stored within the instance variable of the class.
#' @return
#' A scatter plot.
#' (ggplot2::ggplot)
plotRegression = function(){
abs <- dplyr::sym(names(self$model$model)[2])
ord <- dplyr::sym(names(self$model$model)[1])
p <- ggplot2::ggplot(data = self$model$model,
ggplot2::aes_string(x=as.name(abs),
y=as.name(ord)),
na.rm = TRUE)+
ggplot2::geom_point()+
ggplot2::stat_smooth(method = "lm") +
ggplot2::ggtitle("Robust Model\nLinear Regression")
return(p)
},#function
#' @description
#' Creates a histogram of the residual distribution of the model
#' stored within the instance variable of the class.
#' @return
#' A histogram plot.
#' (ggplot2::ggplot)
plotResidualDist = function(){
p <- tibble::enframe(self$model$residuals, name=c("index")) %>%
ggplot2::ggplot(mapping=ggplot2::aes_string(x="value"), na.rm=TRUE)+
ggplot2::geom_histogram() +
ggplot2::ggtitle("Residuals\nBar Plot") +
ggplot2::theme(axis.title.y = ggplot2::element_blank())
return(p)
},#function
#' @description
#' Creates a box plot of the residual distribution of the model
#' stored within the instance variable of the class.
#' @return
#' A box plot.
#' (ggplot2::ggplot)
plotResidualBox = function(){
p <- tibble::enframe(self$model$residuals, name=c("index")) %>%
ggplot2::ggplot(mapping=ggplot2::aes_string(y="value"), na.rm=TRUE)+
ggplot2::geom_boxplot()+
ggplot2::ggtitle("Residuals\nBox Plot") +
ggplot2::theme(axis.title.x = ggplot2::element_blank(),
axis.text.x = ggplot2::element_blank(),
axis.ticks.x = ggplot2::element_blank(),
axis.title.y = ggplot2::element_blank())
return(p)
},#function
#' @description
#' Creates a model of robust linear regression.
#' Executes all graphical exploration functions of the class
#' and creates a composite graph based on their results.
#' @param data
#' The data to be modeled.
#' (tibble::tibble)
#' @param abscissa
#' The name of the attribute which is assigned to the abscissa.
#' (character)
#' @param ordinate
#' The name of the attribute which is assigned to the ordinate.
#' (character)
#' @return
#' A composite graph.
#' (gridExtra::grid.arrange)
plotModel = function(data = "tbl_df", abscissa = "character", ordinate = "character"){
p <- NULL
if(self$featurePairIsValid(abscissa, ordinate)){
self$createModel(data, abscissa, ordinate)
p1 <- self$plotRegression()
p2 <- self$plotResidualBox()
p3 <- self$plotResidualDist()
p <- gridExtra::grid.arrange(p1,p2,p3, layout_matrix = rbind(c(1,1,1,2),c(1,1,1,3)))
}
return(p)
}#function
)#public
)#class
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