R/ldGamma.R

In jasp-stats/jaspDistributions: Distributions Module for JASP

#
# Copyright (C) 2013-2020 University of Amsterdam
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#

LDgammaInternal <- function(jaspResults, dataset, options, state=NULL){
  options <- .recodeOptionsLDgamma(options)

  #### Show gamma section ----
  .ldShowDistribution(jaspResults = jaspResults, options = options, name = gettext("gamma distribution"),
                      parSupportMoments = .ldGammaParsSupportMoments,
                      formulaPDF        = .ldFormulaGammaPDF,
                      formulaCDF        = .ldFormulaGammaCDF,
                      formulaQF         = .ldFormulaGammaQF)

  #### Generate and Display data section ----
  # simulate and read data
  .simulateData(jaspResults, options)

  ready <- options[['variable']] != ""
  errors <- FALSE
  if(ready){
    variable <- dataset[[options[['variable']]]]
    variable <- variable[!is.na(variable)]
    errors <- .hasErrors(dataset, type = c("observations", "variance", "infinity", "limits"),
                         observations.amount = "<2",
                         limits.min = options$support$min, limits.max = options$support$max,
                         exitAnalysisIfErrors = FALSE)
  }

  # overview of the data
  .ldDescriptives(jaspResults, variable, options, ready, errors, "continuous")

  #### Fit data and assess fit ----
  .ldMLE(jaspResults, variable, options, ready, errors, .ldFillGammaEstimatesTable)

  return()
}

### options ----
.recodeOptionsLDgamma <- function(options){
  if(options$parametrization == "scale"){
    options$rate <- 1/options$par2
  } else if(options$parametrization == "mean"){
    options$rate <- options$shape / options$par2
  } else {
    options$rate <- options$par2
  }

  options[['parValNames']] <- c("shape", "par2")

  options[['pars']]   <- list(shape = options[['shape']], rate = options[['rate']])
  options[['pdfFun']] <- stats::dgamma
  options[['cdfFun']] <- stats::pgamma
  options[['qFun']]   <- stats::qgamma
  options[['rFun']]   <- stats::rgamma
  options[['distNameInR']] <- "gamma"

  options <- .ldOptionsDeterminePlotLimits(options)

  options$support <- list(min = 0, max = Inf)
  options$lowerBound <- c(0, 0)
  options$upperBound <- c(Inf, Inf)

  options$transformations <- c(shape = "shape", scale = "1/rate",  rate = "rate", mean = "shape/rate")

  options
}

### text fill functions -----
.ldGammaParsSupportMoments <- function(jaspResults, options){
  if(options$parsSupportMoments && is.null(jaspResults[['parsSupportMoments']])){
    pars <- list()
    pars[[1]] <- switch(options[['parametrization']],
                        scale = gettextf("shape: %s", "k \u2208 \u211D<sup>+</sup>"),
                        mean  = gettextf("shape: %s", "k \u2208 \u211D<sup>+</sup>"),
                                gettextf("shape: %s", "&alpha; \u2208 \u211D<sup>+</sup>"))
    pars[[2]] <- switch(options[['parametrization']],
                        scale = gettextf("scale: %s", "&theta; \u2208 \u211D<sup>+</sup>"),
                        mean  = gettextf("mean: %s",  "&mu; \u2208 \u211D<sup>+</sup>"),
                                gettextf("rate: %s",  "&beta; \u2208 \u211D<sup>+</sup>"))

    support <- "x \u2208 \u211D<sup>+</sup>"

    moments <- list()
    moments$expectation <- switch(options[['parametrization']],
                                  scale = "k&theta;",
                                  mean  = "&mu;",
                                          "&alpha;&beta;<sup>-1</sup>")
    moments$variance <- switch(options[['parametrization']],
                               scale = "k&theta;<sup>2</sup>",
                               mean  = "&mu;<sup>2</sup>k<sup>-1</sup>",
                                       "&alpha;&beta;<sup>-2</sup>")

    jaspResults[['parsSupportMoments']] <- .ldParsSupportMoments(pars, support, moments)
  }
}

.ldFormulaGammaPDF <- function(options){
  if(options[['parametrization']] == "scale"){
    text <- "<MATH>
    f(x; <span style='color:red'>&alpha;</span>, <span style='color:blue'>&beta;</span>) =
(2&pi;<span style='color:blue'>&sigma;&sup2;</span>)<sup>-&frac12;</sup>
exp[-(x-<span style='color:red'>&mu;</span>)&sup2; &frasl; 2<span style='color:blue'>&sigma;&sup2;</span>]
    </MATH>"
  } else if(options[['parametrization']] == "mean"){
    text <- "<MATH>
    f(x; <span style='color:red'>k</span>, <span style='color:blue'>&mu;</span>) =
    (2&pi;<span style='color:blue'>&sigma;</span>&sup2;)<sup>-&frac12;</sup>
    exp[-(x-<span style='color:red'>&mu;</span>)&sup2; &frasl; 2<span style='color:blue'>&sigma;</span>&sup2;]
    </MATH>"
  } else {
    text <- "<MATH>
    f(x; <span style='color:red'>k</span>, <span style='color:blue'>&theta;</span>) =
    (<span style='color:blue'>&tau;&sup2;</span> &frasl; 2&pi;)<sup>&frac12;</sup>
    exp[-(x-<span style='color:red'>&mu;</span>)&sup2; <span style='color:blue'>&tau;&sup2;</span> &frasl; 2]
    </MATH>"
  }

  return(gsub(pattern = "\n", replacement = " ", x = text))
}

.ldFormulaGammaCDF <- function(options){
  if(options$parametrization == "scale"){
    text <- "<MATH>
    F(x; <span style='color:red'>&mu;</span>, <span style='color:blue'>&sigma;&sup2;</span>)
    </MATH>"
  } else if(options$parametrization == "mean"){
    text <- "<MATH>
    F(x; <span style='color:red'>&mu;</span>, <span style='color:blue'>&sigma;</span>)
    </MATH>"
  } else {
    text <- "<MATH>
    F(x; <span style='color:red'>&mu;</span>, <span style='color:blue'>&tau;</span>)
    </MATH>"
  }

  return(gsub(pattern = "\n", replacement = " ", x = text))
}

.ldFormulaGammaQF <- function(options){
  if(options$parametrization == "scale"){
    text <- "<MATH>
    Q(p; <span style='color:red'>&mu;</span>, <span style='color:blue'>&sigma;&sup2;</span>)
    </MATH>"
  } else if(options$parametrization == "mean"){
    text <- "<MATH>
    Q(p; <span style='color:red'>&mu;</span>, <span style='color:blue'>&sigma;</span>)
    </MATH>"
  } else {
    text <- "<MATH>
    Q(p; <span style='color:red'>&mu;</span>, <span style='color:blue'>&tau;</span>)
    </MATH>"
  }

  return(gsub(pattern = "\n", replacement = " ", x = text))
}

#### Table functions ----

.ldFillGammaEstimatesTable <- function(table, results, options, ready){
  if(!ready) return()
  if(is.null(results)) return()
  if(is.null(table)) return()

  par1 <- c(shape = c(scale = "k", rate = "\u03B1", mean = "k")[[options$parametrization]])
  par2 <- c(scale = "\u03B8", rate = "\u03B2", mean = "\u03BC")[options$parametrization]
  res <- results$structured
  res <- res[res$par %in% names(c(par1, par2)),]
  res$parName <- c(par1, par2)

  if(results$fitdist$convergence != 0){
    table$addFootnote(gettext("The optimization did not converge, try adjusting the parameter values."), symbol = gettext("<i>Warning.</i>"))
  }
  if(!is.null(results$fitdist$optim.message)){
    table$addFootnote(results$fitdist$message, symbol = gettext("<i>Warning.</i>"))
  }

  table$setData(res)

  return()
}