R/bd_calc_decay_time_from_peak.R

In MichaelHoltonPrice/BayDem: Bayesian Demography

#' @title For each sample, calculate the time it takes for the density to decrease by half from the peak
#'
#' @details
#' Calculate the relative density for two dates or, more generally, for two
#'
#' @param soln The result of a call to bd_do_inference
#' @param anal The result of a call to bd_analyze_soln
#' @param propChange (Default 0.5) The proportional 
#' @param spec2 The specification for the second density (see details)
#' @param ind (Optional) Indices at which to do the calculation. By default,
#'            all the samples in anal are used.
#' @param anal (Optional) The result of a call to bd_analyze_soln. This is only
#'             needed if either spec1 or spec2 is 'peak'
#'
#' @return A vector of relative densities (f_spec1 / f_spec2)
#'
#' @export
bd_calc_relative_density <- function(soln,spec1,spec2,ind=NA,anal=NA) {
  TH <- bd_extract_param(soln$fit)
  N <- nrow(TH)
  if(all(is.na(ind))) {
    ind <- 1:N
  }


  # Interpret and do error checking on inputs by calling helper function below
  spec1 <- unpack_spec(spec1,soln,T)
  spec2 <- unpack_spec(spec2,soln,F)
  
  if(spec1$type == 'peak' || spec2$type=='peak') {
    if(all(is.na(anal))) {
      anal <- bd_analyze_soln(soln) # If ind is not NA, this may involve unused computation
    }
    summList <- anal$summList[ind]
  }
  
  # Calculate the density for spec1
  if(spec1$type == 'point') {
    f1 <- calc_point_density(TH[ind,],soln,spec1$value)
  } else if(spec1$type == 'range') {
    f1 <- calc_range_density(TH[ind,],soln,spec1$lower,spec1$upper)
  } else if(spec1$type == 'peak') {
    f1 <- calc_peak_density(summList)
  } else {
    # This should not happen, but throw an error regardless
    stop('Unsupported spec type')
  }

  # Calculate the density for spec2
  if(spec2$type == 'point') {
    f2 <- calc_point_density(TH[ind,],soln,spec2$value)
  } else if(spec2$type == 'range') {
    f2 <- calc_range_density(TH[ind,],soln,spec2$lower,spec2$upper)
  } else if(spec2$type == 'peak') {
    f2 <- calc_peak_density(summList)
  } else {
    # This should not happen, but throw an error regardless
    stop('Unsupported spec type')
  }

  return(f1/f2)
}

# A helper function to unpack and do error checking on inputs spec1 / spec2
unpack_spec <- function(spec,soln,isOne) {
  # For more informative error messages, use the input isOne to set the string
  # s to spec1 or spec2
  if(isOne) {
    s <- 'spec1' 
  } else {
    s <- 'spec2' 
  }

  # Handle the supported cases, throwing an error if necessary
  if(is.numeric(spec)) {
    if(length(spec) == 1) { # Numeric / length 1
      point <- spec
      if(point < soln$prob$hp$ymin || soln$prob$hp$ymax < point) {
        stop(paste(s,'is a single date, but not in the range ymin to ymax'))
      }
      return(list(type='point',value=point))
    } else if(length(spec) == 2) { # Numeric / length 2
      lower <- spec[1]
      if(lower < soln$prob$hp$ymin || soln$prob$hp$ymax < lower) {
        stop(paste(s,'is a date range, but lower value is not in the range ymin to ymax'))
      }
      upper <- spec[2]
      if(upper < soln$prob$hp$ymin || soln$prob$hp$ymax < upper) {
        stop(paste(s,'is a date range, but upper value is not in the range ymin to ymax'))
      }
      if(lower > upper) {
        stop(paste(s,'is a date range, but lower value is greater than upper value'))
      }
      return(list(type='range',lower=lower,upper=upper))
    } else { # Numeirc / not length 1 or 2
      stop(paste(s,'is numeric, but is neither a single date nor a date range'))
    }
  } else if(is.character(spec)) { # Character
    if(spec == 'peak') {
      return(list(type='peak'))
    } else {
      stop(paste(s,'is a character, but not equal to peak'))
    }
  } else { # Neither character nor numeric
    stop(paste(s,'is neither numeric nor a character'))
  }
}

# A helper function to calculate point densities
calc_point_density <- function(TH,soln,y) {
  return(as.numeric(bd_calc_gauss_mix_pdf_mat(TH,y,ymin=soln$prob$hp$ymin,ymax=soln$prob$hp$ymax)))
}

# A helper function to calculate the mean density over a range
calc_range_density <- function(TH,soln,ylo,yhi) {
  flo <- as.numeric(bd_calc_gauss_mix_pdf_mat(TH,ylo,ymin=soln$prob$hp$ymin,ymax=soln$prob$hp$ymax,type='cumulative'))
  fhi <- as.numeric(bd_calc_gauss_mix_pdf_mat(TH,yhi,ymin=soln$prob$hp$ymin,ymax=soln$prob$hp$ymax,type='cumulative'))
  return((fhi-flo)/(yhi-ylo))
}

# A helper function to calculate the peak density
calc_peak_density <- function(summList) {
  return(unlist(lapply(summList,function(x){x$fpeak})))
}