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#' Intensity Statistics
#'
#' \code{calc_intensity} calcualtes statisitcs from the intensity column of the PCL data
#'
#' The \code{calc_intensity} function calculates statistics about the intensity
#' data in the PCL data, including min, max, sd, mean, median.
#'
#'
#' @param df data frame of uncorrected PCL data
#' @param filename name of file currently being processed
#' @keywords statisitcs
#' @export
#' @return statisics on the intensity data
#' @examples
#'
#' intensity_stats <- calc_intensity(pcl_adjusted, filename = "UVA")
#'
#####Intensity statistics
calc_intensity <- function(df, filename) {
#Declaring global variables
intensity <- NULL
if (missing(filename)) {
filename <- as.character(c(""))
}
z <- df
z <- subset(z, intensity >= 0)
message("Intensity Statistics")
mean.intensity = mean(z$intensity, na.rm = TRUE)
message("Mean Intensity")
print(mean.intensity)
median.intensity = stats::median(z$intensity, na.rm = TRUE)
message("Median Intensity")
print(median.intensity)
sd.intensity = stats::sd(z$intensity, na.rm = TRUE)
message("Standard Deviation of Intensity")
print(sd.intensity)
max.intensity = max(df$intensity, na.rm = TRUE)
message("Max intensity")
print(max.intensity)
min.intensity = min(df$intensity, na.rm = TRUE)
message("Minimum intensity")
print(min.intensity)
skew.intensity = moments::skewness(df$intensity, na.rm = TRUE)
message("Intensity Skewness")
print(skew.intensity)
kurtosis.intensity = moments::kurtosis(df$intensity, na.rm = TRUE)
message("Intensity Kurtosis")
print(kurtosis.intensity)
intensity.variable.list <- list(plot = filename,
mean.intensity = mean.intensity,
median.intensity = median.intensity,
sd.intensity = sd.intensity,
max.intensity = max.intensity,
min.intensity = min.intensity,
skew.intensity = skew.intensity,
kurtosis.intensity = kurtosis.intensity)
intensity.variable.list <- data.frame(intensity.variable.list)
return(intensity.variable.list)
}
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