RFPM.R
In RFPM: Floating Percentile Model

## ----setup, include = FALSE---------------------------------------------------
require(dplyr)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)


## ----include = F--------------------------------------------------------------
library(RFPM)

## -----------------------------------------------------------------------------
head(h.northport)

## -----------------------------------------------------------------------------
p.northport <- names(h.northport)[1:10] ## all chemical column names
FPM(data = h.northport, paramList = p.northport) ## minimum input - dataset and chemical column names

## -----------------------------------------------------------------------------
plot(chemSigSelect(h.northport[, c("Al", "Cr", "Hit")], paramList = c("Al", "Cr")), type = "boxplot")

## ----fig.width = 7, fig.height = 6--------------------------------------------
## one-way optimization of the FN Limit - vertical lines show best values based on two metrics
optimFPM(h.northport, p.northport, FN_crit = seq(0.1, 0.9, 0.05), alpha.test = 0.05)

## two-way optimization of both FN Limit and alpha - black squares show best values based on two metrics
optimFPM(h.northport, p.northport, 
         FN_crit = seq(0.1, 0.9, 0.05), 
         alpha.test = seq(0.01, 0.2, 0.01))

## ----fig.width = 7, fig.height = 6--------------------------------------------
cvFPM(h.northport, p.northport, k = 10, FN_crit = seq(0.1, 0.9, 0.05), alpha.test = 0.05, which = 2)

## -----------------------------------------------------------------------------

chemVI(h.northport, p.northport)


## -----------------------------------------------------------------------------
FPM(data = h.northport, paramList = p.northport)
FPM(data = h.northport, paramList = c("Cr", "Zn"))

## -----------------------------------------------------------------------------
FPM(h.northport, p.northport, FN_crit = 0.25, alpha.test = 0.15)$FPM
chemVI(h.northport, p.northport, FN_crit = 0.25, alpha.test = 0.15)