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

## ----setup--------------------------------------------------------------------
library(CorMID)

## ----CountChemicalElements----------------------------------------------------
fml <- "C6H12O6T5M1"
CountChemicalElements(x = fml)

## ----CountChemicalElements2---------------------------------------------------
CountChemicalElements(x = fml, ele = c("C", "Si", "T", "Cl"))

## ----echo=FALSE, ShowNaturalIsotopeAbundance----------------------------------
structure(list(
  element = c("H", "H", "C", "C", "O", "O", "O", "Si", "Si", "Si"), 
  isotope = c("1H", "2H", "12C", "13C", "16O", "17O", "18O", "28Si", "29Si", "30Si"), 
  mass = c(1.0078, 2.0141, 12, 13.0034, 15.9949, 16.9991, 17.9992, 27.9769, 28.9765, 29.9738), 
  `abundance [%]` = c(99.99, 0.01, 98.93, 1.07, 99.76, 0.04, 0.21, 92.22, 4.69, 3.09), 
  `abund > 1%` = c(TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE)
), row.names = c(NA, -10L), class = "data.frame")

## ----CalcTheoreticalMDV1------------------------------------------------------
fml <- "C21Si5"
td <- CalcTheoreticalMDV(fml = fml)
round(td, 4)

## ----CalcTheoreticalMDV2------------------------------------------------------
round(CalcTheoreticalMDV(fml = fml, nbio = 21, nmz = 21)[-(5:19), -(5:19)], 4)

## ----recMID-------------------------------------------------------------------
fml <- "C9H20O3Si2"
mid <- c(0.9, 0, 0, 0.1)
r <- list("M+H" = 0.8, "M-H" = 0.1, "M+H2O-CH4" = 0.1)
rMID <- CorMID::recMID(mid = mid, r = r, fml = fml)
round(rMID, 4)
plot(rMID)

## ----CorMID1------------------------------------------------------------------
fml <- "C21Si5"
td1 <- CalcTheoreticalMDV(fml = fml, nbio = 6, nmz = 8)
bMID <- c(0.9, rep(0, 5), 0.1)
md1 <- apply(td1*bMID, 2, sum)
round(md1, 4)

## ----CorMID2------------------------------------------------------------------
CorMID(int=md1, fml=fml, r=unlist(list("M+H"=1)))

## ----CorMID3------------------------------------------------------------------
CorMID(int=md1, fml=fml)

## ----CorMID4------------------------------------------------------------------
md2 <- unlist(list("M-1" = 0, 0.8*md1)) + c(0.2*md1, 0)
round(md2, 4)

## ----CorMID4altern------------------------------------------------------------
fml <- "C21Si5"
bMID <- c(0.9, rep(0, 5), 0.1)
r <- list("M+H" = 0.8, "M+" = 0.2)
rMID <- CorMID::recMID(mid = bMID, r = r, fml = fml)
round(rMID, 4)
plot(rMID, ylim=c(0,0.45))

## ----CorMID5------------------------------------------------------------------
CorMID(int=md2, fml=fml)

## ----poss_local_demo1---------------------------------------------------------
CorMID:::poss_local(vec=c(0.5,0.5,0.5), d=0.5, length.out=3)

## ----poss_local_demo2---------------------------------------------------------
CorMID:::poss_local(vec=c(1,0,0), d=0.25, length.out=3)