pretreatment: Calculate particules accumulation rates for sediment records
In paleofire: Analysis of Charcoal Records from the Global Charcoal Database

Description Usage Arguments Value Author(s) Examples

This is the R version of the CharAnalysis CharPretreatment.m function originally develloped by P. Higuera and available at https://sites.google.com/site/charanalysis

pretreatment(
  params,
  serie,
  Int = TRUE,
  first = NULL,
  last = NULL,
  yrInterp = NULL
)

`params`	A matrix with the following colums: CmTop, CmBot, AgeTop, AgeBot, Volume, in the same order.
`serie`	A proxy record to be transformed in accumulation rates, could be particule counts, surfaces, volumes, etc.
`Int`	Logical specifying whether the function interpolates missing values, default TRUE (missing values specified could be specified as -999 or NA)
`first, last`	Date of the first, last sample for accumulation rate calculation, if NULL first, last are automatically specified as the the minimum and maximum ages of the record respectively
`yrInterp`	Temporal resolution of the interpolated accumulation rates, if NULL, yrInterp is automatically specified as the median resolution of the record

Return an output structure with the following:

`cmI`	interpolated depths
`ybpI`	interpolated ages
`accI`	accumulation rates

O. Blarquez translated from P. Higuera CharPretreatment.m function

## Not run: 
# In this example we will use the charcoal record of the Lac du Loup from Blarquez et al. (2010).
# Blarquez, O., C. Carcaillet, B. Mourier, L. Bremond, and O. Radakovitch. 2010. Trees in the
# subalpine belt since 11 700 cal. BP: origin, expansion and alteration of the modern forest.
# The Holocene 20:139-146.

# Load raw charcoal data in mm^2
A=read.csv("http://blarquez.com/public/code/loupchar.csv")
C_=A[,6] # charcoal areas
P_=A[,1:5] # CmTop, CmBot, AgeTop, AgeBot, Volume

# Calculates charcoal accumulation rate (CHAR, mm2.cm-2.yr-1)
CHAR=pretreatment(params=P_,serie=C_,Int=TRUE)
plot(CHAR)

## End(Not run)