paleofire (version 1.2.4)

pfAddData: Add user defined charcoal data series to paleofire

Description

This function is used to create a "pfAddData" object, from user defined csv files containing charcoal data, to be passed to pfTransform. csv files must contain three columns with Depth, Age, Charcoal quantity in this same order (for type="NONE" argument). A metadata csv file could also be specified with sites location information (three columns with: SITE_NAME, LATITUDE, LONGITUDE). CharAnalysis data files could also be used, in this case the file must include the following columns: DepthTop, DepthBottom, AgeTop, AgeBottom, Volume and Charcoal value in this exact order. Then the files are passed to the pretreatment function in order to calculate Charcoal Accumulation Rates (see pretreatment for details).

Usage

pfAddData(
  files,
  metadata = NULL,
  type = "NULL",
  Int = TRUE,
  first = NULL,
  last = NULL,
  yrInterp = NULL,
  sep = ",",
  dec = "."
)

Arguments

files

Character, names and path to csv files.

metadata

Character, name and path to the (unique) metadata csv file.

type

Character, "NONE": user defined csv (default), "CharAnalysis": CharAnalysis data file.

Int

Logical specifying whether the pretreatment function interpolates particle zero counts, default TRUE.

first, last

Numeric, 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

Numeric, temporal resolution of the interpolated accumulation rates, if NULL, yrInterp is automatically specified as the median resolution of the record.

sep

char, column separator for csv, "," by default

dec

char, decimal "." by default

Value

out

A list with merged data files that can be passed to pfTransform

See Also

pretreatment

Examples

# NOT RUN {

# }
# NOT RUN {
# Ad user own data from CharAnalysis file (csv)
# In this example we will use data from:
# Senici, D., A. Lucas, H. Y. H. Chen, Y. Bergeron, A. Larouche, B. Brossier, O.
# Blarquez, and A. A. Ali. 2013. Multi-millennial fire frequency and tree abundance
# differ between xeric and mesic boreal forests in central Canada. Journal of Ecology:
# 101, 356-367.

files=c("http://blarquez.com/public/data//Ben.csv",
       "http://blarquez.com/public/data/Small.csv")
metadata=c("http://blarquez.com/public/data/metadata.csv")

mydata=pfAddData(files=files,metadata=metadata,type="CharAnalysis")

# Transform and compositing:
TR1=pfTransform(add=mydata, method=c("MinMax","Box-Cox","Z-Score"),
                BasePeriod=c(200,2000))
COMP2=pfCompositeLF(TR1, tarAge=seq(-50,8000,20), hw=500, nboot=100)
plot(COMP2)

# Three columns example (with semicolon csv files):
files=c("http://blarquez.com/public/data/Ben_area.csv",
       "http://blarquez.com/public/data/Small_area.csv")
mydata=pfAddData(files=files, sep=";")
# Transform and compositing:
TR1=pfTransform(add=mydata, method=c("MinMax","Box-Cox","Z-Score"),
               BasePeriod=c(200,2000))
COMP2=pfCompositeLF(TR1, tarAge=seq(-50,8000,20), hw=500, nboot=100)
plot(COMP2)
# }
# NOT RUN {
# }