chlorophyllCalc: chlorophyllCalc Use the relevant local area of influence...

Description Usage Arguments Value

View source: R/chlorophyllCalc.R

Description

chlorophyllCalc Use the relevant local area of influence (calculated using the butterfly algorithm) to find chlorophyll levels over time

Usage

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chlorophyllCalc(input.file, data.variable = "chl", lat.varname = NULL,
  lon.varname = NULL, timeseries = NULL, time.varname = NULL,
  conductance.data, max.day.diff = 10, exclude.nas = TRUE,
  depth.varname = NULL, depth.dimension = NULL, depth.touse = NULL)

Arguments

input.file

.nc file containing chlorophyll levels for the entire area of influence

data.variable

character string corresponding to the relevant data subset within the .nc file (defaults to "chlorophyll")

lat.varname

name of latitude variable, automatic searching is used if NULL

lon.varname

name of longitude variable, automatic searching is used if NULL

timeseries

manually extracted timeseries data as "Date" class, to override automatic extraction from file

time.varname

name of time variable, automatic searching is used if NULL

conductance.data

input for calculation

max.day.diff

integer, number of days to allow as a difference between a conductance array

exclude.nas

should NA values be excluded?

depth.varname

name of depth variable in .nc file, auto matching used if NULL

depth.dimension

if a depth dimension is present, specify which dimension it is. auto-matching used if NULL

depth.touse

if a depth dimension is present, specify which value to use. default NULL will use minimum available depth

Value

A data.table, containing variables for date and chlorophyll level


rossholmberg/pkgButterfly documentation built on March 19, 2018, 4:41 p.m.