fish.wt.cdf: A function to calculate a weighted CDF for XC95 values.

In leppott/InvertExtirp: Extirpation Analysis for Benthic Macroinvertebrates and Fish

Description

Weighted cdf function to calculate XC95 values #'

Usage

fish.wt.cdf(datafile = datafile, ss = ss, plot = T, dogam = T,
  SampleID = "Station_Date", tag = "", sortvect = NULL, np = 61,
  nt = 25, addtrend = T, wd = getwd(), groups = c("BigHUC",
  "ECOREGL3", "WS_AREA"), xvar = "cond")

Arguments

datafile	environmental data, default = "datafile" from global environment.
ss	Species crosstabed data; default = "ss" from global environment.
plot	A boolean to choose if plot cdf and gam plots; default = T.
dogam	A booleen to choose if a gam fit is calculated; default = T.
SampleID	Site/sample id column; default = "Station_Date"
tag	Default = "".
sortvect	to provide a vector of species list so plots will be sorted according to the list; default = NULL.
np	Number of bins; default = 61.
nt	Minimum number of occurence; default = 25.
addtrend	A booleen if a trend should be added ( = ">" etc) in the output (T or F); default = T.
wd	Working directory for saving files.
groups	column names in datafile used for grouping the data; HUC (BigHUC), Ecoregion (ECOREGL3), and Watershed Area (WS_Area)
xvar	variable on which to base calculations; default = "cond"

Value

A dataframe of XC95 values and TIFF files of gam and/or cdf plots in the subdirectory "Results" of the directory specified by "wd".

Examples

# data
data(dta.do)
data(ss.sites)
# run function (~20 seconds)
dftv.do <- fish.wt.cdf(datafile = dta.do, ss = ss.sites, plot = T, dogam = T
                      , SampleID = "Station_Date", tag = "wt", sortvect = NULL
                      , np = 61, nt = 25, addtrend = T
                      , wd = getwd(), groups = c("BigHUC","ECOREGL3","WS_AREA")
                      , xvar = "cond")
View(dftv.do)

leppott/InvertExtirp documentation built on Nov. 8, 2019, 5:58 p.m.