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 on log10 transformed data.

Usage

wt.cdf(data.env, data.sp.wide, plot = T, dogam = F,
  SampleID = "Station_Date", tag = "", sortvect = NULL, np = 61,
  nt = 25, addtrend = F, wd = getwd(), groups = NULL,
  xvar = "cond", groupNames = NULL,
  xvar.PlotName = "Specific Conductivity ( uS/cm)")

Arguments

data.env	environmental data, default = "datafile" from global environment.
data.sp.wide	Species wide (crosstabed) data; default = "ss" from global environment.
plot	A boolean to choose if plot cdf and gam plots; default = F.
dogam	A booleen to choose if a gam fit is calculated; default = F.
SampleID	Site/sample id column used in both data files; 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 = F.
wd	Working directory for saving files.
groups	Three grouping variables (first 2 categorical and third is continuous). Column names in data.env, e.g., HUC (BigHUC), Ecoregion (ECOREGL3), and Watershed Area (WS_Area); default = NULL.
xvar	variable on which to base calculations; default = "cond"
xvar.PlotName	Plot name for xvar; default = paste0("Conductivity ( ", mu, "S/cm)").
groupNamesOut	Group names in output. Keep short.

Details

Grouping variable requires three inputs. The first two are categorical and the third is continuous. For example, HUC, Ecoregion, and Watershed Area. "groups" specifies the column names and "groupNamesOut" species the output names. The function will stop if groups is left as null. The function assumes log10 transformed data.

This function replaces fish.wt.cdf. This function is more generic than fish.wt.cdf.

Value

A dataframe of XC95 values and "gam" and "cdf" subfolders of "wd" with TIFF files of plots.

Examples

# data
data(dta.do)
data(ss.sites) 
# function inputs
data.env     <- dta.do
data.sp.wide <- ss.sites
plot         <- T
dogam        <- F
SampleID     <- "Station_Date"
tag          <- "wt"
sortvect     <- NULL
np           <- 61
nt           <- 25
addtrend     <- F
wd           <- getwd()
groups       <- c("BigHUC","ECOREGL3","WS_AREA")
xvar         <- "cond"
groupNames   <- c("HUC04", "EcoL3", "Area")
xvar.PlotName <- "Conductivity (uS/cm)"
# run function (~20 seconds)
df.xc95 <- wt.cdf (data.env, data.sp.wide, plot = T, dogam = T
                 , SampleID = SampleID, tag = tag, sortvect = NULL
                 , np = 61, nt = 25, addtrend = T, wd = getwd()
                 , groups = groups, xvar = xvar, groupNames = groupNames
                 , xvar.PlotName = xvar.PlotName) 
View(df.xc95)

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