getSSDplot: Species Sentivity Distribution (SSD) Plots

In leppott/CASTfxn: Functions for Causal Assessment Screening Tool (CAST)

Description

Generates plots of the proportion of species affected at different exposure levels in laboratory toxicity tests.

Usage

getSSDplot(Data, ResponseType, Taxa, Exposure)

Arguments

Data	species data set name
ResponseType	column containing endpoint
Taxa	column containing taxa names
Exposure	column containing Exposure amount

Details

https://www.epa.gov/caddis-vol4/ssd-plots

Value

An SSD plot.

Examples

# Example 1
# Define parameters
myDF   <- data_SSD
myRT   <- "ResponseType"
myTaxa <- "Taxa"
myExp  <- "Exposure_mgperL"
# Run function
p1 <- getSSDplot(myDF, myRT, myTaxa, myExp)
print(p1)
# can save output to a file
## Not run: 
library(ggplot2)
fn_p1 <- file.path(getwd(), "Results", "SSD_example1.pdf")
ggsave(fn_p1, p1)

## End(Not run)

#~~~~~~~~~~~~~~~~~~~~~~~~~~

# Example 2
myDF   <- data_SSD_permethrin
myRT   <- "ResponseType"
myTaxa <- "Taxa"
myExp  <- "Exposure"
# Add missing column
myDF[,myRT] <- "LC50"
# Run function
p2 <- getSSDplot(myDF, myRT, myTaxa, myExp)
print(p2)
#' # can save output to a file
## Not run: 
fn_p2 <- file.path(getwd(), "Results", "SSD_example2.pdf")
ggplot2::ggsave(fn_p2, p2)

## End(Not run)

#~~~~~~~~~~~~~~~~~~~~~~~~~~

# Example 3 
# https://www.epa.gov/caddis-vol4/caddis-volume-4-data-analysis-download-software
# ssd_generator_v1.xlsm
myDF <- data_SSD_generator
myRT   <- "ResponseType"
myTaxa <- "Taxa"
myExp  <- "Exposure"
# Run function
p3 <- getSSDplot(myDF, myRT, myTaxa, myExp)
print(p3)
# 
# can save output to a file
## Not run: 
fn_p3 <- file.path(getwd(), "Results", "SSD_example3.pdf")
ggplot2::ggsave(fn_p3, p3)

## End(Not run)
 
#~~~~~~~~~~~~~~~~~~~~~~~~~~
 
# Example 2_mod 
# (same plot as #2 above)
library(ggplot2)
# create points
analyte <- c(0.05, 0.5, 5)
abund <- c(0, 1/3, 2/3)
taxon <- c("Baetis", "Cricotopus", "Simulium")
df.site <- data.frame(analyte, abund, taxon)
# add points to plot and add title (centered)
p2 + 
  geom_point(data=df.site, aes(x=analyte, y=abund), colour="blue", size = 2) + 
  geom_text(data=df.site, aes(x=analyte, y=abund, label=taxon)
                             , hjust="left", nudge_x=0.05, colour="blue") + 
  labs(title="Cluster SSD with site specific taxa") + theme(plot.title=element_text(hjust=0.5))
  

leppott/CASTfxn documentation built on Sept. 6, 2019, 11:04 p.m.