knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 4, fig.height = 4 )
ssdtools
is an R package to fit Species Sensitivity Distributions (SSDs) using Maximum Likelihood and model averaging.
SSDs are cumulative probability distributions that are used to estimate the percent of species that are affected by a given concentration of a chemical. The concentration that affects 5% of the species is referred to as the 5% Hazard Concentration ($HC_5$). For more information on SSDs the reader is referred to @posthuma_species_2001.
In order to use ssdtools
you need to install R (see below) or use the Shiny app.
The shiny app includes a user guide.
This vignette is a user manual for the R package.
ssdtools
provides the key functionality required to fit SSDs using Maximum Likelihood and model averaging in R.
It is intended to be used in conjunction with tidyverse packages such as readr
to input data, tidyr
and dplyr
to group and manipulate data and ggplot2
[@ggplot2] to plot data.
As such it endeavors to fulfill the tidyverse manifesto.
In order to install R [@r] the appropriate binary for the users operating system should be downloaded from CRAN and then installed.
Once R is installed, the ssdtools
package can be installed (together with the tidyverse) by executing the following code at the R console
install.packages(c("ssdtools", "tidyverse"))
The ssdtools
package (and ggplot2 package) can then be loaded into the current session using
library(ssdtools) library(ggplot2)
To get additional information on a particular function just type ?
followed by the name of the function at the R console.
For example ?ssd_gof
brings up the R documentation for the ssdtools
goodness of fit function.
For more information on using R the reader is referred to R for Data Science [@wickham_r_2016].
If you discover a bug in ssdtools
please file an issue with a reprex (repeatable example) at https://github.com/bcgov/ssdtools/issues.
Once the ssdtools
package has been loaded the next task is to input some data.
An easy way to do this is to save the concentration data for a single chemical as a column called Conc
in a comma separated file (.csv
).
Each row should be the sensitivity concentration for a separate species.
If species and/or group information is available then this can be saved as Species
and Group
columns.
The .csv
file can then be read into R using the following
data <- read_csv(file = "path/to/file.csv")
For the purposes of this manual we use the CCME dataset for boron.
ccme_boron <- ssddata::ccme_boron print(ccme_boron)
The function ssd_fit_dists()
inputs a data frame and fits one or more distributions.
The user can specify a subset of the following r length(ssd_dists_all())
distributions
ssd_dists_all()
using the dists
argument.
fits <- ssd_fit_dists(ccme_boron, dists = c("llogis", "lnorm", "gamma"))
The estimates for the various terms can be extracted using the tidyverse generic tidy
function (or the base R generic coef
function).
tidy(fits)
It is generally more informative to plot the fits using the autoplot
generic function (a wrapper on ssd_plot_cdf()
).
As autoplot
returns a ggplot
object it can be modified prior to plotting.
theme_set(theme_bw()) # set plot theme autoplot(fits) + ggtitle("Species Sensitivity Distributions for Boron") + scale_colour_ssd()
Given multiple distributions the user is faced with choosing the "best" distribution (or as discussed below averaging the results weighted by the fit).
ssd_gof(fits)
The ssd_gof()
function returns three test statistics that can be used to evaluate the fit of the various distributions to the data.
ad
) statistic,ks
) statistic andcvm
) statisticand three information criteria
aic
),aicc
) andbic
)Note if ssd_gof()
is called with pvalue = TRUE
then the p-values rather than the statistics are returned for the ad, ks and cvm tests.
Following @burnham_model_2002 we recommend the aicc
for model selection.
The best predictive model is that with the lowest aicc
(indicated by the model with a delta
value of 0.000 in the goodness of fit table).
In the current example the best predictive model is the gamma distribution but the lnorm distribution has some support.
For further information on the advantages of an information theoretic approach in the context of selecting SSDs the reader is referred to @fox_recent_2021.
Often other distributions will fit the data almost as well as the best distribution as evidenced by delta
values < 2 [@burnham_model_2002].
In this situation the recommended approach is to estimate the average fit based on the relative weights of the distributions [@burnham_model_2002].
The aicc
based weights are indicated by the weight
column in the goodness of fit table.
In the current example, the gamma and log-normal distributions have delta
values < 2.
The predict
function can be used to generate model-averaged (or if average = FALSE
individual) estimates by parametric bootstrapping.
Model averaging is based on aicc
unless the data censored is which case aicc
in undefined.
In this situation model averaging is only possible if the distributions have the same number of parameters.
Parametric bootstrapping is computationally intensive.
To bootstrap for each distribution in parallel register the future backend
and then select the evaluation strategy.
doFuture::registerDoFuture() future::plan(future::multisession) set.seed(99) boron_pred <- predict(fits, ci = TRUE)
The resultant object is a data frame of the estimated concentration (est
) with standard error (se
) and lower (lcl
) and upper (ucl
) 95% confidence limits (CLs) by percent of species affected (percent
).
The object includes the number of bootstraps (nboot
) data sets generated as well as the proportion of the data sets that successfully fitted (pboot
).
There is no requirement for the bootstrap samples to converge.
boron_pred
The data frame of the estimates can then be plotted together with the original data using the ssd_plot()
function to summarize an analysis.
Once again the returned object is a ggplot
object which can be customized prior to plotting.
ssd_plot(ccme_boron, boron_pred, color = "Group", label = "Species", xlab = "Concentration (mg/L)", ribbon = TRUE) + expand_limits(x = 5000) + # to ensure the species labels fit ggtitle("Species Sensitivity for Boron") + scale_colour_ssd()
In the above plot the model-averaged 95% confidence interval is indicated by the shaded band and the model-averaged 5% Hazard Concentration ($HC_5$) by the dotted line. Hazard concentrations are discussed below.
The 5% hazard concentration ($HC_5$) is the concentration that affects 5% of the species tested.
set.seed(99) boron_hc5 <- ssd_hc(fits, ci = TRUE) print(boron_hc5)
The ssdtools
package provides four ggplot geoms to allow you construct your own plots.
The first is geom_ssdpoint()
which plots species sensitivity data
ggplot(ccme_boron) + geom_ssdpoint(aes(x = Conc))
The second is geom_ssdsegments()
which plots the range of censored species sensitivity data
ggplot(ccme_boron) + geom_ssdsegment(aes(x = Conc, xend = Conc * 2))
The third is geom_xribbon()
which plots species sensitivity confidence intervals
ggplot(boron_pred) + geom_xribbon(aes(xmin = lcl, xmax = ucl, y = percent/100))
And the fourth is geom_hcintersect()
which plots hazard concentrations
ggplot() + geom_hcintersect(xintercept = c(1, 2, 3), yintercept = c(5, 10, 20) / 100)
They can be combined together as follows
gp <- ggplot(boron_pred, aes(x = est)) + geom_xribbon(aes(xmin = lcl, xmax = ucl, y = percent/100), alpha = 0.2) + geom_line(aes(y = percent/100)) + geom_ssdsegment(data = ccme_boron, aes(x = Conc / 2, xend = Conc * 2)) + geom_ssdpoint(data = ccme_boron, aes(x = Conc / 2)) + geom_ssdpoint(data = ccme_boron, aes(x = Conc * 2)) + scale_y_continuous("Species Affected (%)", labels = scales::percent) + expand_limits(y = c(0, 1)) + xlab("Concentration (mg/L)") print(gp + geom_hcintersect(xintercept = boron_hc5$est, yintercept = 5 / 100))
To log the x-axis add the following code.
gp <- gp + coord_trans(x = "log10") + scale_x_continuous( breaks = scales::trans_breaks("log10", function(x) 10^x), labels = comma_signif ) print(gp + geom_hcintersect(xintercept = boron_hc5$est, yintercept = 5 / 100))
The most recent plot can be saved as a file using ggsave()
, which also allows the user to set the resolution.
ggsave("file_name.png", dpi = 600)
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