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library(ssd4mosaic)When using the MOSAIC SSD web application, a code is provided after each analysis to reproduce the same results directly in R. Here is an example of censored data species sensitivity distribution analysis using {ssd4mosaic} functions.
# Data creation
# Most often, you would archive the same result by reading a table file with a
# function akin to utils::read.delim()
data <- ssd4mosaic::fluazinam
# Which distribution to fit to the data.
# See get_fits function documentation for possible options
distributions <- list("lnorm")
# Whether to display the results plots with a logscale x-axis
logscale <- TRUE
# Concentration unit for plots labels
unit <- "\u03bcg/L"## model fitting
fits <- ssd4mosaic::get_fits(data, distributions, TRUE)
## bootstrapping
bts <- ssd4mosaic::get_bootstrap(fits)[[1]]## Model parameters
lapply(fits, summary)
#> [[1]]
#> Fitting of the distribution ' lnorm ' By maximum likelihood on censored data
#> Parameters
#> estimate Std. Error
#> meanlog 4.976920 0.7422075
#> sdlog 2.687785 0.6056713
#> Loglikelihood: -72.81266 AIC: 149.6253 BIC: 150.9034
#> Correlation matrix:
#> meanlog sdlog
#> meanlog 1.0000000 0.1350239
#> sdlog 0.1350239 1.0000000
## HCx values
lapply(bts, quantile, probs = c(0.05, 0.1, 0.2, 0.5))
#> [[1]]
#> (original) estimated quantiles for each specified probability (censored data)
#> p=0.05 p=0.1 p=0.2 p=0.5
#> estimate 1.743522 4.629205 15.10194 145.0271
#> Median of bootstrap estimates
#> p=0.05 p=0.1 p=0.2 p=0.5
#> estimate 1.943686 5.023317 16.07359 144.5243
#>
#> two-sided 95 % CI of each quantile
#> p=0.05 p=0.1 p=0.2 p=0.5
#> 2.5 % 0.3332222 1.079025 4.034234 35.65986
#> 97.5 % 17.9205455 34.443306 82.766670 771.86244## CDF plot with confidence intervals
p <- ssd4mosaic::base_cdf(fits, unit = unit, logscale = logscale)
ssd4mosaic::add_CI_plot(p, bts, logscale)
## CDF plot with species names
ssd4mosaic::options_plot(fits, unit, logscale, data, use_names = TRUE)
## CDF plot colored by group
ssd4mosaic::options_plot(fits, unit, logscale, data, use_groups = TRUE)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.