# Using ssd4mosaic’s functions in R

    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.

## Defining the inputs

    # 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"

## Fitting to the data

    ## model fitting
    fits <- ssd4mosaic::get_fits(data, distributions, TRUE)

    ## bootstrapping
    bts <- ssd4mosaic::get_bootstrap(fits)[[1]]

## Extracting information from the fit

    ## 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 1.991936 5.148652 16.47329 146.9545
    #>
    #> two-sided 95 % CI of each quantile
    #>            p=0.05     p=0.1     p=0.2     p=0.5
    #> 2.5 %   0.3246611  1.074924  4.073161  36.12596
    #> 97.5 % 18.2851527 35.169329 84.720631 770.04865

    ## 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)