Package: ssd4mosaic 1.0.1

Milena Kaag

ssd4mosaic: Web Application for the SSD Module of the MOSAIC Platform

Web application using 'shiny' for the SSD (Species Sensitivity Distribution) module of the MOSAIC (MOdeling and StAtistical tools for ecotoxICology) platform. It estimates the Hazardous Concentration for x% of the species (HCx) from toxicity values that can be censored and provides various plotting options for a better understanding of the results. See our companion paper Kon Kam King et al. (2014) <doi:10.48550/arXiv.1311.5772>.

Authors:Milena Kaag [cre, aut], Sandrine Charles [aut], UMR5558 LBBE MEPS [cph, fnd], rhandsontable contributors [ctb, cph]

ssd4mosaic_1.0.1.tar.gz
ssd4mosaic_1.0.1.tar.gz(r-4.5-noble)ssd4mosaic_1.0.1.tar.gz(r-4.4-noble)
ssd4mosaic_1.0.1.tgz(r-4.4-emscripten)ssd4mosaic_1.0.1.tgz(r-4.3-emscripten)
ssd4mosaic.pdf |ssd4mosaic.html✨
ssd4mosaic/json (API)
NEWS

# Install 'ssd4mosaic' in R:
install.packages('ssd4mosaic', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • endosulfan - Summary of 48 to 96-hour acute toxicity values for endosulfan
  • fluazinam - 48-hour acute toxicity values for fluazinam
  • salinity_family - 72-hour acute salinity tolerance of macro-invertebrates grouped by family.
  • salinity_order - 72-hour acute salinity tolerance of macro-invertebrates grouped by order.

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.30 score 115 downloads 15 exports 71 dependencies

Last updated 8 months agofrom:78fa799a59. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-linuxOKNov 15 2024

Exports:add_CI_plotbase_cdfcens_lines_plotdllogisget_bootstrapget_fitsgroup_cdf_censoredgroup_cdf_uncensoredname_plot_censoredname_plot_uncensoredoptions_plotpllogisqllogisrllogisrun_app

Dependencies:actuarattemptbase64encbslibcachemclicolorspacecommonmarkconfigcrayondigestevaluateexpintfansifarverfastmapfitdistrplusfontawesomefsggplot2gluegolemgtableherehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpromisesR6rappdirsRColorBrewerRcpprhandsontablerlangrmarkdownrprojrootsassscalesshinyshinybusyshinyjssourcetoolssurvivaltibbletinytexutf8vctrsviridisLitewithrxfunxtableyaml

Getting started

Rendered fromssd4mosaic.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2024-03-20
Started: 2024-03-20

Using ssd4mosaic's functions in R

Rendered fromR_functions.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2024-03-20
Started: 2024-03-20

Readme and manuals

Help Manual

Help pageTopics
Add confidence interval(s) to an existing fitted distribution ggplotadd_CI_plot
Graphical representation of fitted distribution(s)base_cdf
Determines the appropriate bootstrap function based on a fit objectbootdist_fun
Graphical representation of censored datacens_lines_plot
Generate a script according to user in-app inputscode_r_ssd
Combine several bootstrap samples into a single 'bootdist' or 'bootdistcens' objectcombine_boot_samples
Custom ggplot theme created for MOSAIC bioacc overwriting 'theme_bw'custom_theme
Summary of 48 to 96-hour acute toxicity values for endosulfanendosulfan
48-hour acute toxicity values for fluazinamfluazinam
Generate bootstrap sample(s) for a list of fit(s) and check their convergenceget_bootstrap
Fit the specified distributions to the given dataget_fits
Get HCx values from fit or bootstrapget_HCx_table
Get fit(s) parameters in HTML format for shiny outputsget_parameters_html
Create a label for x axis based on concentration unit and log scaleget_xlab
Graphical representation of grouped toxicity censored datagroup_cdf_censored
Graphical representation of grouped toxicity uncensored datagroup_cdf_uncensored
Create a pretty confidence interval ggplotmy_CIcdfplot
Graphical representation of named toxicity censored dataname_plot_censored
Graphical representation of named toxicity uncensored dataname_plot_uncensored
Graphical representation of toxicity data with additional elementsoptions_plot
Take a data.frame of censored toxicity data and order them like 'fitdistrplus' plotsorder_cens_data
Run the Shiny Applicationrun_app
72-hour acute salinity tolerance of macro-invertebrates grouped by family.salinity_family
72-hour acute salinity tolerance of macro-invertebrates grouped by order.salinity_order
Custom toggle switch input for shiny UIswitchInput
Test the approximate equality of the quantiles from several bootstrap samplestest_conv