version 1.0.1

DESCRIPTION

@@ -0,0 +1,43 @@
+Package: ssd4mosaic
+Title: Web Application for the SSD Module of the MOSAIC Platform
+Version: 1.0.1
+Authors@R: c(
+    person("Milena", "Kaag", , "milena.kaag@univ-lyon1.fr", role = c("cre", "aut")),
+    person("Sandrine", "Charles", , "sandrine.charles@univ-lyon1.fr", role = "aut",
+           comment = c(ORCID = "0000-0003-4604-0166")),
+    person("UMR5558 LBBE MEPS", role = c("cph", "fnd")),
+    person("rhandsontable contributors", role = c("ctb", "cph"),
+           comment = "For my_rhandsontable function")
+  )
+Description: 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>.
+License: MIT + file LICENSE
+URL: https://gitlab.in2p3.fr/mosaic-software/mosaic-ssd,
+        https://mosaic.univ-lyon1.fr/
+BugReports: https://gitlab.in2p3.fr/mosaic-software/mosaic-ssd/-/issues
+Depends: R (>= 4.1.0)
+Imports: actuar, config (>= 0.3.1), fitdistrplus (>= 1.1-11), ggplot2,
+        golem (>= 0.3.5), htmltools, htmlwidgets, jsonlite,
+        rhandsontable, rlang, rmarkdown, shiny (>= 1.7.4), shinybusy,
+        shinyjs, stats, utils
+Suggests: knitr, remotes, spelling, testthat (>= 3.0.0)
+VignetteBuilder: knitr
+Config/testthat/edition: 3
+Encoding: UTF-8
+Language: en-US
+LazyData: true
+RoxygenNote: 7.2.3
+NeedsCompilation: no
+Packaged: 2024-03-18 14:28:40 UTC; milenakaag
+Author: Milena Kaag [cre, aut],
+  Sandrine Charles [aut] (<https://orcid.org/0000-0003-4604-0166>),
+  UMR5558 LBBE MEPS [cph, fnd],
+  rhandsontable contributors [ctb, cph] (For my_rhandsontable function)
+Maintainer: Milena Kaag <milena.kaag@univ-lyon1.fr>
+Repository: CRAN
+Date/Publication: 2024-03-19 20:10:02 UTC

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: ssd4mosaic authors

LICENSE.note

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+The ssd4mosaic package as a whole is distributed under MIT.
+
+The ssd4mosaic package includes other open source software components. The following
+is a list of these components (full copies of the license agreements used by
+these components are included below):
+
+- rhandsontable, https://github.com/jrowen/rhandsontable
+- 'Source Sans' fonts, https://fonts.adobe.com/fonts/source-sans
+
+rhandsontable license
+---------------------------------------------------------------------
+(the MIT License)
+
+Copyright (c) 2015-2018 Jonathan Owen and other contributors
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+'Source Sans' fonts
+---------------------------------------------------------------------
+Copyright 2010, 2012, 2014 Adobe Systems Incorporated (http://www.adobe.com/), with Reserved Font Name ‘Source’.
+
+This Font Software is licensed under the SIL Open Font License, Version 1.1.
+This license is copied below, and is also available with a FAQ at:
+http://scripts.sil.org/OFL
+
+
+-----------------------------------------------------------
+SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
+-----------------------------------------------------------
+
+PREAMBLE
+The goals of the Open Font License (OFL) are to stimulate worldwide
+development of collaborative font projects, to support the font creation
+efforts of academic and linguistic communities, and to provide a free and
+open framework in which fonts may be shared and improved in partnership
+with others.
+
+The OFL allows the licensed fonts to be used, studied, modified and
+redistributed freely as long as they are not sold by themselves. The
+fonts, including any derivative works, can be bundled, embedded,
+redistributed and/or sold with any software provided that any reserved
+names are not used by derivative works. The fonts and derivatives,
+however, cannot be released under any other type of license. The
+requirement for fonts to remain under this license does not apply
+to any document created using the fonts or their derivatives.
+
+DEFINITIONS
+"Font Software" refers to the set of files released by the Copyright
+Holder(s) under this license and clearly marked as such. This may
+include source files, build scripts and documentation.
+
+"Reserved Font Name" refers to any names specified as such after the
+copyright statement(s).
+
+"Original Version" refers to the collection of Font Software components as
+distributed by the Copyright Holder(s).
+
+"Modified Version" refers to any derivative made by adding to, deleting,
+or substituting -- in part or in whole -- any of the components of the
+Original Version, by changing formats or by porting the Font Software to a
+new environment.
+
+"Author" refers to any designer, engineer, programmer, technical
+writer or other person who contributed to the Font Software.
+
+PERMISSION & CONDITIONS
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of the Font Software, to use, study, copy, merge, embed, modify,
+redistribute, and sell modified and unmodified copies of the Font
+Software, subject to the following conditions:
+
+1) Neither the Font Software nor any of its individual components,
+in Original or Modified Versions, may be sold by itself.
+
+2) Original or Modified Versions of the Font Software may be bundled,
+redistributed and/or sold with any software, provided that each copy
+contains the above copyright notice and this license. These can be
+included either as stand-alone text files, human-readable headers or
+in the appropriate machine-readable metadata fields within text or
+binary files as long as those fields can be easily viewed by the user.
+
+3) No Modified Version of the Font Software may use the Reserved Font
+Name(s) unless explicit written permission is granted by the corresponding
+Copyright Holder. This restriction only applies to the primary font name as
+presented to the users.
+
+4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+Software shall not be used to promote, endorse or advertise any
+Modified Version, except to acknowledge the contribution(s) of the
+Copyright Holder(s) and the Author(s) or with their explicit written
+permission.
+
+5) The Font Software, modified or unmodified, in part or in whole,
+must be distributed entirely under this license, and must not be
+distributed under any other license. The requirement for fonts to
+remain under this license does not apply to any document created
+using the Font Software.
+
+TERMINATION
+This license becomes null and void if any of the above conditions are
+not met.
+
+DISCLAIMER
+THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
+OTHER DEALINGS IN THE FONT SOFTWARE.

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NAMESPACE

@@ -0,0 +1,32 @@
+# Generated by roxygen2: do not edit by hand
+
+export(add_CI_plot)
+export(base_cdf)
+export(cens_lines_plot)
+export(dllogis)
+export(get_bootstrap)
+export(get_fits)
+export(group_cdf_censored)
+export(group_cdf_uncensored)
+export(name_plot_censored)
+export(name_plot_uncensored)
+export(options_plot)
+export(pllogis)
+export(qllogis)
+export(rllogis)
+export(run_app)
+import(shiny)
+importFrom(actuar,dllogis)
+importFrom(actuar,pllogis)
+importFrom(actuar,qllogis)
+importFrom(actuar,rllogis)
+importFrom(ggplot2,"%+replace%")
+importFrom(golem,activate_js)
+importFrom(golem,add_resource_path)
+importFrom(golem,bundle_resources)
+importFrom(golem,favicon)
+importFrom(golem,with_golem_options)
+importFrom(rlang,.data)
+importFrom(shiny,NS)
+importFrom(shiny,shinyApp)
+importFrom(shiny,tagList)

NEWS.md

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+# ssd4mosaic 1.0.1
+
+## Enhancements
+
+* Changes to comply to CRAN guidelines
+    - Clarification of the authorship and ownership of the package
+    - Completion of the functions documentation
+    - Removed calls to `print()` in bootstrap function
+    - Various syntax changes
+* Update repository url
+## Bug fixes
+
+* Fix the bug of names being displayed in user input order on non-censored data plots, instead of being associated to the correct data point.
+
+* For HCx values, replace medians of the bootstrap samples by quantiles calculated from the fitted distribution in order to match the behaviour of the previous MOSAIC ssd.
+
+## New features
+
+* Added a rate unit (g/ha) in unit selection list
+
+# ssd4mosaic 1.0.0
+
+## Enhancements
+
+* The way to precise the role of each column of the input data column has be reviewed to improve readability.
+
+* More information texts have been added to the website to help users in their choices.
+
+* Group plot readability has been improved by moving the legend to the bottom of the plot instead of the side.
+
+* The colors used in the plot have been modified to improve accessibility for color blindness.
+
+## Bug fixes
+
+* Reports downloaded in markdown format now include required image files.
+
+## New features
+
+* 90% confidence intervals can now be displayed on the plot and computed for the parameter values and HCx values.
+
+* A link toward a Frequently Asked Questions page was added.
+
+* Two vignettes were added to the package: "Getting started" and "Using ssd4mosaic functions in R".
+
+# ssd4mosaic 0.1.0
+
+New features
+
+* Created the package
+* Added a `NEWS.md` file to track changes to the package.