diff --git a/paper/img/ssd_combined.png b/paper/img/ssd_combined.png
new file mode 100644
index 0000000000000000000000000000000000000000..7bdf6c5739e87bde775f58f058dffe9ae944b09a
Binary files /dev/null and b/paper/img/ssd_combined.png differ
diff --git a/paper/paper.bib b/paper/paper.bib
index c2abad5ed0fc5d4c0ad58f0b458d61650fd041fd..f51de73da0c438452c251590e7a903a62f175b29 100644
--- a/paper/paper.bib
+++ b/paper/paper.bib
@@ -19,7 +19,7 @@ issn = {2475-9066},
journal = {Journal of Open Source Software},
number = {31},
pages = {1082},
-title = {{ssdtools: An R package to fit Species Sensitivity Distributions}},
+title = {{ssdtools}: An {R} package to fit Species Sensitivity Distributions},
volume = {3},
year = {2018}
}
@@ -47,7 +47,7 @@ year = {2021}
pages = {2133-2139},
pmid = {24863265},
publisher = {Oxford Academic},
- title = {MOSAIC_SSD: A new web tool for species sensitivity distribution to include censored data by maximum likelihood},
+ title = {{MOSAIC_SSD}: A new web tool for species sensitivity distribution to include censored data by maximum likelihood},
volume = {33},
url = {https://dx.doi.org/10.1002/etc.2644},
year = {2014},
@@ -70,7 +70,7 @@ year = {2021}
}
@Manual{Shiny,
- title = {shiny: Web Application Framework for R},
+ title = {{shiny}: Web Application Framework for {R}},
author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
year = {2025},
note = {R package version 1.10.0.9000,
@@ -79,7 +79,7 @@ year = {2021}
}
@article{fitdistrplus,
- title={fitdistrplus: An R Package for Fitting Distributions},
+ title={{fitdistrplus}: An {R} Package for Fitting Distributions},
volume={64},
url={https://www.jstatsoft.org/index.php/jss/article/view/v064i04},
doi={10.18637/jss.v064.i04},
@@ -91,7 +91,7 @@ year = {2021}
}
@Manual{R,
- title = {R: A Language and Environment for Statistical Computing},
+ title = {{R}: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
@@ -100,7 +100,7 @@ year = {2021}
}
@Manual{ssddata,
- title = {ssddata: Species Sensitivity Distribution Data},
+ title = {{ssddata}: Species Sensitivity Distribution Data},
author = {Rebecca Fisher and Joe Thorley},
year = {2021},
note = {R package version 1.0.0},
diff --git a/paper/paper.md b/paper/paper.md
index 2b9c8a3ff5bc0fcdaade9f0a02ad7cef2dc8abd5..9f2c5ce246b5928163ebbfa874462e01318833a8 100644
--- a/paper/paper.md
+++ b/paper/paper.md
@@ -1,5 +1,5 @@
---
-title: '`ssd4mosaic`: an R package for species sensitivity distributions includin interval-censored data'
+title: '`ssd4mosaic`: an R package for species sensitivity distributions including interval-censored data'
tags:
- R
- ecotoxicology
@@ -8,7 +8,6 @@ tags:
- uncertainty quantification
authors:
- name: Miléna Kaag
- orcid: 0000-0000-0000-0000
equal-contrib: true
affiliation: 1
- name: Sandrine Charles
@@ -18,27 +17,27 @@ authors:
affiliations:
- name: Universite Claude Bernard Lyon 1, UMR CNRS 5558, 43 boulevard du 11 novembre 1918, 69100 Villeurbanne, FRANCE
index: 1
-date: March 2024
+date: February 2025
bibliography: paper.bib
---
# Summary
-Species Sensitivity Distribution analyses (SSDs) are recognized since the 80s as a key support tool for decision in environmental protection and management. More than ten years ago, the MOSAIC ssd web application, based on the *fitdistrplus* R package (`@fitdistrplus`), was created to provide an easy access to these analyses with the specificity of fully supporting interval-censored data (`@MOSAICssd`).
+Species Sensitivity Distribution analyses (SSDs) are recognized since the 80s as a key support tool for decision in environmental protection and management. More than ten years ago, the `MOSAIC ssd` web application, based on the *fitdistrplus* R package [@fitdistrplus], was created to provide an easy access to these analyses with the specificity of fully supporting interval-censored data [@MOSAICssd].
-MOSAIC ssd recently received a major update as a *shiny* R package (`@Shiny`, `@R`) including additional features: easier data input, additional plotting options, choice between 90% and 95% uncertainty quantiles, custom Hazardous Concentration (HCx) computation, better availability, graphical improvements.
+`MOSAIC ssd` recently received a major update as a *shiny* R package [@Shiny; @R], `ssd4mosaic`. This update includes additional features: easier data input, additional plotting options, choice between 90% and 95% uncertainty quantiles, custom Hazardous Concentration (HCx) computation, better availability, graphical improvements.
-This paper describes the new MOSAIC ssd and compares its results with other similar tools via the help of the *ssddata* R package (`@ssddata`) to confirm its capabilities.
+This paper describes the new `MOSAIC ssd` and compares its results with other similar tools via the help of the *ssddata* R package [@ssddata] to confirm its capabilities.
# Statement of need
-The MOSAIC ssd web application was created more than 10 years ago (`@MOSAICssd`). Since then, it has been used across the world and appeared in several papers comparing tools with similar purposes (`@Fox:2021`, `@Binet:2024`).
+The `MOSAIC ssd` web application was created more than 10 years ago [@MOSAICssd]. Since then, it has been used across the world and appeared in several papers comparing tools with similar purposes [@Fox:2021; @Binet:2024].
# Software's new features
- MOSAIC ssd is now implemented using the shiny R package (`@Shiny`). It is available online on the MOSAIC platform (https://mosaic.univ-lyon1.fr/) and also has an R package, *ssd4mosaic* (available on CRAN), which allows users to access MOSAIC ssd's functionalities offline on their own R installation and to easily deploy the application on personal shiny servers if needs be.
+ `MOSAIC ssd` is now implemented using the shiny R package [@Shiny]. It is available online on the MOSAIC platform (https://mosaic.univ-lyon1.fr/) and also has an R package, `ssd4mosaic` (available on CRAN), which allows users to access `MOSAIC ssd`'s functionalities offline on their own R installation and to easily deploy the application on personal shiny servers if needs be.
-A description of the initial version of the MOSAIC ssd web tool can be found in `@MOSAICssd`. Historically, the application has the following features:
+A description of the initial version of the `MOSAIC ssd` web tool can be found from @MOSAICssd. Historically, the application has the following features:
+ Upload or copy and paste of the users' data, or use of a provided test dataset
+ Support of both pointwise and censored data.
@@ -58,18 +57,24 @@ The newer version added the following features:
+ Easier to navigate tabs structure and overall graphical improvements
+ Availability to the users of the "MOSAIC-flavoured" plotting functions via the published *ssd4mosaic* package.
-See Figure ?? for a screenshot of the MOSAIC ssd application.
+See Figure \autoref{fig:mosaic_ssd} for a screenshot of the `MOSAIC ssd` application.
+
+
# Comparison with other tools
-As strongly recommended in `@Fox:2021`, we chose to compare the results of the MOSAIC ssd application to results' of other tools on a series of benchmark datasets stored in the *ssddata* R package (`@ssddata`). This package contains 20 datasets and several hazardous concentrations for each computed with two different tools: *ssdtools* (version 0.3.3 and 0.3.4) and Burrlioz (version v2.0).
+As strongly recommended by @Fox:2021, we chose to compare the results of the `MOSAIC ssd` application to results' of other tools on a series of benchmark datasets stored in the *ssddata* R package [@ssddata]. This package contains 20 datasets and several hazardous concentrations for each computed with two different tools: *ssdtools* (version 0.3.3 and 0.3.4) and Burrlioz (version v2.0).
-We computed the protective concentrations (PC) PC80, PC90, PC95 and PC99 with MOSAIC ssd for each of the datasets using both the lognormal and loglogistic distributions. These protective concentrations corresponds to the hazardous concentrations HC20, 10, 5 and 1 respectively. The comparison of these PCx values can be seen in figure \autoref{fig:historic_PCx}.
+We computed the protective concentrations (PC) PC80, PC90, PC95 and PC99 with `MOSAIC ssd` for each of the datasets using both the lognormal and loglogistic distributions. These protective concentrations corresponds to the hazardous concentrations HC20, 10, 5 and 1 respectively. The comparison of these PCx values can be seen in figure \autoref{fig:historic_PCx}.
-Additionally, we computed HCx values using both MOSAIC ssd and the current version of *ssdtools* (2.1.0) for 7 additional datasets: the "endosulfan" dataset that is available as a test dataset in MOSAIC ssd, the linear alkylbenzene sulfonate (LAS) dataset from `@Fox:2022` (initially from `@Belanger:2016`), and the five produced water datasets from `@Binet:2024`. The comparison of the obtained PCx values can be found in figure \autoref{fig:newer_PCx}.
+Additionally, we computed HCx values using both `MOSAIC ssd` and the current version of *ssdtools* (2.1.0) for 7 additional datasets: the "endosulfan" dataset that is available as a test dataset in `MOSAIC ssd`, the linear alkylbenzene sulfonate (LAS) dataset from @Fox:2022 (initially from @Belanger:2016), and the five produced water datasets from @Binet:2024. The comparison of the obtained PCx values can be found in figure \autoref{fig:newer_PCx}.
-We see no notable discrepancies between the PC values stored in the *ssddata* packages and the ones computed by MOSAIC ssd. The results are equally similar for the new datasets that were added to the analysis, confirming the adequacy of the MOSAIC ssd tool.
+We see no notable discrepancies between the PC values stored in the *ssddata* packages and the ones computed by `MOSAIC ssd`. The results are equally similar for the new datasets that were added to the analysis, confirming the adequacy of the `MOSAIC ssd` tool.
-
\ No newline at end of file
+
+
+# Acknowledgements
+
+# References
\ No newline at end of file