update citations

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ssdtools
 Title: Species Sensitivity Distributions
-Version: 2.2.0.9000
+Version: 2.2.0.9001
 Authors@R: c(
     person("Joe", "Thorley", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7683-4592")),

NEWS.md

@@ -1,9 +1,15 @@
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
+# ssdtools 2.2.0.9001
+
+- Update citations.
+
+
 # ssdtools 2.2.0.9000
 
 - House-keeping on Github actions.
 
+
 # ssdtools 2.2.0
 
 - Added `ssd_label_comma_hc()` function to label numbers with significant digits and comma and offset hazard concentration value if present in breaks.

README.Rmd

@@ -99,6 +99,11 @@ For recent developments in SSD modeling including a review of existing software
 
 *Fox, D.R., et al. 2021. Recent Developments in Species Sensitivity Distribution Modeling. Environ Toxicol Chem 40(2): 293–308. <https://doi.org/10.1002/etc.4925>.*
 
+## Citation
+
+```{r, comment = "", echo = FALSE}
+citation("ssdtools")
+```
 
 ## Installation
 

README.md

@@ -139,6 +139,28 @@ software see:
 Distribution Modeling. Environ Toxicol Chem 40(2): 293–308.
 <https://doi.org/10.1002/etc.4925>.*
 
+## Citation
+
+    To cite package 'ssdtools' in publications use:
+
+      Thorley J, Fisher R, Fox D, Schwarz C (2025). "ssdtools v2: An R
+      package to fit Species Sensitivity Distributions." _Journal of Open
+      Source Software_, *10*(105), 7492. doi:10.21105/joss.07492
+      <https://doi.org/10.21105/joss.07492>.
+
+    A BibTeX entry for LaTeX users is
+
+      @Article{,
+        title = {ssdtools v2: An R package to fit Species Sensitivity Distributions},
+        author = {Joe Thorley and Rebecca Fisher and David Fox and Carl Schwarz},
+        year = {2025},
+        journal = {Journal of Open Source Software},
+        volume = {10},
+        number = {105},
+        pages = {7492},
+        doi = {10.21105/joss.07492},
+      }
+
 ## Installation
 
 ### Release

inst/CITATION

@@ -0,0 +1,11 @@
+bibentry(
+  "Article",
+  title = "ssdtools v2: An R package to fit Species Sensitivity Distributions",
+  author = "Joe Thorley, Rebecca Fisher, David Fox, Carl Schwarz",
+  year = 2025,
+  journal = "Journal of Open Source Software",
+  volume = 10,
+  number = 105,
+  pages = 7492,
+  doi = "10.21105/joss.07492"
+)

vignettes/faqs.Rmd

@@ -44,3 +44,28 @@ ssd_plot(ssddata::ccme_boron, ssdtools::boron_pred, label = "Species", shape = "
 ```{r, results = "asis", echo = FALSE}
 cat(ssd_licensing_md())
 ```
+
+## Censoring
+
+### What is censored data?
+
+Data is censored when the exact value is uncertain. 
+There are three primary types of censoring.
+Right censoring when only the lower bound is known (>), left censoring when only the upper bound is known (<)
+and interval censored when both the lower and upper bound are known (><).
+Uncensored data can be thought of as interval censored data in which the upper and lower bound are identical (=).
+Likewise, missing data can be considered to be censored data in which both the upper and lower bound are unknown (?).
+
+### How is censored data coded in ssdtools?
+
+Censored data is coded by specifying the lower bound values in one column (>) and the upper bound values in a second column (<).
+Unknown lower bounds are coded using NA or 0 while unknown upper bounds are coded using NA or Inf.
+The name of the columns with the lower and upper bound values are then passed to the `left` (>) and `right` (<) arguments in the `ssd_fit_dists()` function, respectively.
+
+### What are the current limitations on analysing censored data?
+
+Currently `ssdtools` has the following limitations on the analysis of censored data:
+
+- distribution fitting to left (<) or interval (><) censored data only, i.e., when the upper bound is known;
+- model averaging when the distributions have the same number of parameters only; and
+- estimation of confidence interval using non-parametric bootstrapping only.