Merge pull request #368 from poissonconsulting/main

vignette naming and order

.Rbuildignore

@@ -21,3 +21,4 @@
 ^COMPLIANCE\.yaml$
 ^CRAN-SUBMISSION$
 ^CODE_OF_CONDUCT\.md$
+^vignettes/articles$

CONTRIBUTING.Rmd

@@ -16,18 +16,19 @@ All contributors retain the original copyright to their stuff, but by contributi
 
 **To track copyright, please use the following:** 
 
-**New code file:** At the top of the file, please ensure copyright is attributed to collaborator and assign the Apache 2.0 license
+**New code file:** At the top of the file, please ensure copyright and year is attributed to collaborator and assign the Apache 2.0 license
 
-**Major addition to code file:** “Copyright Province of British Columbia” and Apache 2.0 remains as a header and either the second collaborator is added if there are changes throughout the code or copyright is listed for specific lines of code.  So it could read:
+**Major addition to code file:** “Copyright YYYY Province of British Columbia” and Apache 2.0 remains as a header and either the second collaborator is added if there are changes throughout the code or copyright is listed for specific lines of code.  So it could read:
 
-Copyright Province of British Columbia and
-Copyright Collaborator
+Copyright 2020-2022 Province of British Columbia
+Copyright 2024 Collaborator
 Apache 2.0 License
 
 Or 
 
-Copyright Province of British Columbia and
-Lines 200-500 Copyright Collaborator
+Copyright 2020-2022 Province of British Columbia
+Copyright 2024 Collaborator Lines 200-500
 Apache 2.0 License
 
-**Minor changes:**  If there are small changes to the code throughout the file then it may be easiest to keep these files as Copyright Province of British Columbia.  However, the contribution will be tracked through GitHub.
+**Minor changes:**  If there are small changes to the code throughout the file then it may be easiest to keep these files as Copyright YYYY Province of British Columbia.  
+However, the contribution will be tracked through GitHub.

_pkgdown.yml

@@ -111,3 +111,11 @@ reference:
   - '`qlgumbel`'
   - '`rlgumbel`'
 
+articles:
+- title: All vignettes
+  contents:
+  - model-averaging
+  - distributions
+  - articles/confidence-intervals
+  - embelishing-plots
+  - additional-technical-details

vignettes/C_confidence_intervals.Rmd → vignettes/articles/confidence-intervals.Rmd

@@ -1,18 +1,12 @@
 ---
-title: "Obtaining Confidence Intervals"
+title: "Confidence Intervals for Hazard Concentrations"
 author: "ssdtools Team"
 date: "`r Sys.Date()`"
 bibliography: references.bib
-output: rmarkdown::html_vignette
-#output: rmarkdown::pdf_document
 csl: my-style.csl
 latex_engine: MathJax
 mainfont: Arial
 mathfont: Courier
-vignette: >
-  %\VignetteIndexEntry{Obtaining Confidence Intervals}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r, include = FALSE}

vignettes/articles/my-style.csl

@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-US">
+  <!-- Generated with https://github.com/citation-style-language/utilities/tree/master/generate_dependent_styles/data/springer -->
+  <info>
+    <title>Statistical Papers</title>
+    <title-short>Stat Papers</title-short>
+    <id>http://www.zotero.org/styles/statistical-papers</id>
+    <link href="http://www.zotero.org/styles/statistical-papers" rel="self"/>
+    <link href="http://www.zotero.org/styles/springer-basic-author-date" rel="independent-parent"/>
+    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_1.0.pdf" rel="documentation"/>
+    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/manuscript-guidelines-1.0.pdf" rel="documentation"/>
+    <category citation-format="author-date"/>
+    <category field="science"/>
+    <issn>0932-5026</issn>
+    <eissn>1613-9798</eissn>
+    <updated>2014-05-18T01:40:32+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+</style>

vignettes/articles/references.bib

@@ -0,0 +1,270 @@
+
+@article{fox_recent_2021,
+	title = {Recent {Developments} in {Species} {Sensitivity} {Distribution} {Modeling}},
+	volume = {40},
+	issn = {0730-7268, 1552-8618},
+	url = {https://setac.onlinelibrary.wiley.com/doi/10.1002/etc.4925},
+	doi = {10.1002/etc.4925},
+	language = {en},
+	number = {2},
+	urldate = {2021-01-25},
+	journal = {Environmental Toxicology and Chemistry},
+	author = {Fox, D.R. and Dam, R.A. and Fisher, R. and Batley, G.E. and Tillmanns, A.R. and Thorley, J. and Schwarz, C.J. and Spry, D.J. and McTavish, K.},
+	month = feb,
+	year = {2021},
+	keywords = {ssdtools},
+	pages = {293--308},
+	file = {Fox et al. - 2021 - Recent Developments in Species Sensitivity Distrib.pdf:/Users/joe/Zotero/storage/MMSH9Q2S/Fox et al. - 2021 - Recent Developments in Species Sensitivity Distrib.pdf:application/pdf},
+}
+
+@article{verdonck_limitations_2003,
+	title = {Limitations of {Current} {Risk} {Characterization} {Methods} in {Probabilistic} {Environmental} {Risk} {Assessment}},
+	volume = {22},
+	issn = {0730-7268, 1552-8618},
+	url = {http://doi.wiley.com/10.1897/02-435},
+	doi = {10.1897/02-435},
+	abstract = {In probabilistic environmental risk assessment, the likelihood and the extent of adverse effects occurring in ecological systems because of exposure(s) to substances are estimated. It is based on the comparison of an exposure/environmental concentration distribution, with a species sensitivity distribution derived from toxicity data. The calculation of a probabilistic risk can be performed in many ways (e.g., area under the curve in joint probability curves). However, several (hypothetical) examples and some theoretical considerations illustrate that the current risk characterisation methods have an integrative character and they focus on the statistical comparison of two distributions without properly considering the environmental interpretation of these underlying distributions. Several scenarios with varying exposure/environmental concentration distribution and species sensitivity distribution standard deviations are discussed.},
+	language = {en},
+	number = {9},
+	urldate = {2019-11-21},
+	journal = {Environmental Toxicology and Chemistry},
+	author = {Verdonck, Frederik A.M. and Aldenberg, Tom and Jaworska, Joanna and Vanrolleghem, Peter A.},
+	year = {2003},
+	pages = {2209},
+	file = {Verdonck et al. - 2003 - LIMITATIONS OF CURRENT RISK CHARACTERIZATION METHO.pdf:/Users/joe/Zotero/storage/I4DFHG9K/Verdonck et al. - 2003 - LIMITATIONS OF CURRENT RISK CHARACTERIZATION METHO.pdf:application/pdf}
+}
+
+@article{burr_cumulative_1942,
+	title = {Cumulative {Frequency} {Functions}},
+	volume = {13},
+	issn = {00034851},
+	number = {2},
+	journal = {The Annals of Mathematical Statistics},
+	author = {Burr, Irving W.},
+	year = {1942},
+	note = {Publisher: Institute of Mathematical Statistics},
+	pages = {215--232},
+	file = {Burr - 1942 - Cumulative Frequency Functions.pdf:/Users/joe/Zotero/storage/IMIF252X/Burr - 1942 - Cumulative Frequency Functions.pdf:application/pdf}
+}
+
+@article{shao_estimation_2000,
+	title = {Estimation for hazardous concentrations based on {NOEC} toxicity data: an alternative approach},
+	abstract = {A common task in environmental studies is to determine toxicant concentrations at which a certain proportion (typically 95 per cent) of the biological species is protected. Extrapolation techniques need to be employed for small sample sizes. By de®nition, our interest focuses on the lower tail of the NOEC (no observed e€ect concentration) distribution, which is very sensitive to the choice of the underlying distribution. In this paper we investigate the use of the three-parameter Burr Type III distribution because of its ¯exibility and ease-of-use. The Constrained Maximum Likelihood (CML) method was used to estimate parameters. Collinearity between parameter estimates was overcome by reparameterisation techniques. As an alternative to the computation of adjustment factors, we estimate the lower con®dence limits of percentile estimates using the Delta-method. When the NOEC sample sizes are small, we employ Bootstrapping, a computer intensive technique. Our technique is easily extended to mixtures of the three-parameter Burr type III distributions, which can be used to model multimodal distributions. Copyright \# 2000 John Wiley \& Sons, Ltd.},
+	language = {en},
+	author = {Shao, Quanxi},
+	year = {2000},
+	keywords = {ssdtools},
+	pages = {13},
+	file = {Shao - 2000 - Estimation for hazardous concentrations based on N.pdf:/Users/joe/Zotero/storage/VFI2YKDE/Shao - 2000 - Estimation for hazardous concentrations based on N.pdf:application/pdf}
+}
+
+
+@article{aldenberg_confidence_1993,
+	title = {Confidence {Limits} for {Hazardous} {Concentrations} {Based} on {Logistically} {Distributed} {NOEC} {Toxicity} {Data}},
+	volume = {25},
+	issn = {01476513},
+	url = {https://linkinghub.elsevier.com/retrieve/pii/S0147651383710067},
+	doi = {10.1006/eesa.1993.1006},
+	language = {en},
+	number = {1},
+	urldate = {2019-12-08},
+	journal = {Ecotoxicology and Environmental Safety},
+	author = {Aldenberg, T. and Slob, W.},
+	month = feb,
+	year = {1993},
+	pages = {48--63}
+}
+
+@techreport{schwarz_improving_2019,
+	address = {Victoria, BC},
+	title = {Improving {Statistical} {Methods} for {Modeling} {Species} {Sensitivity} {Distributions}},
+	number = {WSS2019-07},
+	institution = {Province of British Columbia},
+	author = {Schwarz, Carl and Tillmanns, Angeline},
+	month = jul,
+	year = {2019},
+	keywords = {ssdtools},
+	file = {Schwarz and Tillmanns - 2019 - Improving Statistical Methods for Modeling Species.pdf:/Users/joe/Zotero/storage/M9Z9M872/Schwarz and Tillmanns - 2019 - Improving Statistical Methods for Modeling Species.pdf:application/pdf}
+}
+
+@article{dalgarno_shinyssdtools_2021,
+	title = {shinyssdtools: {A} web application for fitting {Species} {Sensitivity} {Distributions} ({SSDs})},
+	volume = {6},
+	issn = {2475-9066},
+	shorttitle = {shinyssdtools},
+	url = {https://doi.org/10.21105/joss.02848},
+	doi = {10.21105/joss.02848},
+	abstract = {The species sensitivity distribution (SSD) is the most widely used method for getting water quality benchmarks to characterize effects of chemical contaminants for water quality or ecological risk assessment (Fox et al., 2020). This typically involves estimating the concentration of a chemical that affects 5\% of the species considered (Posthuma et al., 2001). The ssdtools R package (Thorley \& Schwarz, 2018) has recently advanced SSD methods by providing model averaging using information-theoretic criteria and the construction of confidence intervals using bootstrapping (Fox et al., 2020).},
+	language = {en},
+	number = {57},
+	urldate = {2021-01-26},
+	journal = {Journal of Open Source Software},
+	author = {Dalgarno, Seb},
+	month = jan,
+	year = {2021},
+	pages = {2848},
+	file = {Dalgarno - 2021 - shinyssdtools A web application for fitting Speci.pdf:/Users/joe/Zotero/storage/CJPKHJ73/Dalgarno - 2021 - shinyssdtools A web application for fitting Speci.pdf:application/pdf}
+}
+
+@book{posthuma_species_2001,
+	title = {Species sensitivity distributions in ecotoxicology},
+	publisher = {CRC press},
+	author = {Posthuma, Leo and Suter II, Glenn W and Traas, Theo P},
+	year = {2001},
+	url = {https://www.routledge.com/Species-Sensitivity-Distributions-in-Ecotoxicology/Posthuma-II-Traas/p/book/9781566705783}
+}
+
+@book{model_averaging,
+	title = {Model Selection and Multimodel Inference - A Practical Information-Theoretic Approach},
+	publisher = {Springer},
+	author = {Burnham, Kenneth and Anderson, David},
+	year = {2002},
+	url = {https://link.springer.com/book/10.1007/b97636}
+}
+
+@book{fletcher,
+	title = {Model Averaging},
+	publisher = {Springer},
+	author = {Fletcher, David},
+	year = {2018},
+	url = {https://link.springer.com/book/10.1007/978-3-662-58541-2}
+}
+
+@Article{fitdistrplus,
+    title = {{fitdistrplus}: An {R} Package for Fitting Distributions},
+    author = {Marie Laure Delignette-Muller and Christophe Dutang},
+    journal = {Journal of Statistical Software},
+    year = {2015},
+    volume = {64},
+    number = {4},
+    pages = {1--34},
+    url = {http://www.jstatsoft.org/v64/i04/}
+  }
+
+@Book{ggplot2,
+  author = {Hadley Wickham},
+   title = {{ggplot2}: Elegant Graphics for Data Analysis},
+   publisher = {Springer-Verlag New York},
+   year = {2016},
+   isbn = {978-3-319-24277-4},
+   url = {https://ggplot2.tidyverse.org}
+ }
+
+ @Manual{r,
+    title = {R: A Language and Environment for Statistical Computing},
+    author = {{R Core Team}},
+    organization = {R Foundation for Statistical Computing},
+    address = {Vienna, Austria},
+    year = {2018},
+    url = {https://www.R-project.org/}
+  }
+
+@book{burnham_model_2002,
+	address = {New York, NY},
+	title = {Model {Selection} and {Multimodel} {Inference}},
+	isbn = {978-0-387-95364-9},
+	url = {https://link.springer.com/10.1007/b97636},
+	language = {en},
+	urldate = {2018-11-23},
+	publisher = {Springer New York},
+	editor = {Burnham, Kenneth P. and Anderson, David R.},
+	year = {2002},
+	doi = {10.1007/b97636}
+}
+
+@techreport{schwarz_improving_2019,
+	address = {Victoria, BC},
+	title = {Improving {Statistical} {Methods} for {Modeling} {Species} {Sensitivity} {Distributions}},
+	number = {WSS2019-07},
+	institution = {Province of British Columbia},
+	author = {Schwarz, Carl and Tillmanns, Angeline},
+	month = jul,
+	year = {2019},
+	file = {Schwarz and Tillmanns - 2019 - Improving Statistical Methods for Modeling Species.pdf:/Users/joe/Zotero/storage/M9Z9M872/Schwarz and Tillmanns - 2019 - Improving Statistical Methods for Modeling Species.pdf:application/pdf}
+}
+
+@book{wickham_r_2016,
+	address = {Sebastopol, CA},
+	edition = {First edition},
+	title = {R for data science: import, tidy, transform, visualize, and model data},
+	isbn = {978-1-4919-1039-9 978-1-4919-1036-8},
+	shorttitle = {R for data science},
+	url = {https://r4ds.had.co.nz},
+	abstract = {"This book introduces you to R, RStudio, and the tidyverse, a collection of R packages designed to work together to make data science fast, fluent, and fun. Suitable for readers with no previous programming experience"--},
+	publisher = {O'Reilly},
+	author = {Wickham, Hadley and Grolemund, Garrett},
+	year = {2016},
+	note = {OCLC: ocn968213225},
+	keywords = {Big data, Computer programs, Data mining, Databases, Electronic data processing, Information visualization, R (Computer program language), Statistics}
+}
+
+@techreport{fox_methodologies_2021,
+	title = {Joint investigation into {statistical} {methodologies} underpinning the {derivation} of {toxicant} {guideline} {values} in {Australia} and {New Zealand}},
+	institution = {Environmetrics Australia and Australian Institute of Marine Science},
+	author = {Fox, David R and Fisher, Rebecca and Thorley, Joseph L and Schwarz, Carl},
+	month = mar,
+	year = {2021},
+  url={https://environmetrics.net/docs/FOX%20and%20FISHER%20Final_final_report_rev2.3.pdf?189db0&189db0}
+}
+
+
+@article{newman_2000,
+	title = {Applying {species-sensitivity distributions} in {ecological} {risk assessment}: Assumptions of
+{distribution type} and sufficient {numbers of species}},
+	volume = {19},
+	url = {https://setac.onlinelibrary.wiley.com/doi/abs/10.1002/etc.5620190233},
+	doi = {10.1002/etc.5620190233},
+	language = {en},
+	urldate = {2024-02-08},
+	journal = {Environmental Toxicology and Chemistry},
+	author = {Newman, Michael C. and Ownby, David R. and Mézin, Laurent C. A. and Powell, David C.  and Christensen, Tyler R. L. and Lerberg, Scott B. and  Anderson, Britt-Anne },
+	month = feb,
+	year = {2000},
+	pages = {508--515}
+}
+
+@techreport{Zajdlik_2005,
+	title = {Statistical analysis of the SSD approach for development of Canadian water quality guidelines},
+	language = {en},
+	year = {2005},
+	number={CCME Project 354‐200/5},
+	author={Zajdlik, B.},
+	institution={Zajdlik and Associates}
+}
+
+@article{chapman_2007,
+	title = {Methods of uncertainty analysis},
+	journal={In: A H (ed) EUFRAM Concerted Action to Develop a European Framework for Probabilistic Risk Assessment of the Environmental Impacts of Pesticides, Vol 2, Detailed Reports on Role, Methods, Reporting and Validation},
+	author = {Chapman,  PF RM and Hart, A and Roelofs, W and  Aldenberg, T and Solomon, K and Tarazona, J LM and Byrne, P and Powley, W and Green, J and Ferson, S and Galicia, H},
+	year = {2007}
+}
+
+@article{fox_2016,
+	title = {Contemporary Methods for Statistical Design and Analysis},
+	url = {https://shop.elsevier.com/books/marine-ecotoxicology/blasco/978-0-12-803371-5},
+	isbn={9780128033715},
+	language = {en},
+	urldate = {2024-02-08},
+	journal = {In: Blasco J, Chapman PM, Campana O, Hampel M (eds) Marine Ecotoxicology.},
+	author = {Fox, David R},
+	month = aug,
+	year = {2016},
+  publisher={Academic Press}
+}
+
+@article{warne2018,
+   author = {Warne, M and Batley, GE and van Dam, RA and Chapman, JC and Fox, DR and Hickey, CW and Stauber, JL },
+   title = {Revised Method for Deriving Australian and New Zealand Water Quality Guideline Values for Toxicants – update of 2015 version},
+   journal = {Prepared for the revision of the Australian and New Zealand Guidelines for Fresh and Marine Water Quality. Australian and New Zealand Governments and Australian state and territory governments, Canberra, 48 pp},
+   year = {2018},
+   type = {Journal Article}
+}
+
+@article{fisher2019,
+   author = {Fisher, Rebecca and van Dam, Rick and Batley, Graeme and Fox, David and Harford, Andrew and Humphrey, Chris and King, Cath and Menendez, Patricia and Negri, Andrew and Proctor, Abigail},
+   title = {KEY ISSUES IN THE DERIVATION OF WATER QUALITY GUIDELINE VALUES: A WORKSHOP REPORT},
+   year = {2019},
+   type = {Journal Article}
+}
+
+