Merge branch 'main' of github.com:pedersen-fisheries-lab/sspm

CITATION.cff

@@ -0,0 +1,15 @@
+cff-version: 1.1.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Lucet
+    given-names: Valentin
+    orcid: https://orcid.org/0000-0003-0268-818X
+  - family-names: Pedersen
+    given-names: Eric
+    orcid: https://orcid.org/0000-0003-1016-540X
+  - family-names: Huynh
+    given-names: Quang
+    orcid: https://orcid.org/0000-0001-7835-4376
+title: pedersen-fisheries-lab/sspm: sspm v1.0.0 Zenodo + JOSS release
+version: v1.0.0
+date-released: 2023-06-07

paper/paper.bib

@@ -326,7 +326,7 @@ @book{wood_generalized_2017
 @techreport{dfo_assessment_2019,
 	type = {techreport},
 	institution = {Canadian Science Advisory Secretariat (CSAS)},
-	title = {An Assessment of {Northern} {Shrimp} (Pandalus borealis) in {Shrimp} {Fishing} {Areas} 4–6 and of {Striped} {Shrimp} (Pandalus montagui) in Shrimp Fishing Area 4 in 2018},
+	title = {An Assessment of {Northern} {Shrimp} ({Pandalus borealis}) in {Shrimp} {Fishing} {Areas} 4–6 and of {Striped} {Shrimp} ({Pandalus montagui}) in Shrimp Fishing Area 4 in 2018},
 	number = {2019/027},
 	author = {{DFO}},
 	year = {2019},

paper/paper.md

@@ -11,10 +11,12 @@ output:
   pdf_document: default
   word_document: default
 authors:
-- name: Valentin Lucet^[co-first author]
+- name: Valentin Lucet
+  equal-contrib: true
   orcid: 0000-0003-0268-818X
   affiliation: 1
-- name: Eric J. Pedersen^[co-first author]
+- name: Eric J. Pedersen
+  equal-contrib: true
   orcid: 0000-0003-1016-540X
   affiliation: "1, 2"
 bibliography: paper.bib
@@ -51,7 +53,7 @@ We have chosen a statistical approach to fitting SPMs. Statistical models allow
 
 In this paper, we use a statistical approach to fitting SPMs using Generalized Additive Models (GAMS), estimated using the `mgcv` R package [@wood_generalized_2017] as the backend. We apply this approach to the population of Northern Shrimp of the Newfoundland and Labrador Shelves, leveraging the smoothing properties of GAMs to account for varying productivity across time and space. The resulting model is a spatial SPM (SSPM), implemented via an R package: `sspm`.
 
-The R package `sspm` is designed to make SSPMs simpler to estimate and apply to any spatially structured stock. The basic model this packages implements was first used to model time-varying production in Newfoundland and Labrador Northern Shrimp stocks [@pedersenNewSpatialEcosystembased2021]. However, the general modelling approach used here will work for any spatially structured fishery with sufficient data. It includes a range of features to manipulate harvest and biomass data. Those features are organized in a stepwise workflow, whose implementation is described in more detail in \autoref{fig:workflow} and in the next section.
+The R package `sspm` is designed to make SSPMs simpler to estimate and apply to any spatially structured stock. The basic model this package implements was first used to model time-varying production in Newfoundland and Labrador Northern Shrimp stocks [@pedersenNewSpatialEcosystembased2021]. However, the general modelling approach used here will work for any spatially structured fishery with sufficient data. It includes a range of features to manipulate harvest and biomass data. Those features are organized in a stepwise workflow, whose implementation is described in more detail in \autoref{fig:workflow} and in the next section.
 
 Although it was developed in a fisheries context, the package is suited to model spatially-structured population dynamics in general.