updated links and version

.github/workflows/test-coverage.yaml

@@ -56,4 +56,4 @@ jobs:
         uses: codecov/codecov-action@v4.0.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          slug: abigailkeller/eDNAjoint
+          slug: ropensci/eDNAjoint

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: eDNAjoint
 Title: Joint Modeling of Traditional and Environmental DNA Survey Data
-Version: 0.1
+Version: 0.2
 Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
 Author: Abigail G. Keller
 Authors@R: 
     c(person("Abigail G.", "Keller", role = c("aut", "cre"), email="agkeller@berkeley.edu"),
     person("Ryan P.", "Kelly", role = "ctb", email="rpkelly@uw.edu"))
 Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: https://bookdown.org/abigailkeller/eDNAjoint_vignette/). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
 License: GPL-3
-URL: https://github.com/abigailkeller/eDNAjoint
-BugReports: https://github.com/abigailkeller/eDNAjoint/issues
+URL: https://github.com/ropensci/eDNAjoint
+BugReports: https://github.com/ropensci/eDNAjoint/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, roclets = c ("namespace", "rd", "srr::srr_stats_roclet"))
 RoxygenNote: 7.3.1

NEWS.md

@@ -1,3 +1,10 @@
+# eDNAjoint 0.2
+
+-   Package source code now hosted at <https://github.com/ropensci/eDNAjoint>
+-   Improved programming (i.e., reduced cyclomatic complexity, spacing, etc.)
+-   Added functionality to accommodate semi-paired data (i.e., traditional samples not collected at all surveyed sites).
+-   Improved integration of package print statements with user guide.
+
 # eDNAjoint 0.1
 
--   First version of eDNAjoint
+-   Initial version of the package on GitHub.

README.Rmd

@@ -22,8 +22,8 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/abigailkeller/eDNAjoint/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abigailkeller/eDNAjoint/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/abigailkeller/eDNAjoint/graph/badge.svg?token=AEVR9NSQ9Z)](https://codecov.io/gh/abigailkeller/eDNAjoint)
+[![R-CMD-check](https://github.com/ropensci/eDNAjoint/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/eDNAjoint/actions/workflows/R-CMD-check.yaml)
+[![codecov](https://codecov.io/gh/ropensci/eDNAjoint/graph/badge.svg?token=AEVR9NSQ9Z)](https://codecov.io/gh/abigailkeller/eDNAjoint)
 [![Status at rOpenSci Software Peer
 Review](https://badges.ropensci.org/642_status.svg)](https://github.com/ropensci/software-review/issues/642)
 [![Lifecycle:
@@ -59,7 +59,7 @@ provided by Cran, the program needs to compile during installation:
 
 ```{r,eval=FALSE}
 library(devtools)
-install_github('abigailkeller/eDNAjoint')
+install_github('ropensci/eDNAjoint')
 ```
 
 ## Example