Dev1.2.2.9000 (#31)

* update readme

* add codecov

* add codecov to test yaml

* forgot to add

.Rbuildignore

@@ -11,3 +11,4 @@
 ^LICENSE\.md$
 ^LICENSE$
 ^\.github$
+^codecov\.yml$

.github/workflows/check-standard.yaml

@@ -54,11 +54,6 @@ jobs:
         # env:
           # RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          # # # # custom hack to ensure correct version of Matrix for TMB
-          # sudo apt-get install -y --allow-downgrades r-cran-matrix=1.2-18-1focal0
-          # R -e "install.packages('TMB', type = 'source')"
-          # # # # custom hack end
-          
           while read -r cmd
           do
             eval sudo $cmd
@@ -76,6 +71,16 @@ jobs:
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Run codecov
+        if: runner.os == 'Linux'
+        run: |
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Upload coverage to Codecov
+        if: runner.os == 'Linux'
+        uses: codecov/codecov-action@v1
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main

DESCRIPTION

@@ -17,6 +17,7 @@ Imports: circular, cowplot, data.table, ggplot2, ggrepel, nloptr, plyr, Rcpp, re
 Suggests: 
     testthat (>= 2.1.0),
     knitr,
-    rmarkdown
+    rmarkdown,
+    covr
 URL: https://github.com/baktoft/yaps
 BugReports: https://github.com/baktoft/yaps/issues

README.Rmd

@@ -20,6 +20,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/baktoft/yaps/workflows/R-CMD-check/badge.svg)](https://github.com/baktoft/yaps/actions)
+[![Codecov test coverage](https://codecov.io/gh/baktoft/yaps/branch/master/graph/badge.svg)](https://codecov.io/gh/baktoft/yaps?branch=master)
 <!-- badges: end -->
 
 
@@ -190,12 +191,19 @@ lines(pl$Y~pl$X, col="red")
 # Papers using or relating to YAPS
 ## 2020
 
+* Baktoft, H., Gjelland, K., Szabo-Meszaros, M. et al (2020). Can energy depletion of wild atlantic salmon kelts negotiating hydropower facilities lead to reduced survival? Sustain. 12, 1–12. https://doi.org/10.3390/SU12187341
+
+* Hubert, J., Campbell, J. & Slabbekoorn, H. (2020). Effects of seismic airgun playbacks on swimming patterns and behavioural states of Atlantic cod in a net pen. Marine Pollution Bulletin. 160. 111680. https://doi.org/10.1016/j.marpolbul.2020.111680  
+
+* Vergeynst, J., Pauwels, I., Baeyens, R. et al. (2020). Shipping canals on the downstream migration route of European eel ( Anguilla anguilla ): Opportunity or bottleneck?. Ecology of Freshwater Fish. 30. https://doi.org/10.1111/eff.12565  
+
 * Vergeynst, J., Vanwyck, T., Baeyens, R. et al. (2020). Acoustic positioning in a reflective environment: going beyond point-by-point algorithms. Anim Biotelemetry 8, 16. https://doi.org/10.1186/s40317-020-00203-1
 
+* Vergeynst, J., Baktoft, H., Mouton, A. et al. (2020). The influence of system settings on positioning accuracy in acoustic telemetry, using the YAPS algorithm. Anim. Biotelemetry, 8, 1–12, https://doi.org/10.1186/s40317-020-00211-1  
+
 ## 2019  
 
-* Baktoft, H., Gjelland, K.Ø., Økland, F., Rehage, J.S., Rodemann, J.R., Corujo, R.S., Viadero, N., Thygesen, U.H. (2019). Opening the black box of fish tracking using acoustic telemetry
-bioRxiv 2019.12.16.877688; doi: https://doi.org/10.1101/2019.12.16.877688
+* Baktoft, H., Gjelland, K.Ø., Økland, F., Rehage, J.S., Rodemann, J.R., Corujo, R.S., Viadero, N., Thygesen, U.H. (2019). Opening the black box of fish tracking using acoustic telemetry. bioRxiv 2019.12.16.877688; doi: https://doi.org/10.1101/2019.12.16.877688
 
 * Silva, A.T., Bærum, K.M., Hedger, R.D., Baktoft, H., Fjeldstad, H., Gjelland, K.Ø., Økland, F. Forseth, T. (2019). Science of the Total Environment The effects of hydrodynamics on the three-dimensional downstream migratory movement of Atlantic salmon. Science of the Total Environment, 135773. https://doi.org/10.1016/j.scitotenv.2019.135773
 

README.md

@@ -3,6 +3,8 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/baktoft/yaps/workflows/R-CMD-check/badge.svg)](https://github.com/baktoft/yaps/actions)
+[![Codecov test
+coverage](https://codecov.io/gh/baktoft/yaps/branch/master/graph/badge.svg)](https://codecov.io/gh/baktoft/yaps?branch=master)
 <!-- badges: end -->
 
 # YAPS - (Yet Another Positioning Solver)<img src="vignettes/yaps_logo.png" align="right" width="120" />
@@ -219,16 +221,36 @@ lines(pl$Y~pl$X, col="red")
 
 ## 2020
 
+-   Baktoft, H., Gjelland, K., Szabo-Meszaros, M. et al (2020). Can
+    energy depletion of wild atlantic salmon kelts negotiating
+    hydropower facilities lead to reduced survival? Sustain. 12, 1–12.
+    <https://doi.org/10.3390/SU12187341>
+
+-   Hubert, J., Campbell, J. & Slabbekoorn, H. (2020). Effects of
+    seismic airgun playbacks on swimming patterns and behavioural states
+    of Atlantic cod in a net pen. Marine Pollution Bulletin. 160.
+    111680. <https://doi.org/10.1016/j.marpolbul.2020.111680>
+
+-   Vergeynst, J., Pauwels, I., Baeyens, R. et al. (2020). Shipping
+    canals on the downstream migration route of European eel ( Anguilla
+    anguilla ): Opportunity or bottleneck?. Ecology of Freshwater
+    Fish. 30. <https://doi.org/10.1111/eff.12565>
+
 -   Vergeynst, J., Vanwyck, T., Baeyens, R. et al. (2020). Acoustic
     positioning in a reflective environment: going beyond point-by-point
     algorithms. Anim Biotelemetry 8, 16.
     <https://doi.org/10.1186/s40317-020-00203-1>
 
+-   Vergeynst, J., Baktoft, H., Mouton, A. et al. (2020). The influence
+    of system settings on positioning accuracy in acoustic telemetry,
+    using the YAPS algorithm. Anim. Biotelemetry, 8, 1–12,
+    <https://doi.org/10.1186/s40317-020-00211-1>
+
 ## 2019
 
 -   Baktoft, H., Gjelland, K.Ø., Økland, F., Rehage, J.S., Rodemann,
     J.R., Corujo, R.S., Viadero, N., Thygesen, U.H. (2019). Opening the
-    black box of fish tracking using acoustic telemetry bioRxiv
+    black box of fish tracking using acoustic telemetry. bioRxiv
     2019.12.16.877688; doi: <https://doi.org/10.1101/2019.12.16.877688>
 
 -   Silva, A.T., Bærum, K.M., Hedger, R.D., Baktoft, H., Fjeldstad, H.,

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true