diff --git a/.Rbuildignore b/.Rbuildignore
index c0b247f..6e9a1d1 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -11,3 +11,4 @@
^LICENSE\.md$
^LICENSE$
^\.github$
+^codecov\.yml$
diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index d0aaecf..ab716aa 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.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 $cmd
@@ -76,6 +71,16 @@ jobs:
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
+ - name: Run codecov
+ if: runner.os == 'Linux'
+ run: |
+ covr::codecov()
+ shell: Rscript {0}
+
+ - name: Upload coverage to Codecov
+ if: runner.os == 'Linux'
+ uses: codecov/codecov-action@v1
+
- name: Upload check results
if: failure()
uses: actions/upload-artifact@main
diff --git a/DESCRIPTION b/DESCRIPTION
index 68f85fa..f353406 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,6 +17,7 @@ Imports: circular, cowplot, data.table, ggplot2, ggrepel, nloptr, plyr, Rcpp, re
Suggests:
testthat (>= 2.1.0),
knitr,
- rmarkdown
+ rmarkdown,
+ covr
URL: https://github.com/baktoft/yaps
BugReports: https://github.com/baktoft/yaps/issues
diff --git a/README.Rmd b/README.Rmd
index e075dd4..73da51d 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -20,6 +20,7 @@ knitr::opts_chunk$set(
[](https://github.com/baktoft/yaps/actions)
+[](https://codecov.io/gh/baktoft/yaps?branch=master)
@@ -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
diff --git a/README.md b/README.md
index 7d2573d..d7a4b4d 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,8 @@
[](https://github.com/baktoft/yaps/actions)
+[](https://codecov.io/gh/baktoft/yaps?branch=master)
# YAPS - (Yet Another Positioning Solver)
@@ -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.
+
+
+- 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.
+
+- 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.
+
- 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.
+- 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,
+
+
## 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:
- Silva, A.T., Bærum, K.M., Hedger, R.D., Baktoft, H., Fjeldstad, H.,
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 0000000..04c5585
--- /dev/null
+++ b/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