[JOSS Review] Add test coverage

[fawda123]

Consider adding test covering to your CI, including the badge showing percentage of the package that's covered. You've got a bunch of tests in tests/testthat, but it would be nice to see how much of the package is covered. This should be pretty straightforward with usethis::use_coverage().

openjournals/joss-reviews#6389

[k-doering-NOAA]

I ran covr::package_coverage() on a clone of the main branch and coverage is indeed high! It would be worth showing off with a badge on the readme.

covr::package_coverage()
SSN2 Coverage: 85.78%
R/SSN_to_SSN2.R: 0.00%
src/init.c: 0.00%     
R/pseudoR2.R: 33.33%
R/create_netgeometry.R: 42.86%
R/utils.R: 44.44%
R/ssn_import_predpts.R: 49.23%
R/AIC.R: 50.00%
R/ssn_get_data.R: 50.00%
R/partition.R: 53.33%
R/laploglik.R: 54.55%
R/ssn_import.R: 58.33%
R/checks.R: 59.32%
R/ssn_put_data.R: 61.29%
R/get_anisotropy_corrected.R: 61.90%
R/get_cholprods.R: 65.22%
R/augment.R: 70.37%
R/get_dist_predbk_object.R: 72.50%
R/random.R: 73.33%
R/deviance.R: 75.00%
R/restruct_ssn_missing.R: 75.00%
R/ssn_update_path.R: 75.00%
R/anova.R: 75.34%
R/local.R: 76.32%
R/get_eigenprods.R: 77.27%
R/optim.R: 78.95%
R/randcov_vector.R: 79.41%
R/get_data_object_glm.R: 79.47%
R/predict_glm.R: 79.80%
R/logLik.R: 80.00%
R/ssn_split_predpts.R: 80.00%
R/createBinaryID.R: 80.56%
R/loocv_glm.R: 80.58%
R/get_cov_matrix.R: 81.48%
R/ssn_write.R: 82.61%
R/predict.R: 82.69%
R/residuals.R: 83.33%
R/get_data_object.R: 84.85%
R/ssn_get_netgeometry.R: 85.71%
R/use_laploglik.R: 85.94%
R/plot.R: 86.07%
R/loocv.R: 86.52%
R/tidy.R: 87.08%
R/get_dist_pred_object.R: 87.08%
R/print.SSN.R: 87.50%
R/ssn_rbinom.R: 87.50%
R/ssn_create_distmat.R: 87.69%
R/ssn_glm.R: 88.46%
R/glances.R: 88.89%
src/test_fc_UNIX.c: 89.47%
R/copy_lsn_to_temp.R: 90.00%
R/cov_initial_search_glm.R: 90.82%
R/ssn_subset.R: 90.85%
R/ssn_get_stream_distmat.R: 90.91%
R/ssn_rinvgauss.R: 90.91%
R/covmatrix.R: 91.07%
R/partition_vector.R: 91.30%
R/ssn_rpois.R: 91.67%
R/ssn_rnorm.R: 92.42%
R/fitted.R: 93.33%
R/ssn_rgamma.R: 93.75%
R/ssn_rnbinom.R: 93.75%
R/coef.R: 94.12%
R/get_Torgegram_initial_object.R: 94.44%
R/cov_initial_search.R: 94.51%
R/get_model_stats_glm.R: 95.86%
R/ssn_rbeta.R: 96.15%
R/get_model_stats.R: 96.27%
R/get_cov_vector.R: 96.97%
R/initial.R: 97.37%
R/initial_NA.R: 97.75%
R/laploglik_products.R: 97.95%
R/Torgegram.R: 98.11%
R/ssn_lm.R: 98.39%
R/use_gloglik.R: 98.39%
R/get_dist_object.R: 98.61%
R/print.R: 99.34%
R/amongSitesDistMat.R: 100.00%
R/confint.R: 100.00%
R/cooks.distance.R: 100.00%
R/cov_betahat_adjust.R: 100.00%
R/cov_estimate.R: 100.00%
R/cov_matrix.R: 100.00%
R/cov_vector.R: 100.00%
R/formula.R: 100.00%
R/get.rid.fc.R: 100.00%
R/getObsRelationshipsDF.R: 100.00%
R/getPredRelationshipsDF.R: 100.00%
R/glance.R: 100.00%
R/gloglik.R: 100.00%
R/gloglik_products.R: 100.00%
R/hatvalues.R: 100.00%
R/influence.R: 100.00%
R/labels.R: 100.00%
R/model.frame.R: 100.00%
R/model.matrix.R: 100.00%
R/names.SSN.R: 100.00%
R/optim2orig.R: 100.00%
R/orig2optim.R: 100.00%
R/params.R: 100.00%
R/ssn_simulate.R: 100.00%
R/summary.R: 100.00%
R/summary.SSN.R: 100.00%
R/transform_anis.R: 100.00%
R/varcomp.R: 100.00%
R/vcov.R: 100.00%

[michaeldumelle]

Thank you for the great suggestion @fawda123, and thanks @k-doering-NOAA for locally running covr::package_coverage(). I would very much love to add this badge, and I recognize the importance of incorporating CI test coverage. Unfortunately, USEPA GitHub does not currently allow their repositories to use certain cloud-based services, one of which is codecov.io. So I cannot incorporate the badge, but maybe there is another way to communicate the coverage of the package as indicated by covr::package_coverage()? Also tagging @mikemahoney218. Thank you!

[fawda123]

@michaeldumelle that's a bummer, but I understand the limitations. It's possible you could fork the repo to your personal account and setup the codecov CI there? Then you could just put the link to the badge from your account on the USEPA readme? This isn't ideal though as it's not really continuous integration - youd' have to make sure that the USEPA repo is always in sync with your personal. So maybe not... just a suggestion, I don't think you should do this. You can close this issue if you like.

[michaeldumelle]

@fawda123 thanks, and I agree it is a total bummer! A few of us are in discussions about adding coverage CI to USEPA repositories, so if this becomes feasible in the future, I will certainly add the codecov CI badge to the SSN2 README.