├── .gitignore ├── .travis.yml ├── README.md ├── document.bash ├── drat.sh ├── pkg ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R │ ├── data_checks.R │ ├── oystercatcher.R │ ├── parse_outfile.R │ ├── read_icv.R │ ├── read_tcf.R │ ├── read_tdf.R │ ├── rtrim-pkg.R │ ├── skylark.R │ ├── trim.R │ ├── trim_estimate.R │ ├── trim_gof.R │ ├── trim_heatmap.R │ ├── trim_index.R │ ├── trim_overall.R │ ├── trim_post.R │ ├── trim_refine.R │ ├── trim_smooth.R │ ├── trim_wald.R │ ├── trim_workhorse.R │ └── utils.R ├── data │ ├── oystercatcher.RData │ ├── skylark.RData │ └── skylark2.RData ├── tests │ ├── testthat.R │ └── testthat │ │ ├── outfiles │ │ ├── skylark-1a.out │ │ ├── skylark-1a.tcf │ │ ├── skylark-1b.out │ │ ├── skylark-1b.tcf │ │ ├── skylark-1c.out │ │ ├── skylark-1c.tcf │ │ ├── skylark-1d.out │ │ ├── skylark-1d.tcf │ │ ├── skylark-1e.out │ │ ├── skylark-1e.tcf │ │ ├── skylark-1f.out │ │ ├── skylark-1f.tcf │ │ ├── skylark-2a.out │ │ ├── skylark-2a.tcf │ │ ├── skylark-2b.out │ │ ├── skylark-2b.tcf │ │ ├── skylark-3a.out │ │ ├── skylark-3a.tcf │ │ ├── skylark-4a.out │ │ ├── skylark-4a.tcf │ │ ├── skylark-4b.out │ │ ├── skylark-4b.tcf │ │ ├── skylark-4c.out │ │ ├── skylark-4c.tcf │ │ ├── skylark-4d.out │ │ ├── skylark-4d.tcf │ │ ├── skylark-4e.out │ │ ├── skylark-4e.tcf │ │ ├── skylark-4f.out │ │ ├── skylark-4f.tcf │ │ ├── skylark-minimal.tcf │ │ ├── skylark-model2-f.csv │ │ ├── skylark-x1.ocv │ │ ├── skylark-x1.out │ │ ├── skylark-x1.tcf │ │ ├── skylark-x2.out │ │ ├── skylark-x2.tcf │ │ ├── skylark-x3.out │ │ ├── skylark-x3.tcf │ │ ├── skylark.dat │ │ ├── skylark_wt.dat │ │ ├── skylark_yr.dat │ │ └── test_skylark_1a_to_2b.R │ │ ├── test_checks.R │ │ ├── test_errors.R │ │ ├── test_tcf.R │ │ ├── test_tdf.R │ │ ├── test_trim.R │ │ ├── test_utils.R │ │ └── testdata │ │ └── 131183.RData └── vignettes │ ├── Skylark_example.Rmd │ ├── TRIM_methods_v2.pdf │ ├── TRIM_methods_v2.pdf.asis │ ├── UIndex_Oystercatcher_output.RData │ ├── rtrim_2_extensions.Rmd │ ├── 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