├── .Rbuildignore ├── .Rprofile ├── .github └── workflows │ ├── binary-build.yml │ ├── r-cmd-check.yml │ └── test-coverage.yml ├── .gitignore ├── BUILD.md ├── DESCRIPTION ├── LICENSE.md ├── Makefile ├── NAMESPACE ├── R ├── anolis.R ├── ape2ouch.R ├── as_data_frame.R ├── bimac.R ├── bootstrap.R ├── brown.R ├── coef.R ├── geospiza.R ├── glssoln.R ├── hansen.R ├── logLik.R ├── ouchtree.R ├── package.R ├── paint.R ├── plot.R ├── print.R ├── rmvnorm.R ├── simulate.R ├── summary.R └── update.R ├── README.md ├── codecov.yml ├── data ├── anolis.ssd.rda ├── bimac.rda └── geospiza.rda ├── examples ├── anolis.R ├── bimac.R ├── bimac1.R ├── bimac2.R ├── bootstrap.R ├── geospiza.R └── paint.R ├── inst ├── CITATION ├── GPL ├── NEWS ├── NEWS.Rd └── doc │ ├── Makefile │ ├── index.html │ └── index.md ├── man ├── anolis_ssd.Rd ├── as_data_frame.Rd ├── bimac.Rd ├── bootstrap.Rd ├── brown.Rd ├── coef.Rd ├── geospiza.Rd ├── glssoln.Rd ├── hansen.Rd ├── logLik.Rd ├── macros │ └── citations.Rd ├── ouchtree.Rd ├── package.Rd ├── paint.Rd ├── plot.Rd ├── print.Rd ├── simulate.Rd ├── summary.Rd └── update.Rd ├── revdep ├── .gitignore ├── Makefile └── Outputs │ ├── check_mvSLOUCH_stderr.txt │ ├── check_mvSLOUCH_stdout.txt │ ├── check_ouch_stderr.txt │ ├── check_ouch_stdout.txt │ ├── check_pmc_stderr.txt │ ├── check_pmc_stdout.txt │ ├── check_surface_stderr.txt │ └── check_surface_stdout.txt ├── rules.mk ├── src ├── covar-matrix.c ├── init.c ├── ouch.h └── weight-matrix.c ├── tests ├── Makefile ├── ape2ouch.R ├── ape2ouch.Rout ├── bapst.R ├── bapst.Rout.save ├── bapst.csv ├── bergmann.R ├── bergmann.Rout.save ├── bergmann.csv ├── boot.R ├── boot.Rout.save ├── brown.R ├── brown.Rout.save ├── exacttree.R ├── exacttree.Rout.save ├── glssoln.R ├── glssoln.Rout.save ├── hansen.R ├── hansen.Rout.save ├── ouchtree.R ├── ouchtree.Rout.save ├── paint.R ├── paint.Rout.save ├── plot.R ├── plot.Rout.save ├── plot01.png ├── plot02.png ├── plot03.png ├── plot04.png ├── plot05.png ├── plot06.png 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