38f74f5732109d038d2f3651bf1029c8 *DESCRIPTION
d229b0734b5537ed6e7d8717dc87b3d2 *NAMESPACE
5078ce8ee09aeb187cdf0c50af7d35ff *NEWS.md
ae0025e00af97ed33d07e467af3cc675 *R/PLN.R
535738109be8cfdd8ce238def742048c *R/PLNLDA.R
23eb1ada7c148edfe2c7e6eb5703d0c2 *R/PLNLDAfit-S3methods.R
8b6a2415e65eabd0f4464aeec4493fcb *R/PLNLDAfit-class.R
05f1bbc77752466429a751a33c15d115 *R/PLNPCA.R
5f1c2c058c29aecc4ab85b5d54db7cc8 *R/PLNPCAfamily-S3methods.R
383b1e1254837fa2dd0ef5002351453c *R/PLNPCAfamily-class.R
cac42c0c01894d08fbe17712eee37d67 *R/PLNPCAfit-S3methods.R
67c935d1a7a7c7340322729df9b4d35f *R/PLNPCAfit-class.R
634b19ea6f44037e460389cef28e630c *R/PLNfamily-S3methods.R
37ec58e6414a6c555b38953d240226ce *R/PLNfamily-class.R
87d88c6336201d80aba27c4c0f40b175 *R/PLNfit-S3methods.R
0cfe392f3ebfae72852301d61dfcb266 *R/PLNfit-class.R
80ca46ed1f4ce4a2daa246a4ce2c446d *R/PLNmixture.R
dee1caa1a53ec364529b835059c43fc1 *R/PLNmixturefamily-S3methods.R
1af6ab305f35dee18b773756c8d3f6b7 *R/PLNmixturefamily-class.R
85afee43cc5b127ed1b5be97ebd8ff2c *R/PLNmixturefit-S3methods.R
edfaa5ee4b9e47f0277639dee5a3bfe7 *R/PLNmixturefit-class.R
d78a53cecc7224bb0d07f77ac9401bfd *R/PLNmodels-package.R
dc8d547cb42b24409a61ee1f30c7759c *R/PLNnetwork.R
6cbf5685b8e37216b384900e81456d06 *R/PLNnetworkfamily-S3methods.R
4ff9981bf50c7850e57841bbf5ec3b90 *R/PLNnetworkfamily-class.R
8d6277276eee83eb4c6f597f952bcad1 *R/PLNnetworkfit-S3methods.R
9e003fe8fe954e9966a7727f13890aa8 *R/PLNnetworkfit-class.R
7a1974b3424a7e9d0f715f060ed7cf97 *R/RcppExports.R
9e002db64d1fe85724c9be3113a12eeb *R/barents.R
3fdacaf07da1106f3f8dd88114ecae87 *R/import_utils.R
1275f472dc1c31454e841e7463b251cf *R/mollusk.R
edf5e4dfbb44b14deb76204ed3bf65cc *R/oaks.R
c28da69534691c405e13a80d0037aa43 *R/plot_utils.R
9af8bc65796472eb9c3189ddaa15f679 *R/trichoptera.R
65cef5e0674056f6fc07dd2b3ca85c13 *R/utils-pipe.R
49360f7322c5fcf330472655610b718b *R/utils.R
6e9e6bbb41da8ba05c651afb2a6d4f4b *R/zzz.R
ea124a494ad7922985532ad3b308e4d5 *build/partial.rdb
c07a0b54305806166ce6911c694e4b1e *build/vignette.rds
e45ed86e18cf600a29bd08dfef643645 *data/barents.rda
2f327773058c2bd66029ab7f7d7b5251 *data/mollusk.rda
3e2ccd2a6b5a8cc32d0f7379d29a8782 *data/oaks.rda
d8fbc101f364e46b994254894974c26c *data/trichoptera.rda
70788621b44cb51154c3e9779870d835 *inst/CITATION
ae9e599ca89528597b4a52b72935c9c0 *inst/WORDLIST
91a6b7147ca85333fa21acc3d4310285 *inst/doc/Import_data.R
96258cc6b7bab62860461ee11c488f6a *inst/doc/Import_data.Rmd
9ff3c64197aa68d86388b4a65df6dfe8 *inst/doc/Import_data.html
b8429aac7581aa83431abed2290cb790 *inst/doc/PLN.R
6e20dea70d1b15e3b3dcfdd14e735fb6 *inst/doc/PLN.Rmd
d5a16a9f2ffdaadf0a391c0ce3a6308a *inst/doc/PLN.html
d02bad25a46dabc32ff4e0c1330b32b0 *inst/doc/PLNLDA.R
60846071275ec051abe832b799665942 *inst/doc/PLNLDA.Rmd
bfa4b03aa1aefa4ea92973d3f5541b00 *inst/doc/PLNLDA.html
b5dee417c86e49746529016066c3035e *inst/doc/PLNPCA.R
7a63e359cf60794c036974080c3fae91 *inst/doc/PLNPCA.Rmd
35dadb16beea6a93841276b8d4b5fa5f *inst/doc/PLNPCA.html
ff48eeb55b45f131ca184259a740d87a *inst/doc/PLNmixture.R
12d59a92638839efca3367bac0e6ddb7 *inst/doc/PLNmixture.Rmd
7483061971246f776be6271889abbed0 *inst/doc/PLNmixture.html
ca0dfe74f4bcf93d570d945bc5e3b610 *inst/doc/PLNnetwork.R
bb1f448ef31f113325627912c7e6a4ff *inst/doc/PLNnetwork.Rmd
1351946367c8e0cc0e264a13a75662fa *inst/doc/PLNnetwork.html
18df2923c3615e799d4cf1e16110bb45 *inst/doc/Trichoptera.R
5310e9f3c42bce25644a1e3357fff1d0 *inst/doc/Trichoptera.Rmd
cc93052ab4bc57194a46768fd78a94ff *inst/doc/Trichoptera.html
76c1ef822e620c54f39dd48420484ca1 *man/PLN.Rd
f1101dfa9f0f0b1293f29a599b6f665b *man/PLNLDA.Rd
670f22c2bbefdfd8893d3ecc2c4daca2 *man/PLNLDA_param.Rd
9b21983983283fc82720fb2c2bbee932 *man/PLNLDAfit.Rd
7979fdf885967e1785dc9f74376374a1 *man/PLNLDAfit_diagonal.Rd
729c56bbd3c0313d3feccd606f2ec16f *man/PLNPCA.Rd
e8ddc3d6fc8aef5ab4d4d4102075fb5c *man/PLNPCA_param.Rd
c6dfe910b703932273ef54a3a832283d *man/PLNPCAfamily.Rd
134caf392f9465223ec5077acbc477fd *man/PLNPCAfit.Rd
6ffcf341e06453f837e2b1746732c738 *man/PLN_param.Rd
d3d1467d452c56e3c1a30996290fab21 *man/PLNfamily.Rd
830f7f02b3390a2e637fc04baf5fa2f1 *man/PLNfit.Rd
1a9c13f261fcbbc669e8d1e21227c12b *man/PLNfit_diagonal.Rd
4fec4c9685aa0010920511120e03924e *man/PLNfit_fixedcov.Rd
06b6c3f8d63dd6fb8f965ffb993acff7 *man/PLNfit_spherical.Rd
2517f97ac5ebe0665098cd75d63e2bad *man/PLNmixture.Rd
da158fbe11595c55495f6a8402d0778e *man/PLNmixture_param.Rd
f7519a8d46532d62f33d15e92efd1911 *man/PLNmixturefamily.Rd
be1cf936440481dc3499a0d54645b43f *man/PLNmixturefit.Rd
d6deaa23a65964d3a679f0dad78e97c1 *man/PLNmodels.Rd
f378f5d978f2fbdd321acd1171496b03 *man/PLNnetwork.Rd
4700705576d3e6ab75e6d7f6907e4bc6 *man/PLNnetwork_param.Rd
51820bb1d76f17beaae170344ac705ec *man/PLNnetworkfamily.Rd
a8c93db6433039f1741050b946dc3e81 *man/PLNnetworkfit.Rd
e083c2469c61777eec9b74cc6fac1cb9 *man/barents.Rd
1fb49f78d35da831799d07341397cbef *man/coef.PLNLDAfit.Rd
99a0ebb1226eff45bf20fd3144b8cd3f *man/coef.PLNfit.Rd
20666df7b3b6067502d6fc5161347c89 *man/coef.PLNmixturefit.Rd
6dd085ee66f2074540af3a891fb1c389 *man/coefficient_path.Rd
bcffc82fb088948f92687d4923defd91 *man/compute_offset.Rd
0f801a6060713abcbddf89bdda5a6594 *man/extract_probs.Rd
ad4fab8aaac566822a2bdab83b802c20 *man/figures/PLN-1.png
e03b5a7338baa6f86571e76cb9107706 *man/figures/PLNLDA-1.png
5aff6b5ed17fb429333b7fa9fb287464 *man/figures/PLNPCA-1.png
311ccfc6ebcdd187952b5f02d6e5aec6 *man/figures/PLNPCA-2.png
ba876de895c7ef4127ff42abf2b33f6e *man/figures/PLNnetwork-1.png
2830cd399b9d2a5cbb83ca1bd18b0933 *man/figures/PLNnetwork-2.png
68946a1f9a3c9d200231229459aa6884 *man/figures/logo.png
bdc12c80267fcce7e4995b128031dfcd *man/fitted.PLNfit.Rd
1cfb01e2f07d9bf668459f208f5d8597 *man/fitted.PLNmixturefit.Rd
8d73b5a734598630b376444cfa46a5fe *man/getBestModel.Rd
5a575c67b7fcd24625a1ef481d531b68 *man/getModel.Rd
dd928b5e8cbff7ce15f4834d5e7395e8 *man/mollusk.Rd
06be0537d1b4473d5db4ee3c6fd0fabf *man/oaks.Rd
4894ca10756199e25f914bfd34f517b0 *man/pipe.Rd
dec5752ca6de2bcd37dcfe3d69a3803a *man/plot.PLNLDAfit.Rd
504a86b4cd667781bc11adffed36b5ba *man/plot.PLNPCAfamily.Rd
89757f4e6edde80408067757113561c6 *man/plot.PLNPCAfit.Rd
9427352e1c67a970168d9194bc1a8201 *man/plot.PLNfamily.Rd
3452dda02cef24ceeffe2293714fbee4 *man/plot.PLNmixturefamily.Rd
974fada0252eb354077843feb4663e52 *man/plot.PLNmixturefit.Rd
9761f15c925c41e315e574c5f431664a *man/plot.PLNnetworkfamily.Rd
1ce0ee5836d7d29dfbf96258f4c78815 *man/plot.PLNnetworkfit.Rd
2afdae406284eadc5fd96cc3f65f16be *man/predict.PLNLDAfit.Rd
5b77a5ddf2c52c151efdd7472397e200 *man/predict.PLNfit.Rd
ec5e124fcf8250dbab3ceafe8efe4aa6 *man/predict.PLNmixturefit.Rd
c15876215dd7dafbd5b241e16e7d7e42 *man/predict_cond.Rd
ff0d8273deeefcd1c582f8de3a176f1b *man/prepare_data.Rd
84af03c6187f55e4debc90d7cb75ca2c *man/rPLN.Rd
8429cee4275a89f12c8e10185c4c52e3 *man/sigma.PLNfit.Rd
d13ffb02aa65f40bfad921b67f8e3329 *man/sigma.PLNmixturefit.Rd
95736cf59bcfe1adfe40b8033d921368 *man/stability_selection.Rd
ac1be6095cf7ced6c8c1753a27d01cfa *man/standard_error.Rd
89820f32077958595f8b6d0ac97e5f49 *man/trichoptera.Rd
9d25bba0bf910092e424b54e03613773 *man/vcov.PLNfit.Rd
fdcb2e0c2502ed804ae55e75cf88055c *src/Makevars
fdcb2e0c2502ed804ae55e75cf88055c *src/Makevars.win
97309eee1edc8c4e5e0736d6bdc00b84 *src/RcppExports.cpp
52bb3667de40f8831180e0798d1e019e *src/nlopt_wrapper.cpp
c5ba6c58b867cdfc087ffa8a878527ab *src/nlopt_wrapper.h
9fd7b79074f6ac4700b068f2928acf77 *src/optim_diag_cov.cpp
de04f36fc81f8cda10b21be621485ef5 *src/optim_fixed_cov.cpp
67995ef40871452a558b4ce89069f61b *src/optim_full_cov.cpp
6f81a17f64393a1cf5401a0d2b40864c *src/optim_genet_cov.cpp
3d481dddb202ca2851be149ac02ee8b2 *src/optim_rank_cov.cpp
373024c1f52991f4ee39cfd7f2bffff9 *src/optim_spherical.cpp
076a1604a1b7059a4e3d25bf0477896c *src/packing.cpp
1e7da738b69d8db732998bb5e0d26ae8 *src/packing.h
4c0ec41194c43751208969b7f986edfe *src/utils.h
18a23834805a479852c3ee8b39ab72be *tests/testthat.R
7aa336eff1d69c10b9a433f422b355a8 *tests/testthat/Rplots.pdf
78c257b160abf361120bc1ad9b271ad3 *tests/testthat/test-cpp.R
293a0de31edb45242295a5e173af1d20 *tests/testthat/test-import-utils.R
605c4f15ecaa278071b35e50e88c2be2 *tests/testthat/test-pln.R
fec6cae403387aa3685f7e2e6961aa9d *tests/testthat/test-plnfamily.R
3674c5053cf86c08df5f1464181e8410 *tests/testthat/test-plnfit.R
330e98e2f24411de9cbacebdf529ffe4 *tests/testthat/test-plnlda-fit.R
c46f9010c72ce2e71ab1c69f84e218fd *tests/testthat/test-plnlda.R
268c3e73737e28fa52f47a88da434083 *tests/testthat/test-plnmixture.R
48dd052792c88ca05682d872bc588403 *tests/testthat/test-plnnetworkfamily.R
d0066fd2e5b527fa9acefd2dfac44d09 *tests/testthat/test-plnnetworkfit.R
6c3c03634e3ce3bf374d4f4fb0abee50 *tests/testthat/test-plnpcafamily.R
8e6d953ba23ed8bb6884dfb8e631ddaa *tests/testthat/test-plnpcafit.R
8f1a85a58c981f6abe5cc6a79f40012e *tests/testthat/test-standard-error.R
96258cc6b7bab62860461ee11c488f6a *vignettes/Import_data.Rmd
6e20dea70d1b15e3b3dcfdd14e735fb6 *vignettes/PLN.Rmd
60846071275ec051abe832b799665942 *vignettes/PLNLDA.Rmd
7a63e359cf60794c036974080c3fae91 *vignettes/PLNPCA.Rmd
12d59a92638839efca3367bac0e6ddb7 *vignettes/PLNmixture.Rmd
bb1f448ef31f113325627912c7e6a4ff *vignettes/PLNnetwork.Rmd
5310e9f3c42bce25644a1e3357fff1d0 *vignettes/Trichoptera.Rmd
5ba4457f5cef9f3ea28eed59fed43d0c *vignettes/article/PLNreferences.bib
5bc5cf5dc71ad7fe0621e36392f00dfa *vignettes/figures/PLN_geometry.jpg
8f03f4dd93836ef21a7341b9fad0419b *vignettes/figures/macronema_zebratum.jpg
