6a9faf3dbac34961ac8c818bc781aa6f *DESCRIPTION
e80a514ef5602ea6c5799dd6c4c3fc83 *NAMESPACE
6e902b9ebc29d3d654519ee03ecfaca6 *NEWS
cfeb7573da848dff66873df501f94ac1 *R/HMMLikelihood.r
696b2ec0092872731bf5b855f2b7f7b5 *R/HMMutilities.r
f487318157b812669e6ba63c2a9a0981 *R/InitialDistribution_functions.r
0e31f70823504dee8c5b03bc91aeaed1 *R/Observation_functions.r
db385d14a375fe513c54dc8d1c183f75 *R/RHMMLikelihood.r
f207be67fa69dae8a5dfbbd63504a540 *R/Transition_functions.r
a61331cd326b75473bf019acc81b977b *R/cjs.R
1ebc745ccb41115db41fdf632627468d *R/cjs.accumulate.R
2ebc83075d0c0a6a61077143ff508b91 *R/cjs.hessian.r
139cfd49c611eb82d979b3e26bbf9cd5 *R/cjs.initial.R
7b7e49bcd1170f6a670f26a0abc319bb *R/cjs.lnl.r
a4e0cd56abdc6f910b87611e3aa5eb2b *R/coef.r
3c866ad5431e8057a1ae12fcf706baec *R/compute.real.R
fbba25aa21041cb01ffbe69fe0afab7a *R/convert.link.to.real.r
27f51dbf74272fd0a9216205336a0a57 *R/create.dm.R
6acdb916f35ceb1c65b7979c32380311 *R/create.dmdf.R
7ff0b2f71c22523cdda71d01b79d663b *R/create.links.r
6d46e57c93ad9f864a5dc0923169827f *R/crm.R
a9fe77272f6ee2bce8f86934d8ce9e8e *R/crm.wrapper.R
edc62ba4f9ee716ba24b02971b9c8af1 *R/deriv.inverse.link.R
1bbdcdf2d4afd936df0cfd1aa8fb57d3 *R/extract.fcts.r
258befcf07bbee8575d6a6be8fb3865d *R/fix.parameters.r
1efd9e1a0de6063577785208908c7796 *R/hmmDemo.r
360d432d3310271e795a738d233ff5cb *R/inverse.link.R
8690ad8303c447739e3717474508508c *R/js.accumulate.R
fdae5badf36ef937f6c523eb009425e1 *R/js.hessian.R
07c3ac3a3b50710b203d8578cb6a2aa7 *R/js.lnl.r
ab491912b918dfb8c63958964edc329c *R/js.r
16d466902f538207720065bb7d7ae9f4 *R/make.design.data.R
16d7024fe322b15884399c21266e9ee9 *R/marked-package.R
45692791473a90588b683e1444d48945 *R/merge.design.covariates.r
496381805c8257ba49b7d2210c099126 *R/mixed.model.r
7fa9e60020af2fc63dbc2503e81f9f87 *R/mscjs.r
bce5da28af77c055f5cccd0dd0d8e02a *R/omega.r
0607f461430bf3e1f0c8d07df3673f64 *R/predict.crm.r
06e79f9f5d7079ad822e40bd91c4b693 *R/print.crm.r
9712387c4dab74a0b16a2d57f3d6e316 *R/probitCJS.R
9983d033e56d49141c175077eea630d9 *R/proc.formula.r
a0c91821349600bf0bfcdc3e6c151660 *R/process.ch.R
c70e7ee411243454097f509fd1125390 *R/process.data.R
d43d8431484f467ad339038ec8c0cfae *R/scale.r
0f508aa4a6eb02134a52e0db8a0e50e1 *R/set.fixed.R
cdf36cec227874a6c633fc8165cb2a81 *R/set.initial.r
ae8c2583a7bf902e6f9ec3b4ecbd2d73 *R/set_mvms.r
d6decb893316620c048d3eb9d99f4de8 *R/setup.model.R
f001c922fbdb56c6fb88a87e8cfb6bb6 *R/setup.parameters.R
9ef1ae425e3dbf0748a8b6c31fb44f9a *R/simHMM.r
13499511e4696f2393819fafe2b40d29 *R/simplify.r
8770267efd153aede8a51712130386d7 *R/splitCH.R
74f1ee4cdcd104cf4c9868977e1a3a7a *R/summary.fcts.R
6be6618e9481274241ef95e1a327de14 *R/utility.R
71acdd849dbbd3e3e939cf17baa46724 *R/valid.parameters.R
a6b222025c12be0cd245f6dae2d38a08 *R/zzz.R
94a4a8cf7acf2064c547edb07655dc9f *build/vignette.rds
86fa75dacd73a1e0c85a547b19b08f0c *data/dipper.rda
4b9eee976b66f48fef85116c4ed6cc6f *data/mstrata.rda
58f69429b47c1db1cc263ff301cc1bd1 *data/sealions.rda
22ae24131afb70bf87d86e44d239a737 *data/tagloss.rda
fa6cad0f5950e6d8e7fa214c41609d6a *demo/00Index
3096feb9785fd012fec79c423cfa9320 *demo/tests.r
1ffa8cd9f4e3cd00dedf776687e365bf *inst/CITATION
28f953c339e702ed56d381d81ef13fa4 *inst/README.txt
fe66014c20038df8afa5f1ce58254712 *inst/cjs.tpl
600468762b822b4fb55551430468087a *inst/cjs_reml.tpl
778242d080cc720c761d554b0d93b670 *inst/cjsre.tpl
c6239015ce2a1de9e66725980b19a22a *inst/df1b2gh.cpp
1143c5d073506731d0e8598ee010157d *inst/df1b2ghmult.cpp
913bfcfc454958ea133abaefb23ad936 *inst/doc/markedVignette.R
9744443e95456b32926b54a13c61504a *inst/doc/markedVignette.Rnw
5d0b6d775575791647d807ef45a57803 *inst/doc/markedVignette.pdf
031b17c7059d5f3cc3550c8e3bfcc6bc *inst/minfil.cpp
a6cb96044224a0acf49b636aacbb82d5 *inst/models.txt
20506d81280de462667067f3fdc47177 *inst/multistate.tpl
de3811d4f2d104416fde367b683a79ad *inst/parameters.txt
e2c6956b7e502038a3b256fcec5c37b6 *inst/xmodelm5.cpp
fc702b1e6c67242c927fd6065c28786b *man/HMMLikelihood.Rd
25d19aa476c36aa90e42acf1b37102cf *man/Phi.mean.Rd
d7da748df0efa185c666838f6776142a *man/R_HMMLikelihood.Rd
6f4e1b096484f2cd6019e6f6e392199e *man/backward_prob.Rd
d6b8ead431fa1e6f4835a316e0a358d2 *man/cjs.Rd
3318f52718a8c8591246bd1ee2da1328 *man/cjs.accumulate.Rd
74ecbbdca240473778cd0c959e311ee8 *man/cjs.hessian.Rd
507a30b7459eb0f61c85fa27587bb985 *man/cjs.initial.Rd
0ff483abc9dfa9dc0e6a33058f78c5c9 *man/cjs.lnl.Rd
ba732b046471e05495890b8690e18c19 *man/cjs_delta.Rd
6e465ceec9246829b22f2e81c4a73547 *man/cjs_gamma.Rd
ddd603f3a4d6818766aa33df38ff8f8c *man/coef.crm.Rd
5524eccd65cb3fd2801f32c3ced107b2 *man/compute.real.Rd
7e97c822a547b5b81a9ef9c2eb11e3a3 *man/compute_matrices.Rd
ce920701449d621943c2d40fd29ae748 *man/convert.link.to.real.Rd
fd48f686be1c307fa6f5240b93963f52 *man/create.dm.Rd
1d6a5fa463e00a9cd945199be51aa83d *man/create.dmdf.Rd
328546abc0fd1f12409101129b2729ab *man/create.fixed.matrix.Rd
0ad49407683809a206da5da8c4b8c2e7 *man/create.links.Rd
5a56d300786c167204ff69b5905eb779 *man/crm.Rd
8471c0ceb37fc43a6c8d5cb80d61e65f *man/crm.wrapper.Rd
2ded5f640d6deec13a7ea3dcfa91b8be *man/deriv_inverse.link.Rd
b27ca17d54a49dd9b9d94c0f3e42da3a *man/dipper.Rd
0664fd85c2db0b4b925b0bb5f19e82a6 *man/fix.parameters.Rd
5ca2777389b88c86d44d920de5b2b65b *man/function.wrapper.Rd
f173b43df21a1f93b88e7aa15361d087 *man/global_decode.Rd
4c11513df03af1eac8272afc775644b3 *man/hmmDemo.Rd
e7040bc9cd82482e22652f08e0edec79 *man/inverse.link.Rd
9ab0d34d0a2c1672c0a83b2eb49bc035 *man/js.Rd
dbcbab87cecd07f979244b31343a9b78 *man/js.accumulate.Rd
a6ddf843b4c02f024a4c8c7b4a31c4b1 *man/js.hessian.Rd
6c8d6ad99a4a67e5d1156262af6dd8df *man/js.lnl.Rd
dcfb5e2238df39f5c534c3ca3a0af93e *man/local_decode.Rd
1bc83104fc2a2224fe9b27484ec77685 *man/make.design.data.Rd
d43f63ae5f90040b00cb7e3508741f0a *man/merge_design.covariates.Rd
161d0e15c1713d9817d2b1c8178a0056 *man/mixed.model.admb.Rd
ccdac19fe46e9e3e2ca490b951853dbb *man/mscjs.Rd
1457e277692178954b3b531fed93989d *man/mstrata.Rd
8061507a0c871852934af3d176378b94 *man/mvms_design_data.Rd
c53004997e99e07651c622ba3764b77a *man/mvms_dmat.Rd
afeedb221079eb86ce1cb99e65314fe8 *man/omega.Rd
bf36cb7f3346aaa72812e01aa9b90b5e *man/predict.crm.Rd
684f88841fa69121664d4c56ac1ab559 *man/print.crm.Rd
aa01c508323d4741e5e2b427e488e596 *man/print.crmlist.Rd
d790af0afea5dee12da85594db9a5db5 *man/probitCJS.Rd
5c096331daa83ad6b436fef1937916db *man/proc.form.Rd
ed3a3dce638aaeff7c2829242af4354b *man/process.ch.Rd
27c6cb597ab43a5c8ba460693356386f *man/process.data.Rd
a81c204aedbcaf5a08d9130fa29cd8cb *man/resight.matrix.Rd
8031860a5ec2b663f3386a19c03cc88f *man/sealions.Rd
c04c5c92324f501d3215bbf97dbaba5d *man/set.fixed.Rd
5511e5b1bd0f194879fe92503dd11c1a *man/set.initial.Rd
4e790ce25b734b5ea0365bb85acb4d05 *man/set.scale.Rd
3bd717c90eaa3b1bc836f127af566dd5 *man/set_mvms.Rd
5b9a240bef2f4ade3988fabe1a7f7dfe *man/setup.model.Rd
0aa7cc892be3f81e4eac7f435669d70b *man/setup.parameters.Rd
6f7be1b0b5171f380a27da9f8dc08700 *man/simHMM.Rd
c9cfede210d2286697ea391890189997 *man/splitCH.Rd
1ed3d0f92fd9b73b8b7cf8b03749979d *man/tagloss.Rd
597370ef47f7312692ac89352441f691 *man/valid.parameters.Rd
b3f86c20b81b51f5162874977d38784d *src/Makevars
73505498722ad4b07b0ddb3067e92523 *src/Makevars.win
2e80757fbe08940fe169c82732e3fce2 *src/bayesCR.cpp
ace5af2bc79c40e34beee755fc027d15 *src/cjs.f
5122673881f927690dadc87343a0097d *src/cjs1tldmat.f
a4e950733857d7fb58eaccd2b0f01ec8 *src/cjs1tlgam.f
1e1eac97d600eef42f64919fbbc59f81 *src/cjs2tldmat.f
f314befef16babc71c9b7c6c9f52aaf5 *src/cjs2tlgam.f
aeb6bf08322a12c91efe77bd05ffa273 *src/cjsdmat.f
46949532ae0e9c6c9c92d98767ac9d51 *src/cjsgamma.f
308617476724aab0aaf0ed47047a4c78 *src/hmm_like.f
d00adbdbce4e07a51403c4f994c35f9c *src/ms2gamma.f
955315de2dce7a9011450b46daef69d4 *src/msdmat.f
976487a9ef69a44a95a759c93e13052c *src/msgamma.f
3fd5ffb06ebed0c15d5b0fede6a2a777 *src/mvmsdmat.f
53e9e7838edfe4dd24cb1b6b325b73bb *src/ums2dmat.f
2db0ec726dcd1c679f6852e0a3b7195d *src/umsdmat.f
9744443e95456b32926b54a13c61504a *vignettes/markedVignette.Rnw
f3ac5cfe03c5f4898e80280ddbfd9a30 *vignettes/markedWriteUpBib.bib
