a91accae7073e5efbebcd920afa54efc *DESCRIPTION
f59186fece2786340fea2e5c5cb0f4e0 *NAMESPACE
6ba865ede61b5f7bef08147dc5b92486 *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
ce1c7af4d811201b343e44d870c64e73 *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
cdbc32905edf1593acf2b11b32cf5753 *R/create.dm.R
6acdb916f35ceb1c65b7979c32380311 *R/create.dmdf.R
7ff0b2f71c22523cdda71d01b79d663b *R/create.links.r
c4cd234607c155f9c4093810ff478c8e *R/crm.R
68b5a1157f295d040a2412f60de739d1 *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
ac0b413b63e1e0ee3d1fc3cb39a05a24 *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
1321893167c466c9a3cace93a5c73bb6 *R/proc.formula.r
a0c91821349600bf0bfcdc3e6c151660 *R/process.ch.R
c70e7ee411243454097f509fd1125390 *R/process.data.R
d43d8431484f467ad339038ec8c0cfae *R/scale.r
0f508aa4a6eb02134a52e0db8a0e50e1 *R/set.fixed.R
a0abe5bba31f2e819bdc953004cfb964 *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
dfa01e5b6b976ce03a19f4a8f4c36f93 *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
7fc90d6ad1f6a27726f6529e57d10d75 *inst/cjs.tpl
600468762b822b4fb55551430468087a *inst/cjs_reml.tpl
778242d080cc720c761d554b0d93b670 *inst/cjsre.tpl
c6239015ce2a1de9e66725980b19a22a *inst/df1b2gh.cpp
1143c5d073506731d0e8598ee010157d *inst/df1b2ghmult.cpp
22934a54ca49db1e1df23a113d1968c9 *inst/doc/markedVignette.R
b50610c8b9911841cf8d27bb7a7eb035 *inst/doc/markedVignette.Rnw
0202720771ce7c7cb676a4ecbdd2df1a *inst/doc/markedVignette.pdf
031b17c7059d5f3cc3550c8e3bfcc6bc *inst/minfil.cpp
a6cb96044224a0acf49b636aacbb82d5 *inst/models.txt
20506d81280de462667067f3fdc47177 *inst/multistate.tpl
de3811d4f2d104416fde367b683a79ad *inst/parameters.txt
e2c6956b7e502038a3b256fcec5c37b6 *inst/xmodelm5.cpp
0d731bf8558d07de47d288d98f9397ac *man/HMMLikelihood.Rd
3edd3987b82aa3f860019a09ff22e709 *man/Phi.mean.Rd
a64ea91c16c56f9156d117eecc007739 *man/R_HMMLikelihood.Rd
99611a46ac6f0dd2e2938b96be72a2e5 *man/backward_prob.Rd
e809d4e4cb2c6a63e42774b419490184 *man/cjs.Rd
e06e632fcabf939920db4ee217e90e59 *man/cjs.accumulate.Rd
12f480daf8ec259239e3f9f3919f2593 *man/cjs.hessian.Rd
8f199c16710912d987c4d87740526139 *man/cjs.initial.Rd
88025c4f5df6be08768532e437033dbb *man/cjs.lnl.Rd
0ccc5f93f5d1667211c3fb3ea786de75 *man/cjs_delta.Rd
d631cea7711c94800abfe79f2a72b9a4 *man/cjs_gamma.Rd
9fc965cd8b79d4e3dc8d48ade6667093 *man/coef.crm.Rd
46dfca2e66c18196b6096dc694975b02 *man/compute.real.Rd
d7e57422339b909a7ae5d7bd628f5798 *man/compute_matrices.Rd
0ce0289f135cfad544d1bab72da7d1bc *man/convert.link.to.real.Rd
68c456557b9e508dc9e7afb981fb6937 *man/create.dm.Rd
8d13ea168e548babd1c48f401a877ab5 *man/create.dmdf.Rd
2c2d1e723440e8ffae0b7e7519db77da *man/create.fixed.matrix.Rd
bcf678c74b7bea71e757d94aa52f0fcc *man/create.links.Rd
5486ed3052bc176be4ae685860d55311 *man/crm.Rd
b1b1b92d25f8ad56d5bac908a2639900 *man/crm.wrapper.Rd
3fc7b830c0c24483faff9bdf4457c40b *man/deriv_inverse.link.Rd
cad5976bc9399a64fcfbda9c61f8ebfc *man/dipper.Rd
63db616db17903a49d80a46911285bbc *man/fix.parameters.Rd
e943dd88704913fe2ca66c63478fa9df *man/function.wrapper.Rd
5fa9d7a119fd4c0688b501c796758eb9 *man/global_decode.Rd
0786665239fb642ccdba5d2f4f6627ed *man/hmmDemo.Rd
bb6933d4a60baf6030c21dad688ffc69 *man/inverse.link.Rd
be6c6655e6aab67be2d436838f32e407 *man/js.Rd
d9bcfccf0c32e6240bb13b099695f410 *man/js.accumulate.Rd
833c9fa28421bb9f3b14c4a1a060c5a7 *man/js.hessian.Rd
479263170ede2e829da2d2f171d539aa *man/js.lnl.Rd
7c0d26bfa72708f55e2d99bf977100c0 *man/local_decode.Rd
e9bc89116be63bd991dc226337170264 *man/make.design.data.Rd
defca986908494bd2dfb89da3fb92020 *man/merge_design.covariates.Rd
d882b2d64d3c56bbba54a711f9473b51 *man/mixed.model.admb.Rd
59f9420be957fd5f7ca13934e24c4361 *man/mscjs.Rd
ae4d70c0ec276d963f61c2995a61e060 *man/mstrata.Rd
ad0eec5bdb9f4c5e3f27d2c14ce622b7 *man/mvms_design_data.Rd
82d9846f2c7c9142f0f5dfe9c301308a *man/mvms_dmat.Rd
a4fe25a9bb94172b6e3b4d8e3ea07877 *man/omega.Rd
a4cff1cee8c59d4052b8e1a61c6bd803 *man/predict.crm.Rd
af1763c33928d458a09368ceee6ad92f *man/print.crm.Rd
d1905bd5ff509e83eab1aace8e156685 *man/print.crmlist.Rd
5e12ffae38f73c29e430e8849c136975 *man/probitCJS.Rd
a05ef55b804006b7ed4c6c30b0ffd851 *man/proc.form.Rd
b1b6d2afa10d7eed9973bc2fd6533336 *man/process.ch.Rd
fd7f2d5234ad1aaf31b8249e2f7ca0b0 *man/process.data.Rd
638f6385905b45691b966c6fbf2edd4b *man/resight.matrix.Rd
0f72882ffad3f56071cf30443501ca0c *man/sealions.Rd
7d8df6d6b5071acb720a00f57ddb0927 *man/set.fixed.Rd
969b3e24102dc77dea62c0c6f6963f3f *man/set.initial.Rd
9f8650bb98984910d785089c05292882 *man/set.scale.Rd
47178823f71a72d8c05c8a18f148ca45 *man/set_mvms.Rd
24fba4012c29b333702995a6a134443d *man/setup.model.Rd
8bf5244e1a224e12e9a72ee87afc0300 *man/setup.parameters.Rd
5beddaa26d54cde9f7e22c53dc89d2ac *man/simHMM.Rd
58b0231a0c2d2d1dcb09cccf8d3a17dc *man/splitCH.Rd
7fae0d307660061e6ef1ae56c36d0ba9 *man/tagloss.Rd
28ab2a7adced1bccafe65322fe6a74e4 *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
b50610c8b9911841cf8d27bb7a7eb035 *vignettes/markedVignette.Rnw
f3ac5cfe03c5f4898e80280ddbfd9a30 *vignettes/markedWriteUpBib.bib
