48fbc9d4330caf8c724ec89d191b13af *DESCRIPTION
5ae5ac1a50f869a4c01b186c2df828c4 *NAMESPACE
0fc151fb71c5c6252f7716fac433d1aa *NEWS
c40627ce643f8effbd3d406ea86be714 *R/HMMLikelihood.r
67ec99ab531dd2b160a6c003b5c74185 *R/HMMutilities.r
bd7ac79a615cbc643a50e6e66e8fe805 *R/InitialDistribution_functions.r
0db4f7d8e2b90865d0507c13d286039a *R/Observation_functions.r
5367a503666117757584ffaa95baa697 *R/RHMMLikelihood.r
41cc092ab5b063e7677f1b926a2b4de1 *R/Transition_functions.r
9b5e7857757e55394e057147825fa380 *R/admbutils.R
f29d4c90f4ca45c8c022b211d448da9c *R/cjs.R
84fb083a2016c8d3ee5644f8c00f6656 *R/cjs.accumulate.R
c0d5090884c584c03a3cfc6625688363 *R/cjs.hessian.r
e7b7b528611356cd28b8600146e37deb *R/cjs.initial.R
86a8b4370c3a6836f48d0f1bc301f025 *R/cjs.lnl.r
52f094af4bb134aa93d0ab21d7d1200e *R/cjs_tmb.R
b5604946a9cd638cba33b4b8519ad8d4 *R/coef.r
cd5cb3c51086d4352f6240d31ef9f15f *R/compute.real.R
b3b9c942b63b057866d91eea7b3ac940 *R/convert.link.to.real.r
99459b2ec132bfbeec503dff55b32051 *R/create.dm.R
5c8d68bc091ac13641dc5efa02ef96a5 *R/create.dmdf.R
7ff0b2f71c22523cdda71d01b79d663b *R/create.links.r
a65a0db79536ea144db84237ea13dd7f *R/crm.R
9190d82deb26db1cfbeca8e0b066465a *R/crm.wrapper.R
a8b3da7e263d59b1cc044ba494d0d2f1 *R/deriv.inverse.link.R
1bbdcdf2d4afd936df0cfd1aa8fb57d3 *R/extract.fcts.r
258befcf07bbee8575d6a6be8fb3865d *R/fix.parameters.r
a5a9c1c49706f05eb8d8809f904126ae *R/hmmDemo.r
62cb5a01ce6e79bed60118d0b7b82da7 *R/hsmm2hmm.r
2d6c087095bf663adb0965757be37698 *R/inverse.link.R
8690ad8303c447739e3717474508508c *R/js.accumulate.R
bf8fd9cd222bd34576397029c84bb052 *R/js.hessian.R
07c3ac3a3b50710b203d8578cb6a2aa7 *R/js.lnl.r
5b22116b9592aa10ff41cc5b864ac1b4 *R/js.r
2f522616bf16de0f4724ad98cf8fcf17 *R/make.design.data.R
4f809e7bbcf5db7c877460a954ccd768 *R/marked-package.R
45692791473a90588b683e1444d48945 *R/merge.design.covariates.r
65c4b6e644b74d9400029ab641069e68 *R/mixed.model.r
b639def49629654d0b6c1b80882f2c46 *R/mscjs.r
a2dd563e6c6d2dac9ec9762dc9fcebf5 *R/mscjs_tmb.r
127d710b1eb22f28b7b35d5cf778cb02 *R/msld_tmb.r
6ea394408af5cf5bc2c4c0d919dbea19 *R/mvmscjs.R
72b03c0bce6997adc4daed5ede5f6e20 *R/mvmscjs_tmb.R
bce5da28af77c055f5cccd0dd0d8e02a *R/omega.r
49db41b6d07a214cec04eacf1fb8931a *R/predict.crm.r
65d50f500421bba45b0a3dfd530d0c21 *R/print.crm.r
41149150a001b527be2872b5522db934 *R/probitCJS.R
dfc17f66096532a4fba1dc50483c4085 *R/proc.formula.r
a0c91821349600bf0bfcdc3e6c151660 *R/process.ch.R
a7ce658a367f27709a1dacad6254ab2e *R/process.data.R
8cba0413d131c354acd8f909baa13a93 *R/scale.r
b719aa4eb76539fff035e2fccb2e142d *R/set.fixed.R
6d7f14a8af4f8eb2f58a14606f16295a *R/set.initial.r
ae8c2583a7bf902e6f9ec3b4ecbd2d73 *R/set_mvms.r
74fe6f6851269b8e926dd4cec8a82432 *R/setup.model.R
f001c922fbdb56c6fb88a87e8cfb6bb6 *R/setup.parameters.R
313367e3ee4b1ebe86d0087e6697b75c *R/simHMM.r
1e15422f079359a504913890c2d8c2d8 *R/simplify.r
04f8df5ac1eb7a3594bd5e8310419f1f *R/splitCH.R
74f1ee4cdcd104cf4c9868977e1a3a7a *R/summary.fcts.R
6be6618e9481274241ef95e1a327de14 *R/utility.R
71acdd849dbbd3e3e939cf17baa46724 *R/valid.parameters.R
561641eebf744b6804c4565e8d8b1ee7 *R/zzz.R
f8fe39806190657d3784ba44dec42896 *build/vignette.rds
af353b1c6010d8919bc357c7187dad15 *data/Paradise_shelduck.rda
86fa75dacd73a1e0c85a547b19b08f0c *data/dipper.rda
4b9eee976b66f48fef85116c4ed6cc6f *data/mstrata.rda
58f69429b47c1db1cc263ff301cc1bd1 *data/sealions.rda
ff63c1e0027064173c0931b40f15ae50 *data/skagit.rda
22ae24131afb70bf87d86e44d239a737 *data/tagloss.rda
0ebf6fec500f52bc34a1f7cc9c683a16 *demo/00Index
3096feb9785fd012fec79c423cfa9320 *demo/tests.r
d629655019983d443e29a3f65ea71ed1 *inst/CITATION
28f953c339e702ed56d381d81ef13fa4 *inst/README.txt
31377c5134e9d67de0d3677b75d0a3ef *inst/cjs.tpl
600468762b822b4fb55551430468087a *inst/cjs_reml.tpl
617999d2ebe6f951244e39e2f6f1463e *inst/cjs_tmb.cpp
778242d080cc720c761d554b0d93b670 *inst/cjsre.tpl
477a36fb8c0720afe416fb69a2e88fa6 *inst/cjsre_tmb.cpp
da6f63bdc35bc32d6f280a0f96a408c3 *inst/df1b2gh.cpp
1102310b4775f7c9331f6b3dd984635b *inst/df1b2ghmult.cpp
74ba2e5cec4b7f753b928edf60f185c7 *inst/doc/markedVignette.R
c59994b684e68564b52f12809ab9772b *inst/doc/markedVignette.Rmd
b6b83d790e79383f9a55bddfe98457b8 *inst/doc/markedVignette.html
b07999fa1b264dbf002a7f72176f5d40 *inst/minfil.cpp
2a4b252fc414d8385a2f74668e43aee8 *inst/models.txt
d710e00f4d7c16b5e61d58255b977c00 *inst/msld_tmb.cpp
117d6ee672943cd4a87f9662e4b8b72d *inst/multistate.tpl
b9ad675edc4fded2c43d26687d72a6e2 *inst/multistate_tmb.cpp
6c490dd7925a7976f321f27400094379 *inst/mvms.tpl
f904ac3ae11829e27487b6f0cd98807b *inst/mvms_tmb.cpp
970cea52c1539c86503dee4383e866e3 *inst/parameters.txt
d748980ac90f84bd03c5843e0c0896b8 *inst/xmodelm5.cpp
eb444891def8a436c152aebdaf9b9a1c *man/HMMLikelihood.Rd
a1b89b9c4bf015bbcab2582941830482 *man/Paradise_shelduck.Rd
22bbe772c22c88e90611434b9dd21628 *man/Phi.mean.Rd
93dcafdfb87a5a4bfb1cb76017c416e5 *man/R_HMMLikelihood.Rd
0b4e6cf05203b0c480ae7d7b992d654d *man/backward_prob.Rd
2fa8acc8d572601c6acc3ee16939821c *man/cjs.accumulate.Rd
8c222694604d2a5af7ac3e533b6d699e *man/cjs.hessian.Rd
c523c9f4675e793b68800a6eb6651c5d *man/cjs.initial.Rd
1d2908a0fd57d9362bf442044420c175 *man/cjs.lnl.Rd
af2baada0353d01c595fa911d4884048 *man/cjs_admb.Rd
d2991699da873463af8791db24b2b52c *man/cjs_delta.Rd
df969db06a1bc90dbdf35ecf8bd3cc4f *man/cjs_gamma.Rd
7aa603ef709354b179298cfa3aa0b04b *man/cjs_tmb.Rd
f26407aa2e1a4dc3660d536ae9711f48 *man/coef.crm.Rd
0c0ed6d476320247e0996ba5abf86852 *man/compute_matrices.Rd
ef52a242e3e8f2925019c30bb4580cca *man/compute_real.Rd
dd9bc1a652744ff1f0f4018734c40ae1 *man/convert.link.to.real.Rd
c878c69307d77e69881ebec0185e3185 *man/create.dm.Rd
fc908b010817d88bc6e3d4321d3a74d1 *man/create.dmdf.Rd
79c762154844e2c5b107919c5ea561d0 *man/create.fixed.matrix.Rd
75f3f8733a739f5cdfe8d3a24f246029 *man/create.links.Rd
b1b213aad29aff5dcb0716f6871cb325 *man/crm.Rd
07833929387285aa1b20bda73ed3efb7 *man/crm.wrapper.Rd
f48b2a7dfcfccb880302ae3f40871909 *man/deriv_inverse.link.Rd
6aae8e9e77bf554eec6d616e7e1ec302 *man/dipper.Rd
c310326d87b3bb275038331cb14db006 *man/dmat_hsmm2hmm.Rd
b850e9533ae60693e9fd26e0f478a8ee *man/fix.parameters.Rd
c49a4b005d3022df0319a845ec10efc0 *man/function.wrapper.Rd
14f7d631ec730f652ceb21afc76fc43c *man/global_decode.Rd
c5ff83bf41775f20904b19f6598fa2fc *man/hmmDemo.Rd
3a8a133c97e9dfa72ce64f635908adee *man/hsmm2hmm.Rd
d4868308d556e667ba9de3a1b410ede3 *man/initiate_pi.Rd
e96dfaa4a5964992031fd3550f6e31bf *man/inverse.link.Rd
e4871331ee0209abe3c3a5c92f9a3f77 *man/js.Rd
d6614872baf0302a8f9293bb96975587 *man/js.accumulate.Rd
62324dfa1b97a237a39e8e0846174f41 *man/js.hessian.Rd
0026d5ce0ad73741ba9213442ee5bae5 *man/js.lnl.Rd
b9bfec68171696565f5342ecadedd74e *man/local_decode.Rd
51364339d81ae7e1981af2eb146c1f89 *man/make.design.data.Rd
b59b00bd30ed7c3d247fc139a1542509 *man/merge_design.covariates.Rd
11ebdda5256faac6058b60e076bf10d5 *man/mixed.model.admb.Rd
b1b907a319718fb12bfdc5843d9bef0b *man/mscjs.Rd
bb60787beb0731b23a227c8829cae36b *man/mscjs_tmb.Rd
cbd929394d9c049597b4d3f807350ff4 *man/msld_tmb.Rd
14361954b60ed218fe43700315673674 *man/mstrata.Rd
4256bc2dc5c0e0795a93bb1549793cfc *man/mvms_design_data.Rd
735e56f2df86aa9c60a4af23a9c62631 *man/mvms_dmat.Rd
0d3259768b324dda9a1675b22076b215 *man/mvmscjs.Rd
e1809fc8c7ad6eeb1a82aa2c06caf3c7 *man/mvmscjs_tmb.Rd
035de714e8f324cd04d8beb37ddea5f7 *man/omega.Rd
28244791e2bb6ff97749f99d318d2698 *man/predict.crm.Rd
d78062494f1ed61d981a95ee40e976ef *man/print.crm.Rd
36b83895b668e5a544a3ed727c3d81fa *man/print.crmlist.Rd
341a5741504fbfd7334f41478cda9696 *man/probitCJS.Rd
516c7a3380675012dba9de61546df893 *man/proc.form.Rd
3f57e6765544930c0bf6cd95962ea3c2 *man/process.ch.Rd
f2c85aa20a96e9568c096912a17a949c *man/process.data.Rd
75c8bafb55415b5b20f2296be729c16f *man/resight.matrix.Rd
767efa00301b860e0540b328b7d7b72e *man/sealions.Rd
effcb1a63734d4afa6996a7113488149 *man/set.fixed.Rd
e496412fa4851e27f18af9b2d6df54c8 *man/set.initial.Rd
e9f52ff06a039939a6bbe56a8a5ea4c9 *man/set.scale.Rd
3456c38e28318aa21d0afe35fc0ab235 *man/set_mvms.Rd
f3c882bb7cc4e4b473831805b16cc77f *man/setup.model.Rd
6ded919df2841ec7fbcae8ad321b6046 *man/setup.parameters.Rd
d4d8fb90908242571c291a487917fb05 *man/setup_admb.Rd
f970565e244f6f8623596e1568fc2282 *man/setup_tmb.Rd
389bc1566196aeaf80951642f1a15787 *man/simHMM.Rd
dd1a1b896b9218409c9d04abb0cb574d *man/skagit.Rd
d0acf37d5d8eed64a7426d82a29f2808 *man/splitCH.Rd
8123625acf4278d5823a8d23917d3592 *man/tagloss.Rd
eee3b66edafbdb4fd1483938fe8a1fd6 *man/valid.parameters.Rd
b3f86c20b81b51f5162874977d38784d *src/Makevars
73505498722ad4b07b0ddb3067e92523 *src/Makevars.win
2e80757fbe08940fe169c82732e3fce2 *src/bayesCR.cpp
8cdb454e2d66b96f9f1a499f198abcbb *src/cjs.f
50f2344e37c1b0cd1caa1cfe2f5666bd *src/cjs1tldmat.f
f0bbb89e2318f1127c51766f10d84823 *src/cjs1tlgam.f
129f1d5f27cc28d2cd4146908331fa00 *src/cjs2tldmat.f
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9dac60a641d807ef1185223d6d7685f3 *src/cjsdmat.f
38889ef693e15bd7124b0627b78039c1 *src/cjsgamma.f
6b0785fb21dd90bf175322ede4589358 *src/hmm_like.f
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a89d517937579a12bab9248c7c4fd00d *src/ms2gamma.f
6a0a7ad01302cdf9fbd2ba359f354f69 *src/msdmat.f
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95c7119de706128749ad4511e2fc0f4c *src/ums2dmat.f
0ff10343c2c771ca31a53006df031999 *src/umsdmat.f
c59994b684e68564b52f12809ab9772b *vignettes/markedVignette.Rmd
b057760c3fce834016d9f3dd9b2acde5 *vignettes/markedWriteUpBib.bib
