61cd2791a2f7845c526be2880dcf8f1c *DESCRIPTION
61888008bfac5c41c79b3e32683aef0d *NAMESPACE
81a6671c751e9dfa446a50fff8e00d1a *NEWS
c40627ce643f8effbd3d406ea86be714 *R/HMMLikelihood.r
3dc3c4de6a193070ad61c1cf56c7369e *R/HMMutilities.r
bd7ac79a615cbc643a50e6e66e8fe805 *R/InitialDistribution_functions.r
0db4f7d8e2b90865d0507c13d286039a *R/Observation_functions.r
5367a503666117757584ffaa95baa697 *R/RHMMLikelihood.r
41cc092ab5b063e7677f1b926a2b4de1 *R/Transition_functions.r
049cdcc7ec798f054790e02d1e8f39c9 *R/admbutils.R
994d3cd2c4d50ae5bf4663317c674edc *R/cjs.R
84fb083a2016c8d3ee5644f8c00f6656 *R/cjs.accumulate.R
e61221901104e611bfca9d0f5a34ff7d *R/cjs.hessian.r
fbfdc5dd5f2ffb800bda2e8771efe302 *R/cjs.initial.R
86a8b4370c3a6836f48d0f1bc301f025 *R/cjs.lnl.r
ff4d6ed395c0538acf2abeb756422d12 *R/cjs_tmb.R
b5604946a9cd638cba33b4b8519ad8d4 *R/coef.r
c5306d2eb28233343538e91a5562e530 *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
67085c04aa379548ab56c241f2b36925 *R/crm.R
452a60264f43ba51a3b709e285469f9f *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
d7c252bdc9b71d389f5ff330e60f4c66 *R/js.hessian.R
07c3ac3a3b50710b203d8578cb6a2aa7 *R/js.lnl.r
906055319bdb431bbdf6172a92b4bbcb *R/js.r
2f522616bf16de0f4724ad98cf8fcf17 *R/make.design.data.R
f4e8584d07deb16976937cc1990dd613 *R/marked-package.R
45692791473a90588b683e1444d48945 *R/merge.design.covariates.r
65c4b6e644b74d9400029ab641069e68 *R/mixed.model.r
c763de9c53b40addaa6bc82c04041c69 *R/mscjs.r
b2a8b8fee6623739b33fe53fc84de7db *R/mscjs_tmb.r
05b0184ba066123149b63615bbeaa8c3 *R/msld_tmb.r
940aaaa155071b54aa6b2cfd00b9a343 *R/mvmscjs.R
bde44e6caf15bbe54933693d07160c75 *R/mvmscjs_tmb.R
bce5da28af77c055f5cccd0dd0d8e02a *R/omega.r
a73760f8b2799323bb23646cdfba174b *R/predict.crm.r
65d50f500421bba45b0a3dfd530d0c21 *R/print.crm.r
eea8d776b9c0f205100ce9e8d367ab7a *R/probitCJS.R
dfc17f66096532a4fba1dc50483c4085 *R/proc.formula.r
a0c91821349600bf0bfcdc3e6c151660 *R/process.ch.R
65298f345a9b4222b384ef086b5f9aa0 *R/process.data.R
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b719aa4eb76539fff035e2fccb2e142d *R/set.fixed.R
6d7f14a8af4f8eb2f58a14606f16295a *R/set.initial.r
ae8c2583a7bf902e6f9ec3b4ecbd2d73 *R/set_mvms.r
74fe6f6851269b8e926dd4cec8a82432 *R/setup.model.R
8a83935306c1868ab6142c3c6cc786dc *R/setup.parameters.R
313367e3ee4b1ebe86d0087e6697b75c *R/simHMM.r
7a3b13a0d5fa10d0b3dd4797845b9612 *R/simplify.r
057b42d8ab556b00436baa74b9360e8e *R/smsld_tmb.r
04f8df5ac1eb7a3594bd5e8310419f1f *R/splitCH.R
74f1ee4cdcd104cf4c9868977e1a3a7a *R/summary.fcts.R
6be6618e9481274241ef95e1a327de14 *R/utility.R
71acdd849dbbd3e3e939cf17baa46724 *R/valid.parameters.R
3e82405b99424e3dd923830d62f37a71 *R/zzz.R
125de8109b9675c5ae9671e5ed87cc03 *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
ab9d88cd2bccee2139dcb68c4ba4ed7b *inst/CITATION
28f953c339e702ed56d381d81ef13fa4 *inst/README.txt
31377c5134e9d67de0d3677b75d0a3ef *inst/cjs.tpl
600468762b822b4fb55551430468087a *inst/cjs_reml.tpl
617999d2ebe6f951244e39e2f6f1463e *inst/cjs_tmb.cpp
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c6239015ce2a1de9e66725980b19a22a *inst/df1b2gh.cpp
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89d1100c51991e5371adea5a9744351a *inst/doc/markedVignette.R
c59994b684e68564b52f12809ab9772b *inst/doc/markedVignette.Rmd
979ab4d74a535555ce870a52560384b9 *inst/doc/markedVignette.html
031b17c7059d5f3cc3550c8e3bfcc6bc *inst/minfil.cpp
d329057b79be3fc2ff230d2b0c2ea475 *inst/models.txt
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117d6ee672943cd4a87f9662e4b8b72d *inst/multistate.tpl
0534153b7ac3558e7425096128a9b117 *inst/multistate_tmb.cpp
6c490dd7925a7976f321f27400094379 *inst/mvms.tpl
00cd344c86f266e9212867d370e49af1 *inst/mvms_tmb.cpp
9aea749278d2736fee8e3bd04671e18c *inst/parameters.txt
465a32cef51de95f01653cf624b577ad *inst/smsld_tmb.cpp
e2c6956b7e502038a3b256fcec5c37b6 *inst/xmodelm5.cpp
eb444891def8a436c152aebdaf9b9a1c *man/HMMLikelihood.Rd
3f17ceae095955535722839dd9b904d3 *man/Paradise_shelduck.Rd
22bbe772c22c88e90611434b9dd21628 *man/Phi.mean.Rd
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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
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0c0ed6d476320247e0996ba5abf86852 *man/compute_matrices.Rd
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c878c69307d77e69881ebec0185e3185 *man/create.dm.Rd
fc908b010817d88bc6e3d4321d3a74d1 *man/create.dmdf.Rd
df0a749a13f86c9e34f6a9ca24e80190 *man/create.fixed.matrix.Rd
75f3f8733a739f5cdfe8d3a24f246029 *man/create.links.Rd
5c3839db9c138aac3172ce435f638126 *man/crm.Rd
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eafab9e446c8e5001aeb8b22b5b4bd67 *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
486b522a943d1fafe66d25311dbe2d0a *man/mscjs_tmb.Rd
d22976b93641a83821c0a387dfe6d874 *man/msld_tmb.Rd
29aca03f1b8fa805be06633d382e08cb *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
ceb0a022e36047256259ffda1f644653 *man/predict.crm.Rd
d78062494f1ed61d981a95ee40e976ef *man/print.crm.Rd
a7eb50705f58513029e27ce76fdcdb4d *man/print.crmlist.Rd
b4ffa7c7f31c139784c500184ad4f11a *man/probitCJS.Rd
516c7a3380675012dba9de61546df893 *man/proc.form.Rd
3f57e6765544930c0bf6cd95962ea3c2 *man/process.ch.Rd
fce7124213de5e42fc2659c01d9bd8b8 *man/process.data.Rd
75c8bafb55415b5b20f2296be729c16f *man/resight.matrix.Rd
c58c3800f7581bb8ae3ba8f03b9990c1 *man/sealions.Rd
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e496412fa4851e27f18af9b2d6df54c8 *man/set.initial.Rd
3456c38e28318aa21d0afe35fc0ab235 *man/set_mvms.Rd
41b6190494e4269f96ac2e044f628401 *man/set_scale.Rd
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6ded919df2841ec7fbcae8ad321b6046 *man/setup.parameters.Rd
d4d8fb90908242571c291a487917fb05 *man/setup_admb.Rd
f970565e244f6f8623596e1568fc2282 *man/setup_tmb.Rd
389bc1566196aeaf80951642f1a15787 *man/simHMM.Rd
688da2a61c0f18426a842d5982ddae23 *man/skagit.Rd
9eb83e31a31c9dcd768ef81162770dc7 *man/smsld_tmb.Rd
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f95e0d2d679c5200bf0d2c523fe928cb *man/tagloss.Rd
eee3b66edafbdb4fd1483938fe8a1fd6 *man/valid.parameters.Rd
b3f86c20b81b51f5162874977d38784d *src/Makevars
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2e80757fbe08940fe169c82732e3fce2 *src/bayesCR.cpp
8cdb454e2d66b96f9f1a499f198abcbb *src/cjs.f
50f2344e37c1b0cd1caa1cfe2f5666bd *src/cjs1tldmat.f
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c59994b684e68564b52f12809ab9772b *vignettes/markedVignette.Rmd
ed9f292cb13eeefa91e076c7e2386c9b *vignettes/markedWriteUpBib.bib
