bac610588b4b4db997ca7aad6ecdb9de *DESCRIPTION
5e04912d3b9b15ee8a7d9b058e3aba20 *NAMESPACE
b91c4216522c141e29cb6180cf14d5dc *NEWS
7199d4e6a637ba1f8ad276f5a51925ad *R/HMMLikelihood.r
f487318157b812669e6ba63c2a9a0981 *R/InitialDistribution_functions.r
3734921d91707603cc125aec730b0219 *R/Observation_functions.r
66925cf470112844aed3ad83badf1ccd *R/Transition_functions.r
fae766d5c1e061769c5c26e2ae6066da *R/cjs.R
1ebc745ccb41115db41fdf632627468d *R/cjs.accumulate.R
224ff44eb94325bfb951235f0c1e4f90 *R/cjs.hessian.r
139cfd49c611eb82d979b3e26bbf9cd5 *R/cjs.initial.R
06d4426059914aa8a3a44af27b590b35 *R/cjs.lnl.r
20565e7c9d9eed84b17f5f35b161099c *R/compute.real.R
37e8bb982ea59045f84958edb798f47e *R/compute_matrices.r
fbba25aa21041cb01ffbe69fe0afab7a *R/convert.link.to.real.r
f4a9f45abf5e575bce4333e0d2cfd196 *R/create.dm.R
fa856cbe6edca84c16031d740abdb1b3 *R/create.dmdf.R
7ff0b2f71c22523cdda71d01b79d663b *R/create.links.r
58e6b7b45517f106df2006907c527ec9 *R/crm.R
65aa2966c346aee4ce97882982701a4f *R/crm.wrapper.R
edc62ba4f9ee716ba24b02971b9c8af1 *R/deriv.inverse.link.R
1bbdcdf2d4afd936df0cfd1aa8fb57d3 *R/extract.fcts.r
258befcf07bbee8575d6a6be8fb3865d *R/fix.parameters.r
1ef637e8534cb63b5cf7b6464a4eb53e *R/hmmDemo.r
360d432d3310271e795a738d233ff5cb *R/inverse.link.R
8690ad8303c447739e3717474508508c *R/js.accumulate.R
fdae5badf36ef937f6c523eb009425e1 *R/js.hessian.R
07c3ac3a3b50710b203d8578cb6a2aa7 *R/js.lnl.r
9021889bdbbb84539e5d147943b9e8fa *R/js.r
1b86e63617f0fb5380158cc5b550cecc *R/make.design.data.R
24908121824ed6790e9a7d72b9ddc3f5 *R/marked-package.R
45692791473a90588b683e1444d48945 *R/merge.design.covariates.r
ac0b413b63e1e0ee3d1fc3cb39a05a24 *R/mixed.model.r
132d281816e422da1b24bc9c7fc7e1dc *R/mscjs.r
5cada0af1f9b6b090eaace26568a756f *R/omega.r
168ef50b18d3e6f3411ca3290096c5c3 *R/predict.crm.r
3d7eb13b3372b6cdf7420c3f01b95183 *R/print.crm.r
715f5a844458eaf7e930a1bd82c4c820 *R/probitCJS.R
1321893167c466c9a3cace93a5c73bb6 *R/proc.formula.r
29b591966cccf77d750ad191e7a776fe *R/process.ch.R
fc45aef44338b8104276249c65596b17 *R/process.data.R
d43d8431484f467ad339038ec8c0cfae *R/scale.r
0f508aa4a6eb02134a52e0db8a0e50e1 *R/set.fixed.R
1fa0691f82dfef94bb8bd0f2c3ac124b *R/set.initial.r
8577532ed8a1cce09ed54df9e7ee9c3f *R/set_mvms.r
0a4c235c01c1504986c8905b294e6d30 *R/setup.model.R
0c95dfae60c3c11c03085af8cb8b1bda *R/setup.parameters.R
2e493c5a2f13aa1d3dc973f25e4fbcba *R/simHMM.r
8770267efd153aede8a51712130386d7 *R/splitCH.R
74f1ee4cdcd104cf4c9868977e1a3a7a *R/summary.fcts.R
6be6618e9481274241ef95e1a327de14 *R/utility.R
71acdd849dbbd3e3e939cf17baa46724 *R/valid.parameters.R
a6b222025c12be0cd245f6dae2d38a08 *R/zzz.R
9f5695c4c439524e5d5b5f96332c2458 *build/vignette.rds
86fa75dacd73a1e0c85a547b19b08f0c *data/dipper.rda
22ae24131afb70bf87d86e44d239a737 *data/tagloss.rda
fa6cad0f5950e6d8e7fa214c41609d6a *demo/00Index
3096feb9785fd012fec79c423cfa9320 *demo/tests.r
28f953c339e702ed56d381d81ef13fa4 *inst/README.txt
603e54756f4aadda75a3b8c06b397c63 *inst/cjs.tpl
6517bef5fe2676548ea0d71425a83881 *inst/cjs_reml.tpl
3136cc5c22e169723bc7d6aed72f2837 *inst/cjsre.tpl
c6239015ce2a1de9e66725980b19a22a *inst/df1b2gh.cpp
1143c5d073506731d0e8598ee010157d *inst/df1b2ghmult.cpp
a3657cf8a811b82b17361ad53ab6326c *inst/doc/markedVignette.R
b50610c8b9911841cf8d27bb7a7eb035 *inst/doc/markedVignette.Rnw
2e232e3f57d4726a3e5ebfbe1d879ccf *inst/doc/markedVignette.pdf
031b17c7059d5f3cc3550c8e3bfcc6bc *inst/minfil.cpp
7931474cce192deeba7c4cafbd0b21ac *inst/models.txt
0a2ad2967d0b45460051a28ceae22986 *inst/multistate.tpl
6a0f40bf45a96160c0762cadc3756075 *inst/parameters.txt
e2c6956b7e502038a3b256fcec5c37b6 *inst/xmodelm5.cpp
d75ddf38009c0438507a8c451f90ca3b *man/HMMLikelihood.Rd
7d86297139584474e40c3d2133e9c576 *man/Phi.mean.Rd
553d3015bdde1bc9a780b1ff58938186 *man/R_HMMLikelihood.Rd
50fbda752f2db431afa12e2fd31c0846 *man/cjs.Rd
6e71c8f092a789675fbc0a14dcf69e6a *man/cjs.accumulate.Rd
97e90a006a920bc86610f66bb7c72095 *man/cjs.hessian.Rd
64de64486ca2c9514a10dbe412ce6be7 *man/cjs.initial.Rd
efdbb3b6ca5e5af47f749c46a2c4e2ca *man/cjs.lnl.Rd
72cd531ae8440556152ae4f434e5f484 *man/cjs_delta.Rd
de333cda8602bbfd56c21a3139408e7a *man/cjs_dmat.Rd
55f07b995a30cc59fe0344362c08b81f *man/cjs_gamma.Rd
11591d87901201cc017cf3dbe5777e89 *man/compute.real.Rd
da9a1c267aae205886c05415e5bb3a0b *man/compute_matrices.Rd
a6788487fedc7af91272c64d68f539c8 *man/convert.link.to.real.Rd
9b9305eec61f542cdaadb46e5012aec8 *man/create.dm.Rd
9ba7d9943ba06c25ebc7458671eb4fb9 *man/create.dmdf.Rd
83b7ed5232964f9063ab2e97619f9805 *man/create.fixed.matrix.Rd
28e07ef6a3e4acf9711f46b4c63229af *man/create.links.Rd
a70aa0b4c482b4866213a101a47fe379 *man/crm.Rd
03a40b1e1918f0a8138fda979bc05afa *man/crm.wrapper.Rd
91e4b1404717e211dd8741cbcf41a231 *man/deriv_inverse.link.Rd
0683e9fa2c3ba2027532ebbe1269a36a *man/dipper.Rd
65b1d13deb3a92b03c2727b5a1b9ab5b *man/fix.parameters.Rd
fa86407ab786cef06cb004cc509720fc *man/function.wrapper.Rd
169e50034f73e5017043200926373775 *man/hmmDemo.Rd
87e14d56323708f63308b54e16143681 *man/inverse.link.Rd
583ffc9eafa6aa2d70304d8c77098339 *man/js.Rd
fb831d74da9029dd89d62b4ff67b75f6 *man/js.accumulate.Rd
0437c9691f498d2079600a5cc3b82b3c *man/js.hessian.Rd
1fd04ec2c969c18e345d8cee5fa042ec *man/js.lnl.Rd
6ab169d7c20aa0ec65b9f9106cda5249 *man/make.design.data.Rd
d2ba8494d02a5869d54b4a2c8b054583 *man/merge_design.covariates.Rd
81ccbad808dd5ca6e0fee24769c315fd *man/mixed.model.admb.Rd
d7149c4a9ff8277f1bf63c574f748745 *man/mscjs.Rd
75c6785e044519a9d5854f95c87ce21b *man/omega.Rd
c1a23513be646a348d9236599b7c02d2 *man/predict.crm.Rd
0bc0f6138b35f390098d30b0939cccd4 *man/print.crm.Rd
ea1e5e131fa8ddf91dd6c3fb70a164b9 *man/probitCJS.Rd
b282817255ca3493f9df30fbfc229ea5 *man/proc.form.Rd
7158d52a64b6e7b74528b87c1eacab33 *man/process.ch.Rd
e4a97040ef2c935360da8936bcfd2f88 *man/process.data.Rd
b4568551867a8caa780b76c33b0f5d3f *man/resight.matrix.Rd
1f9377c8b987fd942591effa1d900b0b *man/set.fixed.Rd
66ffa345e10f4c0a123c582c9074a873 *man/set.initial.Rd
5767f70c5f0de46cd679977cece16044 *man/set.scale.Rd
95d12082007fa2efb7cc51d7cff7f35c *man/set_mvms.Rd
f556e87abc17cbe78da5ded9aa3340d0 *man/setup.model.Rd
de866e2099f37cc23cf9ad00db295867 *man/setup.parameters.Rd
1a8eaec1ce0ced4314bd86f36d046b81 *man/simHMM.Rd
471b5ee7d0d3b1f7638402e893de38e0 *man/splitCH.Rd
05c0d3a5cc061270dcdd50ba4a7f5873 *man/tagloss.Rd
ac281df96cbc0eb0d125d3ba09169e90 *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
25706f6995832d0c534c7e37b940f834 *src/hmm_like.f
d00adbdbce4e07a51403c4f994c35f9c *src/ms2gamma.f
955315de2dce7a9011450b46daef69d4 *src/msdmat.f
779a460e635a31002af816f6a0334192 *src/msgamma.f
53e9e7838edfe4dd24cb1b6b325b73bb *src/ums2dmat.f
96f6f1ff894007c56323dc183ce288fc *src/umsdmat.f
b50610c8b9911841cf8d27bb7a7eb035 *vignettes/markedVignette.Rnw
f3ac5cfe03c5f4898e80280ddbfd9a30 *vignettes/markedWriteUpBib.bib
