a86f2211bcdabbbfa0a74ef5a1891085 *DESCRIPTION
88fad7473d88068e99ffc3162e0ea4dc *NAMESPACE
01e6a6738c1ef8ec78d9452b4390a67f *NEWS.md
b23936242821b69583991cedd5c19adb *R/Ancillary_Indicators.R
e7924c0158ea2334873bfc005506679d *R/Awatea2OM.R
c1accdf637e179c5230d69dca40dcf7b *R/CASAL2OM.R
5455334f646f0dd6bee2a540a4a3f483 *R/HCRs.R
58ade2859ff279fa0e5e3829e77b06fd *R/MMSE_Object.R
464e5799d8f358b1539e9902698a85f8 *R/MMSE_plots.R
0c92ec4dd72acd793e241fd7b266645e *R/MOM_functions.R
498642f8ef47a1498cf40d71becc9f5d *R/MOM_object.R
27a4112aba3c5d0b52f77d135aed55a3 *R/MOM_plots.R
bdb5dbd1a1003ee0b479b8f99c4ac0f1 *R/MSEtool-package.R
596b6ec84a4d74213fa66a629862b58d *R/Misc_fun.R
bc27028c6125ebb10f297bb58167ef5d *R/Movement_calcs.R
a20f4e0f1a4c8cd69e7a16bf599a1380 *R/SRA_scope.R
1e763f8e94d77a498ef01e78c08a2956 *R/SRA_scope_data.R
2e6537379f747d5a42b8dfd185cef083 *R/SS2Data.R
fe86e71e01b106711eabe1d7da0b5308 *R/SS2MOM.R
c3abc96de3c58a2422522fe721ca6e9c *R/SS2OM.R
03ba90471e0427a2f2ad55996841a9e8 *R/SSinternal.R
17ef365e5edea044036ad3913e9ec011 *R/Single_stock_multi_q_REDUNDANT.R
15f1d334d709c701dc4d45c08cff611a *R/VPA2OM.R
d1c1fa09fefd6ae77dde9f11bec094f4 *R/applyMMP.R
c38ad3a5b13fddeed5bdbb0fbdfd5e4f *R/assess_DD.R
5671ab27e71821751487d4ee52de2748 *R/assess_SCA.R
f367100e8bd194d8f600ff5cf05b5cb7 *R/assess_SCA2.R
c3c918888e76d558a741756f20d54c56 *R/assess_SCA_Pope.R
3664440a190d57532dd88c054502423c *R/assess_SP.R
17f2a0c42f5046fd8acdad4f2fa4f83f *R/assess_SSS.R
5b2aceea4060a24dfdf12a13ed432bc7 *R/assess_VPA.R
1d3399cdedb42ead63b8c66d26257bfc *R/assess_cDD.R
c31395624bbaaad72c0350f3d8c1f022 *R/define_S4_class_SRA.R
8edfb5d278f439b63089b09f27f1d5fe *R/define_S4_class_assess.R
2c6bc9b9eed54b9e9becec399aa8bbeb *R/define_S4_class_profile.R
b2189c847e600750b7994e39828e8c53 *R/define_S4_class_project.R
eee40291442fe4e15e78468b43ec9687 *R/define_S4_class_retro.R
4cf5f04e25b8b51226c821c08e0139c4 *R/define_S4_generic_SRA_scope.R
ee3614cbd52e110c5d45d116625e6f4e *R/diagnostic_AM.R
b1b9c76bb8c6820b7340a685e1a77179 *R/document_data.R
9c39cb427e193a3c129edff04af2143d *R/iSCAM2OM.R
fc398226e00e815b4efae713d306fdc4 *R/multiMSE.R
74364946f07d2e1ed89cb503d51f8f66 *R/multiMSE_internal.R
35e12140533c1e1266689bf904c37d5c *R/multi_q_estimation.R
8b5d4331b59e78a02cea94b6db789f71 *R/popdyn_MICE.R
33794646029f924696f02f8181818a8b *R/report_DD_TMB.R
a7b61998a9f7852c26663c6ce00f00bc *R/report_SCA.R
61268bf5d68aaf3dcb3cb96e2cb616e8 *R/report_SCA_Pope.R
a8fc7e50825bf8672eab34aefb3ee823 *R/report_SP.R
e73c770af4fcf68e95bc9534ac7e8000 *R/report_SSS.R
8bd72ddd7f34f768462b05d59c9935c6 *R/report_VPA.R
ec57b0956980581dcd84bd35756cdfe8 *R/report_auxiliary.R
9358067445c3cf535ee951196c09c1f1 *R/report_cDD.R
7c0b839874597440bfc4d289fb4f28fb *R/report_spict.R
5db3f1903c0d4a5368a540e9dec1e540 *R/retrospective_AM.R
f2debf0614b625d1b922519dfae2158a *R/rmd_report.R
bf8bd35076f3c59fd4d1bb9cb0a7d3d0 *R/z_MPs.R
98153683ffd922e7157934012f0588e9 *README.md
38c4271dee28a1de38d1536526731944 *build/vignette.rds
d73b0be62ff2974fc6413e0dbe628092 *data/Albacore_TwoFleet.rda
67c5a33601aa697a0241e71abd12bbe9 *data/swordfish.rda
fb3beda1963f182d517b486026302f9f *inst/doc/Delay_difference.R
2b46a7bd0ffa5af525135cb7539e9024 *inst/doc/Delay_difference.Rmd
96f4a2a01ecef7b748ebf1d2a0f4b580 *inst/doc/Delay_difference.html
859f3705550baf53e4cbd763c49b2757 *inst/doc/MSEtool.R
79b66ae558897739452d7439e89cf609 *inst/doc/MSEtool.Rmd
c4b9ebbf6d726a2116b5885ca62d9be8 *inst/doc/MSEtool.html
fb3beda1963f182d517b486026302f9f *inst/doc/SCA.R
674b0773e805934f3218d487cb22e0b8 *inst/doc/SCA.Rmd
5c7a83c978d0eeb28b065ee80a63065d *inst/doc/SCA.html
412bdf5b99c1ac25146101fd1ef85c39 *inst/doc/SRA_scope.R
1d4df4eb66b8c984518e5b0c4b4408df *inst/doc/SRA_scope.Rmd
bc84bd9068c3fc4dae640c58fe5f34c3 *inst/doc/SRA_scope.html
529a560696f735b16537c81d888ac645 *inst/doc/SRA_scope_eq.R
93d81e2868659c53f49a43452820d9e4 *inst/doc/SRA_scope_eq.Rmd
691625af954840f537c000688f480ab6 *inst/doc/SRA_scope_eq.html
af5a2c2949f926d9ccc3fb6b59ac7307 *inst/doc/SRA_scope_sel.R
158ca95db83dff97feb80ea415e2d8ab *inst/doc/SRA_scope_sel.Rmd
cacf89c5331c3e7491ef00c9b200e842 *inst/doc/SRA_scope_sel.html
fb3beda1963f182d517b486026302f9f *inst/doc/Surplus_production.R
d67a924d4ca5750faf7fe0dbd644e751 *inst/doc/Surplus_production.Rmd
736b4d6ca2a212fd838f6d7ada7cc01e *inst/doc/Surplus_production.html
fb3beda1963f182d517b486026302f9f *inst/doc/VPA.R
b7292ca13452cff2a692f671f193d223 *inst/doc/VPA.Rmd
faf6e04dcaf4467f488d258018cb3353 *inst/doc/VPA.html
fb02e1a0c7bd3a7a11ed489e53f84a05 *inst/doc/multiMSE.R
e598c7ba05d330463b08d19234989448 *inst/doc/multiMSE.Rmd
bff9310a61dccef1f09caeef6b7e5fe1 *inst/doc/multiMSE.html
4e93805508ae3db60a2b63688fccddfa *inst/include/DD.hpp
7800deb4f92ff36633449d017d838b72 *inst/include/SCA.hpp
a7b15775c3b386fff80a41e3331a455d *inst/include/SCA2.hpp
765ff9426042846ee6d33b924444778c *inst/include/SCA_Pope.hpp
d4d8b694d91bfc311bed16e905d8096f *inst/include/SP.hpp
b963cb82ecefd2d24c3f22abf3f9dfcb *inst/include/SRA_scope.hpp
468aca63980ab3f2a1edebbae6b008a6 *inst/include/VPA.hpp
9aba8a1014f252ceb96feef0f05ad73f *inst/include/cDD.hpp
cb63d5aea811e4c568303be49ba0f479 *inst/include/functions.hpp
772aa8c0fe6fe3ea0a92b86b1e83a34a *inst/include/grav.hpp
7064a2215907718bfd8ccd2677fd0010 *inst/include/grav_Pbyarea.hpp
ecae03cc6f7dddfdb81be5dfa311749d *inst/include/ns/ns_SCA.hpp
0089384371cb4d1117fc114c14847b23 *inst/include/ns/ns_SP.hpp
3560ee5e516ebd75e2bf38e8a9d8e91e *inst/include/ns/ns_SRA_scope.hpp
ca8edc360ed3d77e9c635fe0f98b9237 *inst/include/ns/ns_VPA.hpp
8e4b0ade2983b37c1002367b9d80707b *inst/include/ns/ns_cDD.hpp
b955ee9378d27d489d9d9370a7a205e9 *inst/rmarkdown_templates/SS2OM.Rmd
9eeb4328f38e631e1a04dd6e31c20f01 *man/Albacore_TwoFleet.Rd
ab8ce0253bdf08595e83de6d24f097f2 *man/Assessment-class.Rd
85a68ef313444ac2c8aa1372715b1569 *man/Awatea2OM.Rd
969244508383cf6c4e309c6ec6c0ad0c *man/CASAL2OM.Rd
1ad4f4dcdbacdd7c2f0df810bfb74052 *man/CASALpars.Rd
9be7a78ab8da852cf695a0a921ba874e *man/DD_TMB.Rd
1bf3e2f20e43a81ebac9b392c8af0475 *man/HCR_FB.Rd
83f7e394811314e36f62b81ac296de3a *man/HCR_MSY.Rd
e05920241c118b91ece417821f507bf1 *man/HCR_ramp.Rd
629e5cf78cebc2dd7334891a48f14009 *man/HCRlin.Rd
9bafe5b53fe010ad2184e993369dfea2 *man/HistMICE.Rd
cf76400c2275dda5aa10b182fa5dfe64 *man/MMSE-class.Rd
7f3a7d6f638fa743f756d92b368ddfe0 *man/MOM-class.Rd
167cae3f7c6ec1f50c52f148a1927651 *man/MPCalcsNAs.Rd
8a203bca9f87ca44cea7fbe6a6c7a3f0 *man/MSEtool-package.Rd
7d2decfffa007d08a2cea0f86a147632 *man/Model-based-MP.Rd
776573c58f958dfd52f0efdb10f19eae *man/NIL.Rd
838fd32db771ea5fbcfef6f2720acf28 *man/PRBcalc.Rd
2ff10c056dc956d9757cf4584b334bb0 *man/Probs.Rd
2ba25433d1b450f1a1ae78c13a7d4a3d *man/ResFromRel.Rd
ddf2246bdd476703e505ef3a4bd7d0b4 *man/SCA.Rd
7eda41819803e487fbbd31cc84c9b4c1 *man/SIL.Rd
a55d3db13e02b46552bc373d385132b5 *man/SOL.Rd
a9969d9127c56cf25ce6677de1b71ea5 *man/SP.Rd
69cecb2b65f7d7d27a9fe9812dcd468c *man/SP_production.Rd
ed5e1c5a5082cd8b7de55c2474b18acb *man/SRA-class.Rd
d3395a3f984326dd6d1c4b44b83f0e65 *man/SRA_scope.Rd
053ae0689010bfce7eec323896d661a2 *man/SS2Data.Rd
2d065c9b86d655e74a7e32b76cce98d9 *man/SS2MOM.Rd
1548fe5621d12e0079bf4e1a7777d90b *man/SS2OM.Rd
57944eb9b6137bf246b8715140020f2d *man/SSS.Rd
0a74cb3a7c7406bd593e8316a0f79a1f *man/TAC_MSY.Rd
912661c848b6f8a62ac46e79dc0d0680 *man/TEG.Rd
15cc4100a93d987383a37630378a7b71 *man/VPA.Rd
9607853c6c42fed1e3cb73fa12117065 *man/VPA2OM.Rd
632380bed5a0534941effeaa25f7296f *man/avail.Rd
b2ec87be79aba661f79384206229a66a *man/cDD.Rd
3b8df939c5a8adf4647ce1a8a4e26f99 *man/compare_models.Rd
85464aa505ad85c8622ad59ae8bb51a3 *man/diagnostic_AM.Rd
9224fa1f6b61612d6aff65b7109e0964 *man/expandHerm.Rd
cd403575f2b433e57735dc1efe4de4d1 *man/fetch.file.names.Rd
c37f14ef7c528b468efae8201c1bf2b4 *man/getinds.Rd
12baa0c0d5efd5c8feb81d5d608b48e6 *man/getnIVs.Rd
21785b656cfc50a89ccac01099e429a6 *man/getq_multi.Rd
bdc31219de9af12edc70f6e913f79186 *man/getq_multi_MICE.Rd
c62f415481d7cc31174ea86b93be1503 *man/hrate.Rd
56fc2961f0db9a8b778d795f5a79fe25 *man/iSCAM2Data.Rd
465e5253662cb4b5082df117360a3d60 *man/iSCAM2OM.Rd
e76629ce3d47c02c0a84f418f12b53a4 *man/iSCAMcomps.Rd
4e70e1467fc908c270c79013cc88780a *man/iSCAMinds.Rd
87c32b5c267dfaeed392f1feae968135 *man/ldim.Rd
05dd87ad870f14ce2d96dfaa383418fa *man/load.iscam.files.Rd
443763d61a1cc05d17c59832092d016f *man/mahplot.Rd
4c674b023b8b280e489596d7a7ab218b *man/make_MP.Rd
653dc36307c9f968154dfdf23aa20a1c *man/makemov.Rd
458ef8f41823d061678a87c848a2214c *man/multiData.Rd
24c57c67e35d63f8c51025c3ec0324f4 *man/multiDataS.Rd
5a7648b7816bd66647303196d9dc7524 *man/multiMSE.Rd
71c3f58b9f5f17cfd7961daea31b9f89 *man/multidebug.Rd
25fc402454c42cc26c1dc5c23c09b9a2 *man/optQ_multi.Rd
55baa7c3ff89cf613d375fa9b606a83e *man/plot.Assessment.Rd
8ceee4a1b64fdea8fd338ff2900e1079 *man/plot.MMSE.Rd
48a43c081abdf591c4c3d365399039f9 *man/plot.MOM.Rd
f7d1822c4ad99c10d84a2028ccd50dff *man/plot.SRA.Rd
6c269d17898d07075b45f9daa0962171 *man/plot.prof.Rd
fb9a902f929c1ac2a75850daa1d79250 *man/plot.retro.Rd
1de7f498a9bf905b0405eb7e393d89e1 *man/plotRel.Rd
679d10c3eb4f246525089b954303feb8 *man/plot_SR.Rd
9ff828b54fa26ec46d37c3c9426ffd10 *man/plot_betavar.Rd
2c748ce3bb5ee10e82cd9d4da7dd523c *man/plot_composition.Rd
4bc1401c7046e7f1a3769826e76916b8 *man/plot_crosscorr.Rd
86e860d048b77645f7d7379077684069 *man/plot_lognormalvar.Rd
0702a26fe2e3e983a99adfa64c5a8c62 *man/plot_residuals.Rd
e301bcec19553dcd27a9d4bed83cda48 *man/plot_steepness.Rd
6fb537ec1260e8fe2521732d2cb778fe *man/plot_timeseries.Rd
cd53dec6b002a0b1e4a0c2a27636a7df *man/plotmulti.Rd
10e69f9ffd1b64587e8b31be428798a8 *man/plotquant.Rd
d82fc90890bfbfcee83e9acf9c2f3f94 *man/popdynMICE.Rd
f0b1bc4ee16e041ef1e9af6bfb7b874d *man/popdynOneMICE.Rd
3181a081a2b36cc39582898d11c68072 *man/prelim_AM.Rd
5a84f25a38245c0996e82219d4a831b8 *man/prof-class.Rd
caba0bf6b1d339ed7fadc3e04cad83c7 *man/profile.Rd
03d6eaee69f699961dfdf6ea2abaa577 *man/project-class.Rd
ba7a69601b930c528f158fc5b0128a36 *man/projection.Rd
6d726881d5d1e872a8b430ce1c1d11e9 *man/qestMICE.Rd
588753a789a4019edd1f75ef80ede5c9 *man/read.control.file.Rd
339c8c8ba7bf5bfb05e7acf15d507355 *man/read.data.file.Rd
ac1374b8188d587f82a146aefe4ea215 *man/read.mcmc.Rd
dc179c724f50afe2fba030091e34e7bb *man/read.par.file.Rd
952d1d14a37748553faab2ad04e6277f *man/read.projection.file.Rd
f81328c976bbf540540c5a9e917b41a3 *man/read.report.file.Rd
a9fee7ca9ccd578210f73d7dfb89753f *man/retro-class.Rd
a8302050ce19a5282173a2160d207f1a *man/retrospective.Rd
abbb8cdf72efa7b8d7b663ffe02abbd2 *man/retrospective_AM.Rd
6aca8323996411a76380b51b4cba944f *man/simmov.Rd
6a8d5682896358d82efcfd39e1ab5304 *man/summary.Assessment.Rd
fc7af38ab1bf8aa48a9cdb8b65533609 *man/swordfish.Rd
7c1fc07b9196835e5807750917e99d9f *man/tinyErr.Rd
b7da8d8520c9e194520c2a2378881a19 *man/userguide.Rd
dba94f6857697cf238081286bd635af9 *src/MSEtool.cpp
81f111de4f0d7e765db94fed2154df8d *vignettes/DLMtool_logo.png
2b46a7bd0ffa5af525135cb7539e9024 *vignettes/Delay_difference.Rmd
79b66ae558897739452d7439e89cf609 *vignettes/MSEtool.Rmd
674b0773e805934f3218d487cb22e0b8 *vignettes/SCA.Rmd
1d4df4eb66b8c984518e5b0c4b4408df *vignettes/SRA_scope.Rmd
93d81e2868659c53f49a43452820d9e4 *vignettes/SRA_scope_eq.Rmd
158ca95db83dff97feb80ea415e2d8ab *vignettes/SRA_scope_sel.Rmd
d67a924d4ca5750faf7fe0dbd644e751 *vignettes/Surplus_production.Rmd
b7292ca13452cff2a692f671f193d223 *vignettes/VPA.Rmd
b4a0bf41a1eaf1559efa8e3250bce96a *vignettes/fig_assess/DD_TAC.png
3ec197c7fe04d9cb496b1b34080251cd *vignettes/fig_assess/DD_Tplot2.png
684863c6f4e4639408773e03d66b3883 *vignettes/fig_assess/DD_diagnostic_AM.png
a91f511c35ab8c13652486a5d03352f9 *vignettes/fig_assess/DD_profile.png
aca8c73b11a1c272977c925edf833f69 *vignettes/fig_assess/DD_retrospective_AM.png
be67fe5fabbca2a8ddefee128df7be2c *vignettes/fig_assess/DLMtool_design.png
2a6350673808da9e6e1f4f443950914c *vignettes/fig_assess/DLMtool_process.jpg
6f04e98d1655abb7d0772d36ef5c9636 *vignettes/fig_assess/MSEtool_design.png
1fcbabee70935ffb47721fe8c93a1c5e *vignettes/fig_multiMSE/MICE.png
8884abb77ab9224457b14111cdebf54b *vignettes/fig_multiMSE/MICE_F.png
58cf28f8d781aac534a1479ae179fc46 *vignettes/fig_multiMSE/MICE_sel.png
c3fa144fccba274b6fcd7b9552e84ed5 *vignettes/fig_multiMSE/MICE_stock.png
e598c7ba05d330463b08d19234989448 *vignettes/multiMSE.Rmd
