70bcc76ceb7f733eff5e0c55f8c0ed24 *DESCRIPTION
4c1e25e0644dc46837f6f258d96d017a *NAMESPACE
2ce38d363442ce4d04b0f944015d5fe6 *NEWS.md
2ba5c0355a1308adb13e769ccda23dce *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
925f4d1967ee62364150d2001a5854d9 *R/MSEtool-package.R
d772229be8b67e997f705e210104a6c2 *R/Misc_fun.R
bc27028c6125ebb10f297bb58167ef5d *R/Movement_calcs.R
c045239d0ca97a8a4f22c8317c1b0002 *R/SRA_scope.R
7d7b9bc8707aca349810077c8a2d07c3 *R/SRA_scope_data.R
ed1c247d2f2848c4d1d5abe491098de7 *R/SS2Data.R
41b99abb84df1228166b890230a5d6b3 *R/SS2OM.R
17ef365e5edea044036ad3913e9ec011 *R/Single_stock_multi_q_REDUNDANT.R
d1c1fa09fefd6ae77dde9f11bec094f4 *R/applyMMP.R
c6ee004a45aeab806a39a799597cffe4 *R/assess_DD.R
d5a1b6e11b996b1f7682c93a94b172f1 *R/assess_SCA.R
4bf335f4e762d194193baba63b75681c *R/assess_SCA2.R
2f11de8eab9601207dd68125009c6077 *R/assess_SCA_Pope.R
870e56fff801ac8c8543ad80c2f1bbff *R/assess_SP.R
58eb64c53da2953deb602638ccb721aa *R/assess_VPA.R
ecdc50f274413338812bdc2ee9306d59 *R/assess_cDD.R
1587da4f56ff9b46e22f42d480cfd2ce *R/define_S4_class_SRA.R
b5e9e0c24517c53d16fea89b707b8208 *R/define_S4_class_assess.R
2162c5f619810667350a83916c4b2ade *R/define_S4_class_profile.R
b2189c847e600750b7994e39828e8c53 *R/define_S4_class_project.R
eee40291442fe4e15e78468b43ec9687 *R/define_S4_class_retro.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
462f531e76eedd5e6d3999a136557572 *R/report_DD_TMB.R
8559b8237209d01a7790b534070c6f9e *R/report_SCA.R
f8c23df5f8fa26657b74c9cf657b6c15 *R/report_SCA_Pope.R
598782e6c1407ec389a9b8e59b3c5b37 *R/report_SP.R
90fec3bd5c57b7fcd839ba7bc9454833 *R/report_VPA.R
b599337a45b73bfe7c91a7a580c83835 *R/report_auxiliary.R
bc6aa898550e528980529f25c3fabf00 *R/report_cDD.R
ca4db23ddd6a44d5a72bf70c972e580b *R/report_spict.R
5db3f1903c0d4a5368a540e9dec1e540 *R/retrospective_AM.R
df71b1e27ab7d86d32c4f27629ea8b0e *R/rmd_report.R
91c393156fcb8ab00e3b44eb6696860f *R/z_MPs.R
a742cbd6ef02f32471bfd90056543195 *README.md
b582546c6f079c3cb6dce0c73656197d *build/vignette.rds
d73b0be62ff2974fc6413e0dbe628092 *data/Albacore_TwoFleet.rda
410db88575328a1de265f89bcdee8c4d *data/swordfish.rda
fb3beda1963f182d517b486026302f9f *inst/doc/Delay_difference.R
d5934511ced95640e700904ae74a4b35 *inst/doc/Delay_difference.Rmd
ab4e67cf8ca8acc4d68dd534de47d435 *inst/doc/Delay_difference.html
20d5d4e3c4c52386f70e1156179db31a *inst/doc/MSEtool.R
5a8059618143679698fc911f14787659 *inst/doc/MSEtool.Rmd
efabbad489764532d85d3093bdd377c1 *inst/doc/MSEtool.html
fb3beda1963f182d517b486026302f9f *inst/doc/SCA.R
9a4665a072f526d349eecc5baf5d19e2 *inst/doc/SCA.Rmd
d3f81c5bee7470c29bd6ac08c6dca0b1 *inst/doc/SCA.html
846942cf94360a3afaa8ee399fd1fa40 *inst/doc/SRA_scope.R
fba375e4127bd0829b2920f9849e9cb2 *inst/doc/SRA_scope.Rmd
c3622321e27b6cc1da6d0d69b608c93b *inst/doc/SRA_scope.html
fb3beda1963f182d517b486026302f9f *inst/doc/Surplus_production.R
24025707b2861469e9ea78dd283eab5c *inst/doc/Surplus_production.Rmd
80a57924c630f721b55f711ba6224794 *inst/doc/Surplus_production.html
fb3beda1963f182d517b486026302f9f *inst/doc/VPA.R
6ba9c03d1412fac7a38266f9c34635dc *inst/doc/VPA.Rmd
5dee6ffc5f62ae944ade4f5be8a72db8 *inst/doc/VPA.html
1448b148f561a756385ee5c067d49d81 *inst/doc/multiMSE.R
e6170b0b5dba3bdf8887b8ccf37d38e2 *inst/doc/multiMSE.Rmd
b53165acd1e2284e69448c9478b489c5 *inst/doc/multiMSE.html
e4408ae7cbc0d030f29048ad8dfd2e05 *inst/include/DD.hpp
179dc20fabefd1f40a28254f78e7c683 *inst/include/DD_SS.hpp
b7898d3e8feac5d0cb3520b09585e9e9 *inst/include/SCA.hpp
ba109c41ae64d3191c1a4b20f6104cd4 *inst/include/SCA2.hpp
64af310a686f806a1912ca1083338ade *inst/include/SCA_Pope.hpp
3bef010b4228ea5179667c2c3aa559ad *inst/include/SP.hpp
4cff8fd7681800eb7abc2431622bdaae *inst/include/SRA_scope.hpp
0db02ab62f07f6f33b6f08673008746c *inst/include/VPA.hpp
8226cda1380430c5f1e371a698b1f105 *inst/include/cDD.hpp
2c9268f48a5f7411ad745ee5e7fb37bd *inst/include/cDD_SS.hpp
d79f036bc5e4044d4199688b9937140f *inst/include/functions.hpp
772aa8c0fe6fe3ea0a92b86b1e83a34a *inst/include/grav.hpp
7064a2215907718bfd8ccd2677fd0010 *inst/include/grav_Pbyarea.hpp
1bf970e94985a480e7b0cac94a10cbdf *inst/include/ns/ns_SCA.hpp
b4cb49cbd763681b05a2a41914eba26c *inst/include/ns/ns_SP.hpp
c373b9a7621b25dcb44949df0f699db4 *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
88eada78caf3241630ded4f0c329ffcd *man/Albacore_TwoFleet.Rd
a48506654172ea07325820573fe22496 *man/Assessment-class.Rd
4cf9d1246c1d784b4f6f48298af003bb *man/Awatea2OM.Rd
227694457bde49172db042342e0c8ba8 *man/CASAL2OM.Rd
1ad4f4dcdbacdd7c2f0df810bfb74052 *man/CASALpars.Rd
f044dd1dc8f388acedacf5ec53bf0308 *man/DD_TMB.Rd
2a7391713d29837c891ec72e5dacc5a1 *man/Data-rich-MP.Rd
1bf3e2f20e43a81ebac9b392c8af0475 *man/HCR_FB.Rd
83f7e394811314e36f62b81ac296de3a *man/HCR_MSY.Rd
64e4975165c4678f577fff3f9772003c *man/HCR_ramp.Rd
629e5cf78cebc2dd7334891a48f14009 *man/HCRlin.Rd
0eb1293a2480274a873efe17753ab6e7 *man/HistMICE.Rd
cf76400c2275dda5aa10b182fa5dfe64 *man/MMSE-class.Rd
7f3a7d6f638fa743f756d92b368ddfe0 *man/MOM-class.Rd
167cae3f7c6ec1f50c52f148a1927651 *man/MPCalcsNAs.Rd
9a15c2c44979539a3724cde922ee87d0 *man/MSEtool-package.Rd
776573c58f958dfd52f0efdb10f19eae *man/NIL.Rd
15b4c762a7200530e17a9cdf505c0f39 *man/PRBcalc.Rd
ff49c5db1fd4ed5766a1375337b3decd *man/Probs.Rd
2ba25433d1b450f1a1ae78c13a7d4a3d *man/ResFromRel.Rd
814860fd3e3b86e755c8a88daeb715e6 *man/SCA.Rd
7eda41819803e487fbbd31cc84c9b4c1 *man/SIL.Rd
a55d3db13e02b46552bc373d385132b5 *man/SOL.Rd
3bbc59bf9b59d4ba9011b2d1472e5ef1 *man/SP.Rd
69cecb2b65f7d7d27a9fe9812dcd468c *man/SP_production.Rd
31e9f39f159df23763083a05c5d38685 *man/SRA-class.Rd
a26e890da4071088604bbbb03d0c9be0 *man/SRA_scope.Rd
3b060221859de176f51cfc60121349a3 *man/SS2Data.Rd
921944fb75e2522da036fb8ded4ad044 *man/SS2OM.Rd
0a74cb3a7c7406bd593e8316a0f79a1f *man/TAC_MSY.Rd
912661c848b6f8a62ac46e79dc0d0680 *man/TEG.Rd
859376bcaaf2d2e411ed8cb041e48db1 *man/VPA.Rd
632380bed5a0534941effeaa25f7296f *man/avail.Rd
f628a8504964f28ee4e155373a2c5cb5 *man/cDD.Rd
3b8df939c5a8adf4647ce1a8a4e26f99 *man/compare_models.Rd
4b37786c767225e527957dd11bf5e7ad *man/diagnostic_AM.Rd
9224fa1f6b61612d6aff65b7109e0964 *man/expandHerm.Rd
cd403575f2b433e57735dc1efe4de4d1 *man/fetch.file.names.Rd
9bdb68488496b1069fa49923a79347af *man/getinds.Rd
12baa0c0d5efd5c8feb81d5d608b48e6 *man/getnIVs.Rd
b5096621d1ead0c445497a6106b36f44 *man/getq_multi.Rd
17e6a1c6a8a61eb3677e085204694a61 *man/getq_multi_MICE.Rd
c62f415481d7cc31174ea86b93be1503 *man/hrate.Rd
65245a303cd7e5b846e47668c8526cca *man/iSCAM2Data.Rd
81ddb0d9fd35a604d49901bf2722cd6f *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
a8a0a9289c80a7534f774ee107400558 *man/multiMSE.Rd
dd35aa5167784066f5a595ea35c0076c *man/multidebug.Rd
33908934e728c510b8c0540d23313dbe *man/optQ_multi.Rd
2f887d18e4dc6fb898aed7fdf1a17347 *man/plot.Assessment.Rd
882a92b28541ba0e5a073fdb0db0a289 *man/plot.MMSE.Rd
1fe6038b69f900b5fb3a1695b668ecdd *man/plot.MOM.Rd
5a0d95dce5515f41589c181cf8e0df35 *man/plot.SRA.Rd
048b5903638e978b3c007e542864888a *man/plot.prof.Rd
a83ffe51f1c53ad04c82c7bde64904b7 *man/plot.retro.Rd
1de7f498a9bf905b0405eb7e393d89e1 *man/plotRel.Rd
f3de5c9fedf78c0e7319825724aa2caf *man/plot_SR.Rd
9ff828b54fa26ec46d37c3c9426ffd10 *man/plot_betavar.Rd
4b26461a5d022b5d86ce63aa2bfc300a *man/plot_composition.Rd
a46cfebbef46acfa653a8701f3ac519f *man/plot_crosscorr.Rd
a1cac7b30471405c51231a1d00347e31 *man/plot_lognormalvar.Rd
b3f3be154b3bc7d77105cd6a651b85d5 *man/plot_residuals.Rd
5f536c4f11ed74717d9db4f5cf056ac2 *man/plot_steepness.Rd
cdba2e4ef17a1c40434004dbfa099c8f *man/plot_timeseries.Rd
cd53dec6b002a0b1e4a0c2a27636a7df *man/plotmulti.Rd
008e253fccd1aaddf9a89a162e422448 *man/plotquant.Rd
b0522646ba9e74bd77566828f4c068d3 *man/popdynMICE.Rd
b880be7f386bc641ebd8bc0ecad95e3b *man/popdynOneMICE.Rd
3181a081a2b36cc39582898d11c68072 *man/prelim_AM.Rd
5a84f25a38245c0996e82219d4a831b8 *man/prof-class.Rd
3372d7629578bfed2f96d5868c154c9f *man/profile.Rd
03d6eaee69f699961dfdf6ea2abaa577 *man/project-class.Rd
e3c5aabaf417ed3f5c9c97426c4d1045 *man/projection.Rd
ad296fc5036dce40debc94a08c22341c *man/qestMICE.Rd
af36b07151dc668197d1f289fb6b727e *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
37d25223409dd0fa8150b615489b53c5 *man/retrospective.Rd
a75b26331acd436adcdca9e1112d3652 *man/retrospective_AM.Rd
90e2bc2ee513596b599eca6b7a2a3a81 *man/simmov.Rd
ea212eb79ed9a1d6b2f16ee0dae9f9d0 *man/summary.Assessment.Rd
fc7af38ab1bf8aa48a9cdb8b65533609 *man/swordfish.Rd
87aea78acabd94b5de529c15510480e7 *man/tinyErr.Rd
b7da8d8520c9e194520c2a2378881a19 *man/userguide.Rd
6dc24efe0058e7fbc296cf92e9b1efca *src/MSEtool.cpp
81f111de4f0d7e765db94fed2154df8d *vignettes/DLMtool_logo.png
d5934511ced95640e700904ae74a4b35 *vignettes/Delay_difference.Rmd
5a8059618143679698fc911f14787659 *vignettes/MSEtool.Rmd
9a4665a072f526d349eecc5baf5d19e2 *vignettes/SCA.Rmd
fba375e4127bd0829b2920f9849e9cb2 *vignettes/SRA_scope.Rmd
24025707b2861469e9ea78dd283eab5c *vignettes/Surplus_production.Rmd
6ba9c03d1412fac7a38266f9c34635dc *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
e6170b0b5dba3bdf8887b8ccf37d38e2 *vignettes/multiMSE.Rmd
