Code

Size- and age- dependent mortality #599

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glemieux merged 31 commits intoNGEET:masterNGEET/fates:masterfrom JessicaNeedham:JessicaNeedham-IO-sizeagemortalityJessicaNeedham/fates:JessicaNeedham-IO-sizeagemortalityCopy head branch name to clipboardMar 26, 2020

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Commits on Jan 9, 2020

• Squashed commit of the following:

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  Jessica Needham

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• [ Fix bug in parameter file - cohort age classes must be defined ]

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• [ Update FatesPFTindexSwapper to be compatible with python 3]

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• [ Change the logic for how the size and age mortality functions are

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Commits on Jan 10, 2020

• [Fix bug in FatesHistoryInterfaceMod ]

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Commits on Jan 17, 2020

• [Fix the small simple things like indentations and forgotten _r8s ]

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Commits on Jan 20, 2020

• [Change the switch for age dependent mortality ]

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  Jessica Needham

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• [Update param file with metadata and add checks on param values ]

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Commits on Jan 21, 2020

• [ Fix bug in flags for mortality params ]

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• [In EDCohortDynamicsMod increase maxCohortsPerPatch to 300 if cohort

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• [ More detailed flags for mortality parameter checks in

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Commits on Jan 22, 2020

• [ Change the cap on mortality ]

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Commits on Jan 23, 2020

• [ Remove cap on mortality ]

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Commits on Jan 30, 2020

• [Change check on initialised params to use the check_initialized

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  Jessica Needham

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Commits on Mar 11, 2020

• [ Fix some minor bugs/make changes suggested by Rosie Fisher ]

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• [ Cohort age units to years ]

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• [ Bug fix - .eqv. to .TRUE. for cohort_age_tracking check ]

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Commits on Mar 12, 2020

• [Remove the cohort age tracking parameter and make

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• [Fix bug with hlm_use_cohort_age_tracking flag ]

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Commits on Mar 14, 2020

• Merge remote-tracking branch 'ngeet_repo/master'

  

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• Merge branch 'master' into JessicaNeedham-IO-sizeagemortality

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Commits on Mar 17, 2020

• [Add one additional test to ensure age-dependent

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Commits on Mar 18, 2020

• [ Fix bug in error message for cohort age tracking flag ]

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• [ifalse to 0 in a test of hlm_use_cohort_age_flag ]

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Commits on Mar 19, 2020

• [ Update parameter file]

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Commits on Mar 20, 2020

• [ Remove checks on cohort age bin edges ]

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Commits on Mar 24, 2020

• Merge branch 'master' into JessicaNeedham-IO-sizeagemortality-merged

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• Fixed order of operations on mortality condition for age mortality, conditioned some history variables when age is off

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• Merge pull request #1 from rgknox/JessicaNeedham-IO-sizeagemortality-merged-rkfixes

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• [ Fix bug in mortality change in number density - logging

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Commits on Mar 26, 2020

• [Change maxCohortsPerPatch back to 100]

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