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Age size observation 202206 #397

Merged
merged 26 commits into from
Jul 20, 2022
Merged

Age size observation 202206 #397

merged 26 commits into from
Jul 20, 2022

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Craig44
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@Craig44 Craig44 commented Jul 20, 2022

The main contribution from this pull request is to add a fully tested (with CASAL) and documented observation class of age-size observations

minor contributions include

  • Add initial value for @Estimates
  • Add Bernoulli likelihood
  • Add Github actions to test the R-package
  • CHG: instantaneous mortality to report years with catches not model years.
  • CHG: accessors for combined categories so now we can access a specific category from the partition

Craig44 added 26 commits June 30, 2022 15:32
@Craig44
ADD: observation class
9300677 
ADD: functions to AgeLength parent class to calculate observations.
still incomplete
@Craig44
UPD: AgeLength obs
3e5b2b7 
ADD: unique labels for TestModel/Simple
@Craig44
Test R library GH workflow
80ef215
@Craig44
CHG: R-lib GH so sub-directory found for dependencies
afa237a
@Craig44
FIX: r-lib GH github_install command
802af12
@Craig44
DEL: extra command
6834588
@Craig44
r-lib GH test different devtools command
bb0ad4b
@Craig44
UPD: r-lib GH from windows to ubuntu
84f6ef1
@Craig44
Test workflow sequence GH actions
7475bfb
@Craig44
ADD: dependency GH action GH
1134c78
@Craig44
UPD: GH r-lib actions
4502ca7
@Craig44
UPD: r-library yml
32c2bb0
@Craig44
UPD: test GH rlib
32b5897
@Craig44
UPD: r-lib test .yml
40ebda5
@Craig44
ADD: R-tests into main validation
83c9cee
@Craig44
UPD: R-lib GH actions
6cc567f 
remove duplicate @estimate in Simple TestModel
@Craig44
FIX: years reported in InstantaneousMortality only prints years with …
58c9b01 
…catches now was model years
@Craig44
UPD: length based instantanesous mortality to only report years when …
ba25bcc 
…there is catch

FIX: rlibrary to stop on warnings.
@Craig44
UPD: manual and AgeLength obs class
02afb7e 
the AgeLength class is not working yet
@Craig44
ADD: accessors methods for combined categories partitions
44a30dc
@Craig44
UPD: AgeLength obs
dd15f0b
@Craig44
UPD: Age length observation
8ad348a 
ADD unit tests
ADD: bernoulli likelihood
@Craig44
ADD: initial value for estimates
b3e4cd3
@Craig44
UPD: bernoulli likeihood
01f9be4
@Craig44
UPD: Usermanual for AgeLength observation
8cc9305
@Craig44
Merge branch 'master' into AgeSizeObservation_202206
1d1a6e7
@Craig44 Craig44 merged commit 61b6651 into master Jul 20, 2022
@Casal2 Casal2 deleted the AgeSizeObservation_202206 branch June 26, 2024 04:13
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@Craig44