Ecosyste.ms: Issues

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GitHub / noaa-fims/fims issues and pull requests

#241 - [Refactor]: refactor the add_to_fims_TMB method

Issue - State: closed - Opened by ChristineStawitz-NOAA almost 2 years ago - 5 comments
Labels: status: wishlist, kind: refactor, P1

#241 - [Refactor]: refactor the add_to_fims_TMB method

Issue - State: closed - Opened by ChristineStawitz-NOAA almost 2 years ago - 5 comments
Labels: status: wishlist, kind: refactor, P1

#241 - [Refactor]: refactor the add_to_fims_TMB method

Issue - State: closed - Opened by ChristineStawitz-NOAA almost 2 years ago - 5 comments
Labels: status: wishlist, kind: refactor, P1

#235 - [Feature]: Link FIMS.cpp to model.hpp to test MakeADFun

Issue - State: closed - Opened by Andrea-Havron-NOAA about 2 years ago - 2 comments
Labels: status: help wanted

#235 - [Feature]: Link FIMS.cpp to model.hpp to test MakeADFun

Issue - State: closed - Opened by Andrea-Havron-NOAA about 2 years ago - 2 comments
Labels: status: help wanted

#235 - [Feature]: Link FIMS.cpp to model.hpp to test MakeADFun

Issue - State: closed - Opened by Andrea-Havron-NOAA about 2 years ago - 2 comments
Labels: status: help wanted

#232 - [Feature]: Update selectivity and recruitment interfaces

Issue - State: closed - Opened by Bai-Li-NOAA about 2 years ago - 2 comments
Labels: kind: feature, status: help wanted

#232 - [Feature]: Update selectivity and recruitment interfaces

Issue - State: closed - Opened by Bai-Li-NOAA about 2 years ago - 2 comments
Labels: kind: feature, status: help wanted

#232 - [Feature]: Update selectivity and recruitment interfaces

Issue - State: closed - Opened by Bai-Li-NOAA about 2 years ago - 2 comments
Labels: kind: feature, status: help wanted

#220 - [Question/help] Why do we parameterize fishing mortality and recruitment using mean and deviations?

Issue - State: open - Opened by JaneSullivan-NOAA about 2 years ago - 17 comments
Labels: kind: question, status: needs discussion, P2, theme: NLL refactor

#220 - [Question/help] Why do we parameterize fishing mortality and recruitment using mean and deviations?

Issue - State: open - Opened by JaneSullivan-NOAA about 2 years ago - 17 comments
Labels: kind: question, status: needs discussion, P2, theme: NLL refactor

#210 - [Refactor]: when should FIMS switch to TMBad?

Issue - State: open - Opened by Andrea-Havron about 2 years ago - 9 comments
Labels: status: wishlist, kind: refactor, P3, theme: code cleanup

#210 - [Refactor]: when should FIMS switch to TMBad?

Issue - State: open - Opened by Andrea-Havron about 2 years ago - 4 comments
Labels: kind: feature, status: wishlist, attribute: needs discussion, P3, theme: NLL refactor

#203 - [INPUT NEEDED] A first pilot stock in your region that could use FIMS

Issue - State: closed - Opened by ChristineStawitz-NOAA about 2 years ago - 15 comments
Labels: status: help wanted, kind: question, status: wishlist, theme: pilot studies

#203 - [INPUT NEEDED] A first pilot stock in your region that could use FIMS

Issue - State: open - Opened by ChristineStawitz-NOAA about 2 years ago - 15 comments
Labels: status: help wanted, kind: question, status: wishlist, theme: pilot studies

#193 - [Feature]: Rcpp interface to call module, likelihoods

Issue - State: closed - Opened by ChristineStawitz-NOAA about 2 years ago - 6 comments

#193 - [Feature]: Rcpp interface to call module, likelihoods

Issue - State: closed - Opened by ChristineStawitz-NOAA about 2 years ago - 6 comments

#193 - [Feature]: Rcpp interface to call module, likelihoods

Issue - State: closed - Opened by ChristineStawitz-NOAA about 2 years ago - 6 comments

#192 - Vectorize distributions

Issue - State: open - Opened by Andrea-Havron-NOAA about 2 years ago - 4 comments
Labels: status: wishlist, kind: refactor, theme: NLL refactor

#192 - Vectorize distributions

Issue - State: open - Opened by Andrea-Havron-NOAA about 2 years ago - 2 comments
Labels: status: wishlist, kind: refactor, theme: NLL refactor

#190 - [Bug]: call doc and style r GHA is failing and R styler returns an error

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago
Labels: kind: bug

#190 - [Bug]: call doc and style r GHA is failing and R styler returns an error

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago
Labels: kind: bug

#190 - [Bug]: call doc and style r GHA is failing and R styler returns an error

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago
Labels: kind: bug

#187 - Separate the "recruitment" of the population being tied to an SRR

Issue - State: open - Opened by Bai-Li-NOAA over 2 years ago - 2 comments
Labels: status: wishlist, theme: NLL refactor

#187 - Separate the "recruitment" of the population being tied to an SRR

Issue - State: open - Opened by Bai-Li-NOAA over 2 years ago - 2 comments
Labels: status: wishlist, theme: NLL refactor

#187 - Separate the "recruitment" of the population being tied to an SRR

Issue - State: open - Opened by Bai-Li-NOAA over 2 years ago - 2 comments
Labels: status: wishlist, theme: NLL refactor

#186 - [Feature]: recruitment deviations vector options

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago - 2 comments
Labels: kind: feature, status: wishlist, theme: NLL refactor

#186 - [Feature]: recruitment deviations vector options

Issue - State: open - Opened by Bai-Li-NOAA over 2 years ago - 1 comment
Labels: kind: feature, status: wishlist, attribute: needs discussion, theme: NLL refactor

#186 - [Feature]: recruitment deviations vector options

Issue - State: open - Opened by Bai-Li-NOAA over 2 years ago - 1 comment
Labels: kind: feature, status: wishlist, attribute: needs discussion, theme: NLL refactor

#185 - [Feature]: Do we need to put bias adjustment fraction within the likelihood?

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago - 37 comments
Labels: kind: question, P1

#183 - [Bug]: Error in Google test GHA when CXX compiler is GNU 11.2.0

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago - 5 comments
Labels: kind: bug, P2

#183 - [Bug]: Error in Google test GHA when CXX compiler is GNU 11.2.0

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago - 5 comments
Labels: kind: bug, P2

#183 - [Bug]: Error in Google test GHA when CXX compiler is GNU 11.2.0

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago - 5 comments
Labels: kind: bug, P2

#180 - [Feature]: Develop population loop module

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 5 comments
Labels: kind: feature

#180 - [Feature]: Develop population loop module

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 5 comments
Labels: kind: feature

#179 - [Feature]: Develop fleet module

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 7 comments
Labels: kind: feature

#179 - [Feature]: Develop fleet module

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 7 comments
Labels: kind: feature

#179 - [Feature]: Develop fleet module

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 7 comments
Labels: kind: feature

#177 - [FEATURE] Create formula interface (w/ notes from data group)

Issue - State: open - Opened by kellijohnson-NOAA over 2 years ago
Labels: kind: feature, attribute: needs discussion, theme: r interface

#174 - [Feature]: plot(FIMSFrame(data_mile1))

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 6 comments
Labels: kind: question, status: triage_needed

#174 - [Feature]: plot(FIMSFrame(data_mile1))

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 6 comments
Labels: kind: question, status: triage_needed

#174 - [Feature]: plot(FIMSFrame(data_mile1))

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 6 comments
Labels: kind: question, status: triage_needed

#173 - [Feature]: add ability to toggle between ADMB-style sum to zero constraint and k-1 style

Issue - State: open - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: status: wishlist, status: needs discussion, theme: NLL refactor

#170 - [Refactor]: Distributions base to share more parameters

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: status: wishlist, attribute: needs discussion, theme: NLL refactor

#170 - [Refactor]: Distributions base to share more parameters

Issue - State: open - Opened by ChristineStawitz-NOAA over 2 years ago - 9 comments
Labels: status: wishlist, status: needs discussion, theme: NLL refactor

#170 - [Refactor]: Distributions base to share more parameters

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: status: wishlist, attribute: needs discussion, theme: NLL refactor

#169 - check validity of data object using the weight-at-age module

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 2 comments
Labels: kind: feature

#169 - check validity of data object using the weight-at-age module

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 2 comments
Labels: kind: feature

#169 - check validity of data object using the weight-at-age module

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 2 comments
Labels: kind: feature

#167 - [Feature]: Easy functionality to plot input data object

Issue - State: open - Opened by Cole-Monnahan-NOAA over 2 years ago
Labels: kind: feature, status: wishlist, theme: r interface

#167 - [Feature]: Easy functionality to plot input data object

Issue - State: open - Opened by Cole-Monnahan-NOAA over 2 years ago
Labels: kind: feature, status: wishlist, theme: r interface

#167 - [Feature]: Easy functionality to plot input data object

Issue - State: open - Opened by Cole-Monnahan-NOAA over 2 years ago
Labels: kind: feature, status: wishlist, theme: r interface

#160 - [Bug]: testthat test-use-module.R does not work on GHA

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago - 2 comments
Labels: kind: bug

#160 - [Bug]: testthat test-use-module.R does not work on GHA

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago - 2 comments
Labels: kind: bug

#160 - [Bug]: testthat test-use-module.R does not work on GHA

Issue - State: closed - Opened by Bai-Li-NOAA over 2 years ago - 2 comments
Labels: kind: bug

#148 - [Feature]: an R function to create the Rcpp interface for new modules from a template file

Issue - State: open - Opened by ChristineStawitz-NOAA over 2 years ago - 9 comments
Labels: kind: feature, theme: r interface

#148 - [Feature]: an R function to create the Rcpp interface for new modules from a template file

Issue - State: open - Opened by ChristineStawitz-NOAA over 2 years ago - 9 comments
Labels: kind: feature, status: wishlist, theme: r interface

#147 - Empirical maturity at age[Feature]:

Issue - State: open - Opened by JonBrodziak over 2 years ago
Labels: kind: feature, status: wishlist, theme: more features

#147 - Empirical maturity at age[Feature]:

Issue - State: open - Opened by JonBrodziak over 2 years ago
Labels: kind: feature, status: wishlist, theme: more features

#147 - Empirical maturity at age[Feature]:

Issue - State: open - Opened by JonBrodziak over 2 years ago
Labels: kind: feature, status: wishlist, theme: more features

#141 - [Feature]: should input R data ages always start at zero?

Issue - State: open - Opened by ChristineStawitz-NOAA over 2 years ago - 6 comments
Labels: kind: question, status: needs discussion, theme: r interface

#139 - [FEATURE] logistic maturity ogive

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 1 comment
Labels: kind: feature

#139 - [FEATURE] logistic maturity ogive

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 1 comment
Labels: kind: feature

#139 - [FEATURE] logistic maturity ogive

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 1 comment
Labels: kind: feature

#137 - [BUG] repeats of fims::exp() and fims::log()

Issue - State: closed - Opened by JaneSullivan-NOAA over 2 years ago - 1 comment
Labels: kind: bug

#137 - [BUG] repeats of fims::exp() and fims::log()

Issue - State: closed - Opened by JaneSullivan-NOAA over 2 years ago - 1 comment
Labels: kind: bug

#137 - [BUG] repeats of fims::exp() and fims::log()

Issue - State: closed - Opened by JaneSullivan-NOAA over 2 years ago - 1 comment
Labels: kind: bug

#136 - What type of uncertainty should be used for each data type?

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 8 comments
Labels: kind: question, theme: r interface

#136 - What type of uncertainty should be used for each data type?

Issue - State: open - Opened by kellijohnson-NOAA over 2 years ago - 8 comments
Labels: kind: question, attribute: needs discussion, theme: more features

#134 - [FEATURE] implement differentiable max function to scale selectivity functions

Issue - State: closed - Opened by JaneSullivan-NOAA over 2 years ago - 16 comments
Labels: kind: feature, status: help wanted

#134 - [FEATURE] implement differentiable max function to scale selectivity functions

Issue - State: closed - Opened by JaneSullivan-NOAA over 2 years ago - 16 comments
Labels: kind: feature, status: help wanted

#134 - [FEATURE] implement differentiable max function to scale selectivity functions

Issue - State: closed - Opened by JaneSullivan-NOAA over 2 years ago - 16 comments
Labels: kind: feature, status: help wanted

#126 - [FEATURE]: Use issue forms instead of issue templates for issue submission

Issue - State: closed - Opened by k-doering-NOAA over 2 years ago - 2 comments
Labels: kind: feature, status: help wanted

#126 - [FEATURE]: Use issue forms instead of issue templates for issue submission

Issue - State: closed - Opened by k-doering-NOAA over 2 years ago - 2 comments
Labels: kind: feature, status: help wanted

#126 - [FEATURE]: Use issue forms instead of issue templates for issue submission

Issue - State: closed - Opened by k-doering-NOAA over 2 years ago - 2 comments
Labels: kind: feature, status: help wanted

#123 - [FEATURE] update doxygen github action to push to FIMS-docs

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 4 comments
Labels: kind: feature

#123 - [FEATURE] update doxygen github action to push to FIMS-docs

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 4 comments
Labels: kind: feature

#123 - [FEATURE] update doxygen github action to push to FIMS-docs

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 4 comments
Labels: kind: feature

#120 - column names and/or order of the input data frame

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 21 comments
Labels: status: help wanted, kind: question

#120 - column names and/or order of the input data frame

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 21 comments
Labels: status: help wanted, kind: question

#120 - column names and/or order of the input data frame

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 21 comments
Labels: status: help wanted, kind: question

#112 - [FEATURE] Dirichlet-multinomial likelihood for composition data

Issue - State: open - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: kind: feature, status: wishlist, theme: more features

#112 - [FEATURE] Dirichlet-multinomial likelihood for composition data

Issue - State: open - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: kind: feature, status: wishlist, theme: more features

#112 - [FEATURE] Dirichlet-multinomial likelihood for composition data

Issue - State: open - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: kind: feature, status: wishlist, theme: more features

#111 - [FEATURE] Non standard evaluation of function in input data frame

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 7 comments
Labels: kind: question

#111 - [FEATURE] Non standard evaluation of function in input data frame

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 7 comments
Labels: kind: question

#111 - [FEATURE] Non standard evaluation of function in input data frame

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 7 comments
Labels: kind: question

#108 - [FEATURE] Pull TMB R-style distributions into FIMS objective function

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: kind: feature

#108 - [FEATURE] Pull TMB R-style distributions into FIMS objective function

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: kind: feature

#108 - [FEATURE] Pull TMB R-style distributions into FIMS objective function

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: kind: feature

#107 - [FEATURE] Implement empirical weight-at-age module for FIMS

Issue - State: closed - Opened by ChristineStawitz-NOAA over 2 years ago - 3 comments
Labels: kind: feature