Blue-Matter/MSEtool issues and pull requests

#107 - proyears argument to SS2OM doesn't work

Issue - State: open - Opened by tcarruth 5 months ago
Labels: bug

#106 - An MP that returns the PPD after n projected years given a specified directory for the PPD

Issue - State: open - Opened by tcarruth 6 months ago
Labels: enhancement

#105 - A generic tuning function tune_MP(MP, MP_parname, OM_list, PM_tune)

Issue - State: open - Opened by tcarruth 6 months ago
Labels: enhancement

#104 - Release MSEtool 3.7.2

Issue - State: open - Opened by AdrianHordyk 7 months ago

#103 - I_beta should not be calculated directly from indices when they are supplied in OM@Data

Issue - State: open - Opened by AdrianHordyk 8 months ago

#102 - addMPs(): the merging of the N arrays is currently along the second dimension but I think it should be the third

Issue - State: closed - Opened by tcarruth 8 months ago - 1 comment
Labels: bug

#101 - Record MP interval in the MSE object

Issue - State: open - Opened by AdrianHordyk 8 months ago

#100 - Difference between Hist@Data and Hist@OM@cpars$Data not clear??

Issue - State: open - Opened by tcarruth 9 months ago

#99 - Time-varying hermaphroditism

Issue - State: closed - Opened by quang-huynh 10 months ago

#98 - Add salmonMSE functionality

Pull Request - State: closed - Opened by quang-huynh 10 months ago

#97 - move time series OM figures to the top of plot(OM) report, Imp and Obs properties to bottom

Issue - State: open - Opened by tcarruth 12 months ago
Labels: enhancement

#96 - disable checkMPs = T by default!

Issue - State: closed - Opened by tcarruth 12 months ago
Labels: enhancement

#95 - Descriptive figure to show derivation of statistical properties of data (particularly indices and catches)

Issue - State: open - Opened by tcarruth 12 months ago

#94 - Can't turn off plusgroup in multiMSE

Issue - State: closed - Opened by quang-huynh 12 months ago

#93 - iSCAM2OM needs a spawn_time_frac argument

Issue - State: closed - Opened by quang-huynh 12 months ago

#92 - SS2OM is failing to populate the Wt_age_C array for the first age class:

Issue - State: open - Opened by tcarruth about 1 year ago
Labels: bug

#91 - cpars$SLarray error message when resampling for depletion

Issue - State: open - Opened by tcarruth about 1 year ago
Labels: bug

#90 - predictMK returns error with inpars argument

Issue - State: closed - Opened by tcarruth about 1 year ago - 1 comment
Labels: bug

#89 - Add website to DESCRIPTION

Pull Request - State: closed - Opened by olivroy about 1 year ago

#88 - Format of PPD in MMSE object

Issue - State: closed - Opened by tcarruth about 1 year ago - 1 comment
Labels: enhancement

#87 - Erroneous simulation of length composition for anchovy

Issue - State: closed - Opened by tcarruth about 1 year ago
Labels: bug

#86 - When calculating statistical properties of indices, this fails if the index only has a recent year or two years of data

Issue - State: open - Opened by tcarruth about 1 year ago
Labels: bug

#85 - OM@L50 and OM@L50_95 not worked as expected for some OMs when using plot(OM) at least

Issue - State: closed - Opened by tcarruth over 1 year ago - 2 comments
Labels: bug

#84 - Massive CAL_nsamp slows down entire projection

Issue - State: open - Opened by quang-huynh over 1 year ago - 1 comment
Labels: enhancement

#83 - Better control of spatial TAC and Effort in the Rec object

Issue - State: open - Opened by tcarruth over 1 year ago
Labels: enhancement

#82 - Add an argument to runMSE to allow the MSE@PPD slot to include the Data@Misc$StockPars information to be reported

Issue - State: open - Opened by tcarruth over 1 year ago
Labels: enhancement

#81 - new("OM") fails

Issue - State: closed - Opened by quang-huynh over 1 year ago
Labels: bug

#80 - Interpretation with 2 area OM

Issue - State: open - Opened by quang-huynh over 1 year ago
Labels: enhancement

#79 - Code overwrites OM@cpars$AddIerr

Issue - State: open - Opened by quang-huynh over 1 year ago
Labels: bug

#78 - Issue when length(OM@interval) > 2

Issue - State: open - Opened by quang-huynh over 1 year ago
Labels: bug

#77 - Assess2OM should use cpars$spawn_timing

Issue - State: closed - Opened by quang-huynh over 1 year ago - 1 comment
Labels: enhancement

#76 - Deprecating/archiving CRAN version of {r4ss} package

Issue - State: closed - Opened by iantaylor-NOAA over 1 year ago - 2 comments

#75 - Data@Obs data frame is breaking

Issue - State: closed - Opened by quang-huynh almost 2 years ago

#74 - Update Cheatsheets and add to openMSE site

Issue - State: open - Opened by AdrianHordyk about 2 years ago
Labels: enhancement

#73 - Update `OM@CurrentYr` if `OM@cpars$Data@Year` exists

Issue - State: open - Opened by AdrianHordyk about 2 years ago
Labels: enhancement

#72 - plot(OM) and plot(RCMfit) plots would be greatly improved by simple addition of grid() or equivalent

Issue - State: open - Opened by tcarruth about 2 years ago - 2 comments
Labels: enhancement

#71 - Merge flexible SRR developments

Pull Request - State: closed - Opened by AdrianHordyk about 2 years ago

#70 - Bug when `report=TRUE` in `SS2OM`

Issue - State: closed - Opened by AdrianHordyk about 2 years ago
Labels: bug

#69 - SS2OM doesn't calculate V, retL, etc correctly for GFMC blackspot seabream

Issue - State: closed - Opened by AdrianHordyk about 2 years ago - 1 comment
Labels: bug

#68 - Calculate VB reference points from fishery weight at age?

Issue - State: open - Opened by quang-huynh over 2 years ago

#67 - Add overall F by stock in multi-MSE

Issue - State: open - Opened by AdrianHordyk almost 3 years ago - 1 comment

#66 - add `plot(MOM`) function back to package

Issue - State: closed - Opened by AdrianHordyk almost 3 years ago - 1 comment

#65 - default lag-1 autocorrelation for simulated indices should be minimum value 0

Issue - State: closed - Opened by tcarruth almost 3 years ago
Labels: enhancement

#64 - Allowing for in-season timing of surveys (data) relative to exploitation

Issue - State: open - Opened by tcarruth about 3 years ago
Labels: enhancement

#63 - Age-year survival deviations for copying state-space models like WHAM and SAM

Issue - State: open - Opened by tcarruth about 3 years ago

#62 - Implementation error by year

Issue - State: open - Opened by tcarruth about 3 years ago
Labels: enhancement

#61 - Retrospective MP evaluation

Issue - State: open - Opened by tcarruth about 3 years ago
Labels: enhancement

#60 - Need to document WHAM2OM (when completed) on the openMSE help pages etc

Issue - State: open - Opened by tcarruth about 3 years ago
Labels: documentation

#59 - Fdisc as a Stock vs. Fleet parameter

Issue - State: closed - Opened by quang-huynh over 3 years ago - 1 comment

#58 - Generate message for invalid custom parameters

Issue - State: closed - Opened by quang-huynh over 3 years ago

#57 - t0bias is NaN when OM@t0 = 0 and cpars$Data@vbt0 = 0

Issue - State: closed - Opened by quang-huynh over 3 years ago - 1 comment

#56 - new('OM') needs default values

Issue - State: closed - Opened by tcarruth over 3 years ago

#55 - Function that checks for OM completeness

Issue - State: closed - Opened by tcarruth over 3 years ago
Labels: enhancement

#54 - runMSE returns negative SSB

Issue - State: closed - Opened by quang-huynh over 3 years ago

#53 - Ad retro feature for showing MP performance over the last x historical years

Issue - State: open - Opened by AdrianHordyk over 3 years ago
Labels: enhancement

#52 - Strange LinInterp behavior

Issue - State: closed - Opened by quang-huynh over 3 years ago - 2 comments

#51 - Package crashing with Rcpp 1.0.7

Issue - State: closed - Opened by quang-huynh over 3 years ago - 1 comment

#50 - Calculate SPR

Pull Request - State: closed - Opened by AdrianHordyk over 3 years ago

#49 - Fix plus group calcs

Issue - State: closed - Opened by AdrianHordyk over 3 years ago
Labels: bug

#48 - plot(OM) returning error fairly often with OMs made using RCM

Issue - State: closed - Opened by tcarruth almost 4 years ago
Labels: bug

#47 - get an acf() error when submitting data with an index with only one observation

Issue - State: closed - Opened by tcarruth almost 4 years ago - 1 comment

#46 - XL2Data returns error if empty CAA data fields are provided in the excel data file

Issue - State: closed - Opened by tcarruth almost 4 years ago - 1 comment

#45 - Add example CSVs to package

Issue - State: open - Opened by AdrianHordyk almost 4 years ago
Labels: enhancement

#44 - Skipjack_IO_IOTC OM from MSEtool Extra not compatible

Issue - State: closed - Opened by tcarruth almost 4 years ago - 1 comment
Labels: bug

#43 - Update OM Report

Issue - State: open - Opened by AdrianHordyk about 4 years ago
Labels: enhancement

#42 - Export functions for AddIbeta and AddIerr calculations

Issue - State: closed - Opened by quang-huynh about 4 years ago - 2 comments
Labels: enhancement

#41 - Report(Data) does not plot time series of discontinuous catch (is a line without points) or effort

Issue - State: closed - Opened by tcarruth about 4 years ago
Labels: enhancement

#40 - Zero y-axis intercepts needed for most plot(OM) figures (e.g. depletion)

Issue - State: closed - Opened by tcarruth about 4 years ago
Labels: enhancement

#39 - Error in Report(Data) if ALL 'reference' fields are empty in the csv or xlsx data file,

Issue - State: closed - Opened by tcarruth about 4 years ago
Labels: bug

#38 - plot(Data) does not plot other indices such as VInd

Issue - State: closed - Opened by tcarruth about 4 years ago
Labels: enhancement

#37 - Add a percentile range to the LH2OM sampling as an alternative to truncation using filterMK

Issue - State: closed - Opened by tcarruth about 4 years ago
Labels: enhancement

#36 - runMSE errors when calculating F from TAC

Issue - State: closed - Opened by quang-huynh about 4 years ago - 4 comments

#35 - SS2OM - Add Linf, K, and t0 to OM@cpars

Issue - State: closed - Opened by AdrianHordyk about 4 years ago - 2 comments
Labels: enhancement

#34 - add beta to validcpars()

Issue - State: closed - Opened by AdrianHordyk about 4 years ago - 1 comment
Labels: bug

#33 - new('Data', dir) does not load CAL data but XL2Data(dir) does

Issue - State: closed - Opened by tcarruth about 4 years ago
Labels: bug

#32 - Alternative CAA/CAL distributions

Issue - State: closed - Opened by quang-huynh about 4 years ago - 2 comments

#31 - Allow for variable width length bins

Issue - State: closed - Opened by quang-huynh about 4 years ago - 3 comments

#30 - Additional reference points for OM

Issue - State: closed - Opened by quang-huynh about 4 years ago

#29 - Required() not working in vectored mode

Issue - State: closed - Opened by tcarruth about 4 years ago

#28 - include the cpars_info object so that validcpars() works ok

Issue - State: closed - Opened by tcarruth about 4 years ago

#27 - Add density-dependent M to OM and SCA (and RCM)

Issue - State: closed - Opened by robynforrest about 4 years ago - 1 comment