r4atlantis atlantisom issues

r4atlantis / atlantisom

Atlantis operating model. Generates data sets from Atlantis scenarios.

https://r4atlantis.github.io/atlantisom

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issues

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revise column names used in SS3 input files

#58 iantaylor-NOAA opened 1 month ago
0
New functions for biomass pools and total catch by fleet

#57 sgaichas closed 10 months ago
0
get dimensioning from output file in case Atlantis run doesn't finish

#56 sgaichas opened 1 year ago
0
wt at age interpolation fails for initial agecl > 1

#55 sgaichas closed 2 years ago
1
annual wt at age output incomplete

#54 sgaichas closed 11 months ago
1
Need to cast as data.table to use dcast in `reformat_compositions`

#53 ChristineStawitz-NOAA closed 1 month ago
1
reformat load_catch output

#52 andybeet opened 3 years ago
0
read_savedfisheries() function couldn't been used

#51 Bai-Li-NOAA closed 3 years ago
1
DetaileDietCheck.txt contents - load_detailed_diet_comp

#50 andybeet opened 3 years ago
0
Andy agebiomind

#49 andybeet closed 3 years ago
0
Updated vignettes to allow for pkgdown site

#48 andybeet closed 3 years ago
0
return species code in load_bioind

#47 andybeet closed 3 years ago
0
create package down site

#46 andybeet opened 3 years ago
3
installation issue

#45 andybeet closed 3 years ago
1
kwsr or kswr

#44 vonStadarhraun closed 2 years ago
6
Multispecies and multi-survey functions into master

#43 sgaichas closed 3 years ago
0
add sample_ages to wrappers to simulate ageing a subset of lengthed fish

#42 sgaichas opened 3 years ago
5
Save run_truth output as .rds rather than .Rdata?

#41 sgaichas opened 3 years ago
2
links to create_fishery_data.r

#40 andybeet closed 4 years ago
3
Annage

#39 sgaichas closed 4 years ago
0
Improve robustness across Atlantis models

#38 sgaichas opened 4 years ago
1
should package bbmle be added as a dependency?

#37 andybeet closed 4 years ago
2
check birthday for each species when assigning age

#36 ChristineStawitz-NOAA opened 4 years ago
0
stock assessment skill assessment functions

#35 sgaichas opened 4 years ago
0
wrapper functions to generate stock assessment inputs

#34 sgaichas opened 4 years ago
2
modify run_truth and load_nc to allow full age structure

#33 sgaichas closed 4 years ago
4
add calculate M function

#32 sgaichas opened 5 years ago
1
add more life history info to load_biolprm

#31 sgaichas closed 5 years ago
1
Add code to write growth parameter initial conditions and bounds based on atlantisom "data"

#30 cstawitz opened 5 years ago
0
Add function to write empirical weight-at-age

#29 cstawitz opened 5 years ago
0
load_prm doesn't work if tags in run .xml end with </Attribute>

#28 cstawitz closed 5 years ago
1
Code example in sample_survey_biomass has an error

#27 cstawitz closed 5 years ago
1
Standard survey specifications list

#26 sgaichas opened 7 years ago
1
calc_Z survival at time step or year

#25 kellijohnson-NOAA opened 8 years ago
2
Change run_ to convert_

#24 slucey closed 8 years ago
4
add callgraphs

#23 kellijohnson-NOAA opened 8 years ago
0
list all items ever eaten

#22 kellijohnson-NOAA opened 8 years ago
2
catch.nc and catch.txt do not add up

#21 alketh opened 8 years ago
4
load_meta challenge

#20 ghost closed 8 years ago
1
Filestructure of input data

#19 alketh closed 8 years ago
2
Try to avoid filenames explicitly

#18 alketh closed 8 years ago
1
Loading functions from packages!

#17 alketh closed 8 years ago
5
Fishing stage classes

#16 kellijohnson-NOAA closed 8 years ago
1
function run_atlantis

#15 ghost closed 8 years ago
1
function load_groups

#14 kellijohnson-NOAA closed 8 years ago
1
function load_bio

#13 kellijohnson-NOAA closed 8 years ago
2
function load_meta

#12 kellijohnson-NOAA closed 8 years ago
1
function create_env

#11 kellijohnson-NOAA opened 8 years ago
0
Finalize package

#10 ghost opened 8 years ago
0
functions sample_

#9 kellijohnson-NOAA opened 8 years ago
4