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NEWS
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CHANGES in planetfish VERSION 0.5.5
o disable warning on 'init_age_comp'
o replacing print statements in 'M3_CASAL1_Data.r' with warning()
CHANGES in planetfish VERSION 0.5.3
o bug fix: method 'defined' in 'stock_recruit' now takes a series of recruitment
values (previously only accepted a single value)
o bug fix: fill now implemented in 'create_array', previously arrays filled with
zeroes
o Function 'initial_ages' replaces 'init_age_comp' in generating the initial age
structure of the population and provides methods for user defined age structures
o estimate_selectivity now controls which selectivities that are estimated by the
CASAL assessment.
CHANGES in planetfish VERSION 0.5.1
o 'move_fish_dframe' now permits separate movement for tagged and untagged
population by specifing 'om$move_tag_rules'
CHANGES in planetfish VERSION 0.5
o individual ogive functions have been replaced by 'ogive' which has a type
argument. These functions will be removed in version 0.7
o move rules now implemented as dataframes, old parameter specifications will no
longer work.
o 'create_move_rule' is now redundant and will be removed in version 0.6
o new function 'expand_move_matrix' for array based movement
o new function 'ogive' combines all the ogive functions
o new argument for 'move_init' to specify the number of years to move the initial
population prior to the first model timestep. The previously hardcoded number of
100 is the default.
o changing object names from '.' to '_'
o new names in movement matrix "Sex", "Year" and "Season (default = "all"). "From"
and "To" changed to "Origin" and "Destination"
o Implementation of new movement method. Movement array added to 'pop' object in
'setup_om_objects'.
o argument 'para' removed from 'get_om_data'
o argument 'res' removed from 'setup_om_objects'
CHANGES in planetfish VERSION 0.4.0
o Minor release after correction of bugs in 0.3.z series
CHANGES in planetfish VERSION 0.3.5
o bug fix calculation of mod$ssb0 is more robust, previous method was specified
with an integer and comments describing options 1 and 3 were transposed. New
implementation has options "casal", "stoch" and "init_age", see ?get_initial_pop
for details
CHANGES in planetfish VERSION 0.3.4
o new function 'rel_err' calculates relative error from OM/AM scenario runs
CHANGES in planetfish VERSION 0.3.3
o bug fix 'sample.length' was overestimating by one length bin resulting in
biomass being over-estimated in CASAL assessment
CHANGES in planetfish VERSION 0.3.2
o bug fix fleet[[ff]]$landings.n array not indexed by sex in 'run_annual_om'
o bug fix SSB by sex not allocating correctly to mod$ssb in 'run_annual_om'
o 'run_complete_casal_assessment' now checks mpd.dat and output.log exist before
trying to delete, previously a warning was generated when these files did not exist
CHANGES in planetfish VERSION 0.3.1
o numerous bug fixes to new functions in version 0.3.0 (don't use version 0.3.0)
o intern now an argument of 'run_casal_pointest' and functions that call it. Setting
intern=FALSE sends CASAL output to R console, can be useful for debugging
o bug fix, length data now used in CASAL assessment (catchlen_N), was using age
data (catchage_N)
o Sample sizes for the catch and length data in the CASAL assessment moved to
the Fish object in 'get_casal_para'
CHANGES in planetfish VERSION 0.3.0
o minor doc updates passes CHECK
o new functions 'om_control', 'om_study', 'om_biol', 'om_movement',
'om_fisheries', 'om_sampling', 'am_study', 'am_fisheries', 'am_seqence',
'am_movement', 'am_recruit', 'am_biol', 'am_sampling', 'am_tags', 'am_est',
'am_out_print', 'am_out_quants' and 'am_natage' provide an alternative to
'get_om_data', 'get_casal_para' and 'get_casal_data'. These functions specify
parameters within function arguments.
o removal of redundant om$move_rules from get_casal_para
CHANGES in planetfish VERSION 0.2.0
o Tagging data implemented as dataframe instead of multiple arrays
CHANGES in planetfish VERSION 0.1.3
o additional removing of redundant comments
CHANGES in planetfish VERSION 0.1.2
o removing batch file implementation of CASAL assessment
o some minor bug fixes (see git repo is interested)
o removing redundant comments, see original planetfish if interested
in these comments
CHANGES in planetfish VERSION 0.1.1
o Functions updated and documented
o Unused functions removed
CHANGES in planetfish VERSION 0.0.1
o An empty package to convert the planetfish scripts to a package