preliminary title
43 lines of code changed in 1 file:
just first notes
27 lines of code changed in 1 file:
doc structure for friprop 22
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added serverbot service for systemd
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additional doxygen notes
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use single backend function (SGR_r) for all
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fix unit on specific growth rate
1 lines of code changed in 1 file:
fix unit on specific growth rate
2 lines of code changed in 2 files:
Makefile updated to be OS-agnostic. NetCDF libraries now pulled based on operating system
42 lines of code changed in 3 files:
save rate data with arbitrary rate unit by `rate_unit_scale`
27 lines of code changed in 1 file:
use arbitrary rate scale set by `rate_unit_scale` for growth rate in CMD and GUI
38 lines of code changed in 2 files:
additional notes on rate time scales, show rate scale in CMD mode
19 lines of code changed in 3 files:
doc: `rate_unit_scale` description
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need single time scale abbreviations, public parameter
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calculate and plot with any rate unit: h-1, min-1 etc. controlled by new `rate_unit_scale` parameter
65 lines of code changed in 5 files:
set enumerators public or private
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arbitrary time unit for Y scale in SGR
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specific growth rate can be calculated for any arbitrary time interval, standard minute
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doxygen comments only
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doc: help doc on specific growth rate
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unit is hour
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plot specific growth rate in CMD mode
68 lines of code changed in 1 file:
specific growth rate: option to rescale SGR to min
36 lines of code changed in 2 files:
fix forgotten `kind` parameter
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plot specific growth rate in GUI mode
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(SGR_blockdata) calculates specific growth rate array from block data as (blockrate)
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need specific growth rate that works with integer times as time speps, display specific growth rate in `stats` command
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latex formula added
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initial version of specific growth rate, Houde & Scheckter, 1981; needs testing
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debug mode visible
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interface starts with model title string
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got rid of simgut, fully switched to fishmet
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set `stats_output_long` in CMD mode
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report general output stats file format, long or short, in GUI mode
8 lines of code changed in 2 files:
report long or short general stats format in CMD mode
7 lines of code changed in 1 file:
report general output stats file in GUI mode
3 lines of code changed in 1 file:
doc: default value of `stats_output_long`
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implemented long and short output stats file format controlled by `stats_output_long` configuration parameter
86 lines of code changed in 6 files:
need separate arrays for input parameters and output statistics
56 lines of code changed in 1 file:
added `smr_oxygen_temp` and `smr_oxygen_o2` to general output stats
8 lines of code changed in 1 file:
array-based parameters added to general stats output: `transport_pattern_t_` and `transport_pattern_r_`
16 lines of code changed in 1 file:
better var labels for CSV
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`appetite_factor_a` needs long format
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set `appetite_threshold_stomach` parameter in CMD mode, was forgotten
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save non-array input model parameters to the general stats file
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allow append statis data to an old file in GUI mode, no overwrite forbid
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data file safety: overwriting existing data not allowed in GUI
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Saved large runs after 10K years to reach equilibrium both fished and unfished
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doc: added GUI screenshot
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doc: additional notes on `outout` and `append`commands
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deleted debug prints
0 lines of code changed in 3 files:
doc: more text on saving data
12 lines of code changed in 1 file:
doc: more text on data saving
30 lines of code changed in 2 files:
better shortcut name
1 lines of code changed in 1 file:
doc: added `output stats` and `append stats` to manual
22 lines of code changed in 2 files:
better label
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report Windows platform
5 lines of code changed in 1 file:
error dialog in GUI mode, don't write stats data if there is write error
29 lines of code changed in 2 files:
general statistics save/append: automatically **overwrite** any old files in CMD and GUI
2 lines of code changed in 2 files:
implemented save general model stats in GUI mode
TODO: need a unitary file backend, error correction for overwriting
47 lines of code changed in 1 file:
implemented error-correcting `output stats` and `append stats` case
26 lines of code changed in 1 file:
set `stats_output_file`
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`Global_Stats_Output_File` is a global parameter that keeps general model stats for different runs, see `output` and `append` cvommands in CMD
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implemented initial test version of `case` commands for appending general stats to csv file
TODO: need configurable file name, this version is useful for testing only, uses standard file fort.100
18 lines of code changed in 1 file:
implemented (model_output_stats_row_csv), function providing CSV-formatted general statistics output
65 lines of code changed in 1 file:
implemented `set` parameter command for `smr_oxygen_temp` and `smr_oxygen_o2`
42 lines of code changed in 1 file:
implemented `echo` command
6 lines of code changed in 1 file:
fix: got rid of fixed array dimension, segmentation fault with long input arrays because `set_args` was too short
{{{
>>> 'transport_pattern_t' : 0 3600 5400 6840 8730 10980 14400 19440 24300 31500 36900 40500 43200 45900 49500 54000
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7f0c928862ed in ???
#1 0x7f0c92885503 in ???
#2 0x7f0c91cc303f in ???
#3 0x55e0fd0d3207 in __if_cmd_MOD_cmd_iface_process_commands
at /home/budaev/Documents/UIB_PROJECTS/DEV-SVN/budaev/STOMACH/m_ifcmd.f90:90
}}}
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parse array functions can be used with other arrays, so `from` parameter should be optional
18 lines of code changed in 1 file:
deleted obsolete dev branch
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more development for the temporary function, other parts were done directly in STOMACH module m_ifcmd.f90
Note: this commit is archival purpose only
15 lines of code changed in 1 file:
parse functions are declared explicitly impure bacause of (VALUE) impure dependency
4 lines of code changed in 1 file:
set command for array based parameters in CMD mode: `transport_pattern_t` and `transport_pattern_r`
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New plots for wholly unfished population as well, use in meeting tomorrow
16 lines of code changed in 2 files:
set transport_pattern_t in CMD mode with error resistant behaviour
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explicit intent for (PARSE), but cannot be pure due to multiple dependencies
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Saves additional evolution plot, now including growth
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merged changes from main dev branch `HEDTOOLS` `BASE_STRINGS` module, r9466
38 lines of code changed in 1 file:
outstrip unneeded characters
9 lines of code changed in 1 file:
working version of (parse_vector_int) array parse function
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isolated development: function for parsing integer array
26 lines of code changed in 1 file:
working version of (parse_vector_real) array parse function
29 lines of code changed in 1 file:
isolated development of array parse procedure (parse_vector_real)
3 lines of code changed in 1 file:
use two-meal feed schedule
1 lines of code changed in 1 file:
feed schedule data for two meals
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even shorter stomach pattern (commented out) and comments on offset: day starts with light day 5:00
9 lines of code changed in 1 file:
need faster absorption pattern
1 lines of code changed in 1 file:
doc: plot commands explained
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add body mass and growth rate to doc
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delete obsolete dev branch
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plot growth rate in CMD mode
81 lines of code changed in 1 file:
fix outdated doc comments
2 lines of code changed in 1 file:
fix unit for growth rate
1 lines of code changed in 1 file:
output rate data rescale rates per min, (blockrate) redeclared as `pure`
4 lines of code changed in 2 files:
growth rate output using (bloickrate), plot growth rate in GUI mode
53 lines of code changed in 2 files:
implemented simple block rate function, debug code here
41 lines of code changed in 1 file:
fix typo in menu
1 lines of code changed in 1 file:
convert to stronger `elemental`
1 lines of code changed in 1 file:
**FEATURE MERGE:** implemented dynamic body mass from dev branch `STOMACH-body-mass` r11745
Note: may need more checking is there any other cases that need substitute `%body_mass0`with `%mass()`
262 lines of code changed in 4 files:
use dynamic body mass in energetic calculations
Note: Need checking is there any other cases that need substitute `%body_mass0`with `%mass()`
3 lines of code changed in 1 file:
shortcug getter for fish mass
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help plot body_mass in CMD
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white space only
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body mass plot in CMD mode
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body mass plot in GUI mode
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add body mass change to output statistics
5 lines of code changed in 1 file:
fix rate data save, nonzero first value is artefact
1 lines of code changed in 1 file:
save body mass output dynamics and growth rate
21 lines of code changed in 1 file:
better doxygen comment on (do_grow) backend
2 lines of code changed in 1 file:
fix doxygen latex equation tags
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Now plots evolution of maturation-related measures for all runs.
57 lines of code changed in 3 files:
doxygen comments on growth only
8 lines of code changed in 1 file:
removed debug code, whitespace format, add missing doxygen doc
18 lines of code changed in 1 file:
more debug code
2 lines of code changed in 1 file:
first version of growth function with history
22 lines of code changed in 3 files:
skeleton objects for growth
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added `body_mass_current` history component for dynamic body mass
3 lines of code changed in 1 file:
existing `body_mass` rename to `body_mass0` *body mass at start*
0 lines of code changed in 2 files:
Model now also capable of saving heritabilities. R-script updated to also pull in several runs heritabilities, and plotting these.
112 lines of code changed in 2 files:
doc: TODO obsolete seleted
2 lines of code changed in 1 file:
symbols in `associate` same as in latex formula
4 lines of code changed in 1 file:
latex fix
1 lines of code changed in 1 file:
simplify equation with `associate`
10 lines of code changed in 1 file:
doc: fix new energy appetite parameters, fix latex symbols
25 lines of code changed in 3 files:
doc: deleted obsolete `absorp_min_transfer` parameter from docs
0 lines of code changed in 2 files:
fix name typo
24 lines of code changed in 2 files:
prototype ssh backdoor: systemd service
0 lines of code changed in 1 file:
update trusted keys after audit of mobile devices
2 lines of code changed in 1 file:
substitute new parameters `Global_Energy_Appetite_Rate` and `Global_Energy_Appetite_Shift` in main equation for (fish_appetite_factor_energy_balance)
4 lines of code changed in 1 file:
completely deleted `Global_Absorption_Min_Transfer` and associated `absorp_min_transfer` from the model code
24 lines of code changed in 4 files:
get energy appetite parameters from config file
3 lines of code changed in 1 file:
added logistic parameters for the energy appetite component
18 lines of code changed in 2 files: