smaller figs in pdf
4 lines of code changed in 1 file:
small fix on fix
1 lines of code changed in 1 file:
cleanup doxygen
4 lines of code changed in 1 file:
micro fix class separator
2 lines of code changed in 1 file:
doxygen cleanup links in (eat_food_item_do_this)
12 lines of code changed in 1 file:
fixed doxygen links
4 lines of code changed in 1 file:
doxygen fix subtitles in (eat_food_item_do_this)
8 lines of code changed in 1 file:
increased to 400 px
8 lines of code changed in 1 file:
reduced to 300 px
8 lines of code changed in 1 file:
fixed plot
1566 lines of code changed in 3 files:
module of universal subroutines e.g. matrix_to_binary_real8, which saves fortran array to .bin file
33 lines of code changed in 1 file:
deleted image from non-horiz
0 lines of code changed in 1 file:
added image for below/above food perception
680 lines of code changed in 3 files:
added doxygen image for below/above
16 lines of code changed in 1 file:
'implementation details' subtitle added
6 lines of code changed in 1 file:
links to generic interfaces in doxygen
12 lines of code changed in 1 file:
generic interface (food_mass_above) done
24 lines of code changed in 1 file:
generic interface (food_mass_below) done
13 lines of code changed in 1 file:
Started fixing code for the stochastic environemnt so it can be run in fortran, still not finished.
60 lines of code changed in 1 file:
Updated Makefile to include functions.f90
1 lines of code changed in 1 file:
Added parameters used for the stochastic environment.
7 lines of code changed in 1 file:
done (perception_food_mass_above_horiz_calculate)
79 lines of code changed in 1 file:
New module with functions and parameters used for calculations.
57 lines of code changed in 1 file:
small changes in comments
5 lines of code changed in 1 file:
started implementation of horizon-based 'above' and 'below' functions for food item mass: (perception_food_mass_below_horiz_calculate) done
68 lines of code changed in 1 file:
generic interfaces to all 'items' functions (food_items_below) and (food_items_above)
28 lines of code changed in 1 file:
implemented the horizon-based 'above' function (perception_food_items_above_horiz_calculate)
44 lines of code changed in 1 file:
implemented logical function (is_within) and spatial perception (perception_food_items_below_horiz_calculate), an analogue of 'below' but within specific horizon
125 lines of code changed in 1 file:
Folder file adding binary files to current folder.
1 lines of code changed in 1 file:
small fix doxygen
5 lines of code changed in 1 file:
changelog updated
90 lines of code changed in 1 file:
food perception above / below declared elemental
6 lines of code changed in 1 file:
micro fix formatting
2 lines of code changed in 1 file:
small fix doxygen
2 lines of code changed in 1 file:
fixed wrong interface name for (food_mass_above)
1 lines of code changed in 1 file:
implemented (food_mass_below) and (food_mass_above), fixed, use now a simplr 'get_mass' method rather than size
59 lines of code changed in 1 file:
included lat_loop; organized parameter for subroutine input in table like structure; included "feed" and "pred" array
145 lines of code changed in 1 file:
moved all parameters to made code, adapted in a way that subroutine can be used both for feeding and predation of mesopelagic fish, through change of "role" input statement
52 lines of code changed in 1 file:
Added svn tags.
8 lines of code changed in 4 files:
Adding new folder with stochastic hormone model and modules
682 lines of code changed in 4 files:
Coded together - environmental stochasticity. Added general equations and calculation of probabilities - integration in code is next.
73 lines of code changed in 1 file:
Coded together - environmental stochasticity. Added some parameters.
1 lines of code changed in 1 file:
implemented (perception_food_mass_below_calculate)
40 lines of code changed in 1 file:
refactored (food_items_below) and (..._above) procedures, moved into PERCEPTION class; also had to redeclare (has_food) as elemental
99 lines of code changed in 1 file:
init method for (go_down_depth_init_zero) fixed
3 lines of code changed in 1 file:
added subtitle
1 lines of code changed in 1 file:
another fix on fix
1 lines of code changed in 1 file:
fix of fix
0 lines of code changed in 1 file:
minor fix on usage log_dbg
12 lines of code changed in 1 file:
another small fix formatting
1 lines of code changed in 1 file:
Added possibility to make 2D real arrays.
29 lines of code changed in 1 file:
Coded together. Included example of table of parameters for visual subroutine.
23 lines of code changed in 1 file:
Trying to reshape arrays into dataframes, but I have not been sucessful so far.
51 lines of code changed in 1 file:
Coded together. Looked at code, restructured loops, moved huge predation rate array to shrink it, coded example of loop counters that can be trasnferred to matlab/R.
125 lines of code changed in 1 file:
additional small fixes in (system_init)
6 lines of code changed in 1 file:
small fix doxygen titles in (system_init)
2 lines of code changed in 1 file:
reordered predation loop structure to make it run faster
11 lines of code changed in 1 file:
references to user-defined operators for doxygen docs
8 lines of code changed in 1 file:
small fix
1 lines of code changed in 1 file:
added interface operators .within. and .contains. for spatial objects
21 lines of code changed in 1 file:
operators don't render links, deleted
2 lines of code changed in 1 file:
fix doxygen docs for (is_above) and (is_below) procedures
8 lines of code changed in 1 file:
implemented user operators for spatial objects .above. and .below.
71 lines of code changed in 1 file:
fix links to implementation procedures spatial
3 lines of code changed in 1 file:
minot fixes comments
6 lines of code changed in 1 file:
debug code
3 lines of code changed in 1 file:
included loop structure to write predation rate matrix in main program, added timing statement at the start and end of main program, muted qsw0 and SURLIGH subroutines, preliminary parametrization of predation calculation
467 lines of code changed in 4 files:
debug code
3 lines of code changed in 1 file:
implemented logical indicator functions (is_below) and (is_above)
40 lines of code changed in 1 file:
started implementation of the GO_DOWN_DEPTH class objects
42 lines of code changed in 1 file:
added arbitrary cost exponent in (condition_cost_swimming_burst) as an optional dummy parameter
28 lines of code changed in 1 file:
local parameters do not seem to allow linking in in doxygen, returned non-linked uppercase
1 lines of code changed in 1 file:
test local param link in doxygen
1 lines of code changed in 1 file:
small changes, added link to DOI URI scheme
10 lines of code changed in 1 file:
small reformat debug logger
3 lines of code changed in 1 file:
small reformat logger calls
9 lines of code changed in 1 file:
doxygen links fixed in (food_item_capture_probability_calc)
14 lines of code changed in 1 file:
very small fix
1 lines of code changed in 1 file:
finished refactoring (reproduce_do_probability_reproduction_calc): deleted obsolete interpolation grid parameters, final probability of reproduction limited by baseline value rather than 1.0 in 'within' function, fixed/added doxgen comments
25 lines of code changed in 1 file:
Changed i individuals into n invididuals to make it easier to understand.
43 lines of code changed in 2 files:
refactor in (reproduce_do_probability_reproduction_calc) : debug plot only when same-sex nonzero, added logging
44 lines of code changed in 1 file:
fix interpolation parameter ordinatre for (reproduce_do_probability_reproduction_calc)
3 lines of code changed in 1 file:
refactor (reproduce_do_probability_reproduction_calc) to ensure prob. reproduction = p0 when no same-sex in perception
21 lines of code changed in 1 file:
fix dosy formulas
3 lines of code changed in 1 file:
updated plot
2306 lines of code changed in 2 files:
fix doxygen formula
1 lines of code changed in 1 file:
in (reproduce_do_probability_reproduction_calc) limit prob. of reproduction within 0.0 and 1.0
5 lines of code changed in 1 file:
Modified variable names from "larval" (Fouzai 2015) to meaningful names for mesopelagic project
11 lines of code changed in 1 file:
added doc for grid parameters defining probability of reproduction
8 lines of code changed in 1 file:
in probability of reproduction fixed range strictly within 0.0 and 1.0, added comments on parameters
21 lines of code changed in 1 file:
edited comments, wrote preliminary subroutines:
(1) import_light subroutine imports light data generated in R from .bin file
(2) visual_range subroutine calculates visual range, adopted from Fouzai N, Opdal AF, Jørgensen C, Fiksen Ø. 2015. Marine Ecology-Progress Series
(3) visual_predation subroutine calculates predation risk, adopted from Fouzai N, Opdal AF, Jørgensen C, Fiksen Ø. 2015. Marine Ecology-Progress Series
476 lines of code changed in 6 files:
Coded together. Rewrote outline/structure for northern barriers code, based on old version of other model. Included sample subroutine.
96 lines of code changed in 1 file:
Minor changes.
7 lines of code changed in 1 file:
First upload of code for summer barriers in mesopelagic fish. Code copied from draft life history model, to be modified.
101 lines of code changed in 1 file:
0 lines of code changed in 6 files:
creating several projects in mesopelagic fodler for Tom.
0 lines of code changed in 1 file:
Added some lines to check when individuals die, reach max length or if they did not reach max length during t_max.
3 lines of code changed in 1 file:
Rewrote j_max into i_max and j into i, to make it easier to understand.
39 lines of code changed in 1 file:
Changed j_max into i_max to make it easier to understand.
1 lines of code changed in 1 file:
0 lines of code changed in 2 files:
Updated to print some values while running.
1 lines of code changed in 1 file:
Reformatted some comments to make the module more Camilla-readable
4 lines of code changed in 1 file:
Reformatted som comments and some code to make it more Camilla-readable
166 lines of code changed in 1 file:
Removed code for debuggin reserves as it is no longer in use.
0 lines of code changed in 1 file:
Removed surplus_after_growth and iftest as they are no longer in use.
1 lines of code changed in 1 file:
Removed alternate growth function.
2 lines of code changed in 1 file:
Added description for how to compare old and new versions of a file, both in meld and with regular diff.
6 lines of code changed in 1 file:
fix style as @nSee doesn't render correctly
154 lines of code changed in 1 file:
changed doxygen reference link to interface implementation (use See...)
154 lines of code changed in 1 file:
continued documenting interfaces in the individual and population modules
42 lines of code changed in 1 file:
changelog updated
72 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: all motivation states
8 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: all neurobio module so far
7 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: behaviours
32 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: reproduce class
20 lines of code changed in 1 file:
small fix
2 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: GOS main
6 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: appraisal class
10 lines of code changed in 1 file:
small fix
4 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: emotional memory
23 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: motivatio class
22 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: root motivation class
35 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: perceptual components of motivation
13 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: PERCEPTION class
57 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: perceptual memory stack
17 lines of code changed in 1 file:
continued documenting interfaces in THE_NEUROBIO: perception objects
110 lines of code changed in 1 file:
document interfaces in SPATIAL_PERCEPT_COMPONENT
4 lines of code changed in 1 file:
started fixing doxygen comments in the_neurobio: percept_food interfaces done
17 lines of code changed in 1 file:
documented in-class interfaces in THE_CONDITION
32 lines of code changed in 1 file:
documented interfaces in THE_HORMONES
14 lines of code changed in 1 file:
started documenting interfaces for the_hormones
2 lines of code changed in 1 file:
documented interfaces in the_genonme
32 lines of code changed in 1 file:
documented all interfaces in THE_ENVIRONMENT using the style
43 lines of code changed in 1 file:
added doxygen interface documentation style
7 lines of code changed in 1 file:
use shorter interface doc for timer
5 lines of code changed in 1 file:
shorter doxygen interface doc style
25 lines of code changed in 1 file:
doxygen uinterfaces for spatial types
25 lines of code changed in 1 file:
doxygen fix functions in commondata
4 lines of code changed in 1 file:
fix doxygen function ref
1 lines of code changed in 1 file:
doxygen cleanup in commondata, functions references
13 lines of code changed in 1 file:
Replaced with parameter module from trunk.
4 lines of code changed in 1 file:
Replaced with model from trunk
27 lines of code changed in 1 file:
doxygen (parse_svn_version) fixed
10 lines of code changed in 1 file:
fix doxygen comments for plotting procedures
93 lines of code changed in 1 file:
small fix
2 lines of code changed in 1 file:
doxygen comments in (debug_interpolate_plot_save) fixed
27 lines of code changed in 1 file:
merged from branch
33004 lines of code changed in 6 files:
added piece on parallel do concurrent, plus index
26 lines of code changed in 1 file:
doxygen cleanup logger and init
79 lines of code changed in 1 file:
fixed logger formatting in (population_save_data_all_agents_csv)
2 lines of code changed in 1 file:
IS_SCREEN_OUTPUT separately controls stdout; fixes logger for debug test procedure
53 lines of code changed in 1 file:
minor addition, note the neuronal response function in expectancies calculate methods
6 lines of code changed in 1 file:
very small change
4 lines of code changed in 1 file:
added subsections for notable local vars in doxygen
5 lines of code changed in 1 file:
isolated fake perceptions into separate local variables in (reproduce_motivations_expect)
18 lines of code changed in 1 file:
isolated fake perceptions into separate local variables in (eat_food_item_motivations_expect)
43 lines of code changed in 1 file:
changelog updated
124 lines of code changed in 1 file:
refactored (eat_food_item_motivations_expect)and (reproduce_motivations_expect): separated fake perceptions and subjective probabilities into separate local variables; (reproduce_motivations_expect) now update fake energy perception; update now the 'decrement_mass' in (do_this) for 'REPRODUCE' object
115 lines of code changed in 1 file:
separate function (reproduction_cost_unsuccessful_calc); added 'decrement_mass' into reproduction class, so far did only for (init)
68 lines of code changed in 1 file:
small changes from yesterday
9 lines of code changed in 1 file:
another small dix doxygen
2 lines of code changed in 1 file:
another small fix doxygen
7 lines of code changed in 1 file:
another small fix
1 lines of code changed in 1 file:
small fix
4 lines of code changed in 1 file:
fix doxygen for reproduction procedures
14 lines of code changed in 1 file:
further small changes; reproduction cost fix increased to 0.2
5 lines of code changed in 1 file:
minor fix doxygen comments
6 lines of code changed in 1 file:
in (reproduction_cost_energy_dynamic) implemented two low-order functions using full body mass and residual body mass after offspring are subtracted
108 lines of code changed in 1 file: