August 2017 Commit Log

Number of Commits:
363
Number of Active Developers:
4
sbu062 2017-08-31 12:41

doc: small fix

5 lines of code changed in 2 files:

sbu062 2017-08-31 12:37 Rev.: 5094

doc: warning renders wrongly

3 lines of code changed in 1 file:

sbu062 2017-08-31 12:35 Rev.: 5093

(behaviour_select_optimal): the procedure is now ready, small fix doc

5 lines of code changed in 1 file:

sbu062 2017-08-31 12:29 Rev.: 5092

(behaviour_select_optimal): final part, return control after execution of behaviour unit, final check and logging, the procedure is now ready

22 lines of code changed in 1 file:

sbu062 2017-08-31 12:29 Rev.: 5091

(behaviour_select_optimal): final part, test conditions done, doc on them done

13 lines of code changed in 1 file:

sbu062 2017-08-31 12:29 Rev.: 5090

(behaviour_select_optimal): final part, doing doc for conditions

6 lines of code changed in 1 file:

sbu062 2017-08-31 12:29 Rev.: 5089

(behaviour_select_optimal): final part, select action and execute

109 lines of code changed in 1 file:

sbu062 2017-08-31 12:29 Rev.: 5088

(is_minval): functions and generic interface

18 lines of code changed in 1 file:

sbu062 2017-08-31 12:29 Rev.: 5087

(behaviour_select_optimal): started minimisation part, skeleton for (is_minval), so far just copied from (is_maxval)

107 lines of code changed in 1 file:

sbu062 2017-08-31 10:30 Rev.: 5086

(behaviour_select_optimal): fix name, must be _select

4 lines of code changed in 1 file:

sbu062 2017-08-31 10:30 Rev.: 5085

(behaviour_select_optimal): standardised interfaces, second internal parameter 'selected'

40 lines of code changed in 1 file:

sbu062 2017-08-31 10:00 Rev.: 5084

(behaviour_select_optimal): standardised interfaces, use not 'expected_gos' first internal parameter

56 lines of code changed in 1 file:

sbu062 2017-08-31 09:40 Rev.: 5083

doc: did notes on lower scope procedures in (behaviour_select_optimal)

16 lines of code changed in 1 file:

sbu062 2017-08-31 09:27 Rev.: 5082

doc: started notes on higher scope procedure (behaviour_select_optimal)

3 lines of code changed in 1 file:

sbu062 2017-08-31 09:27 Rev.: 5081

doc: notes on the procedure scope

18 lines of code changed in 1 file:

sbu062 2017-08-31 09:19 Rev.: 5080

(go_up_step): reformatted doc, set intent

9 lines of code changed in 1 file:

sbu062 2017-08-31 09:19 Rev.: 5079

(migrate_select) and (go_down_select): reformatted doc, set intent

15 lines of code changed in 1 file:

sbu062 2017-08-31 09:19 Rev.: 5078

(approach_consp_select): reformatted doc, set intent

8 lines of code changed in 1 file:

sbu062 2017-08-31 09:04 Rev.: 5077

(escape_dart_select): reformatted doc, set intent

8 lines of code changed in 1 file:

sbu062 2017-08-31 09:04 Rev.: 5076

(freeze_select): reformatted doc, set intent

11 lines of code changed in 1 file:

sbu062 2017-08-31 09:04 Rev.: 5075

(walk_random_select): reformatted doc, set intent

15 lines of code changed in 1 file:

sbu062 2017-08-31 09:04 Rev.: 5074

(eat_food_select): reformatted doc, set intent, also deleted obsolete init's in higher order procedure

18 lines of code changed in 1 file:

sbu062 2017-08-31 08:40 Rev.: 5073

(behaviour_select_optimal): go_up part moved to inner subroutines

61 lines of code changed in 1 file:

sbu062 2017-08-31 08:40 Rev.: 5072

(behaviour_select_optimal): go_down part moved to inner subroutines

45 lines of code changed in 1 file:

sbu062 2017-08-31 08:40 Rev.: 5071

(behaviour_select_optimal): migrate part moved to inner subroutines

63 lines of code changed in 1 file:

sbu062 2017-08-31 08:40 Rev.: 5070

(behaviour_select_optimal): approach conspecifics part moved to inner subroutines

56 lines of code changed in 1 file:

sbu062 2017-08-31 08:40 Rev.: 5069

(behaviour_select_optimal): escape part moved to inner subroutines

74 lines of code changed in 1 file:

sbu062 2017-08-31 08:40 Rev.: 5068

(behaviour_select_optimal): walks and freezing parts moved to inner subroutines

57 lines of code changed in 1 file:

sbu062 2017-08-31 06:33 Rev.: 5067

(behaviour_select_optimal): reproduction doc fixed

2 lines of code changed in 1 file:

sbu062 2017-08-31 06:33 Rev.: 5066

(behaviour_select_optimal): reproduction part finally moved into included subroutine (reproduce_select)

21 lines of code changed in 1 file:

sbu062 2017-08-31 06:33 Rev.: 5065

(behaviour_select_optimal): continue skeleton, food selection part finally moved into included subroutine (eat_food_select)

5 lines of code changed in 1 file:

sbu062 2017-08-31 06:07 Rev.: 5064

(behaviour_select_optimal): continue skeleton, copied food selection part into included subroutine (eat_food_select)

43 lines of code changed in 1 file:

sbu062 2017-08-30 20:15 Rev.: 5063

(behaviour_select_optimal): continue skeleton, selection part done

18 lines of code changed in 1 file:

sbu062 2017-08-30 20:15 Rev.: 5062

(behaviour_select_optimal): continue skeleton, just copied down for up

30 lines of code changed in 1 file:

sbu062 2017-08-30 20:14 Rev.: 5061

(behaviour_select_optimal): continue skeleton

33 lines of code changed in 1 file:

sbu062 2017-08-30 19:51 Rev.: 5060

(behaviour_select_optimal): continue skeleton

31 lines of code changed in 1 file:

sbu062 2017-08-30 19:28 Rev.: 5059

(behaviour_select_optimal): continue skeleton

33 lines of code changed in 1 file:

sbu062 2017-08-30 18:45 Rev.: 5058

(spatial_get_environment_in_pos): small fix comments

6 lines of code changed in 1 file:

sbu062 2017-08-30 18:32 Rev.: 5057

doc: small reformat

2 lines of code changed in 1 file:

sbu062 2017-08-30 18:30 Rev.: 5056

tests: test for (find_environment)

110 lines of code changed in 2 files:

sbu062 2017-08-30 17:05 Rev.: 5055

(spatial_get_environment_in_pos): comment obsolete

6 lines of code changed in 1 file:

sbu062 2017-08-30 17:05 Rev.: 5054

(spatial_get_environment_in_pos): now accepts optional environment/habitat, with default from Global_Habitats_Available

56 lines of code changed in 1 file:

sbu062 2017-08-30 17:05 Rev.: 5053

(behaviour_select_optimal): continue skeleton

24 lines of code changed in 1 file:

sbu062 2017-08-30 15:52

(behaviour_select_optimal): continue skeleton

56 lines of code changed in 2 files:

sbu062 2017-08-30 15:52 Rev.: 5050

(behaviour_select_optimal): continue skeleton, pasted from predator to change in conspecific

43 lines of code changed in 1 file:

sbu062 2017-08-30 14:34 Rev.: 5049

(behaviour_select_optimal): continue skeleton

51 lines of code changed in 1 file:

sbu062 2017-08-30 13:50

(behaviour_select_optimal): continue skeleton

32 lines of code changed in 2 files:

sbu062 2017-08-30 12:43 Rev.: 5046

(behaviour_select_optimal): continue skeleton

42 lines of code changed in 1 file:

sbu062 2017-08-30 11:46

(behaviour_select_optimal): continue skeleton

109 lines of code changed in 2 files:

sbu062 2017-08-30 09:58 Rev.: 5043

doc: updated links

4 lines of code changed in 1 file:

sbu062 2017-08-30 08:41 Rev.: 5042

doc: small fix

1 lines of code changed in 1 file:

sbu062 2017-08-30 08:36 Rev.: 5041

doc: small fix

15 lines of code changed in 1 file:

sbu062 2017-08-30 08:20 Rev.: 5040

doc: fixed global motivation and behaviour scheme

5718 lines of code changed in 4 files:

sbu062 2017-08-29 20:11 Rev.: 5039

doc: small change

2 lines of code changed in 1 file:

sbu062 2017-08-29 20:04 Rev.: 5038

(behaviour_select_optimal): initial skeleton

10 lines of code changed in 1 file:

sbu062 2017-08-29 19:35 Rev.: 5037

doc: small fix

1 lines of code changed in 1 file:

sbu062 2017-08-29 17:54 Rev.: 5036

doc: fix arrow

521 lines of code changed in 3 files:

sbu062 2017-08-29 17:49 Rev.: 5035

doc: fix header text

15 lines of code changed in 1 file:

sbu062 2017-08-29 17:38 Rev.: 5034

doc: more info on complex links, updated scheme

7975 lines of code changed in 4 files:

sbu062 2017-08-29 16:58 Rev.: 5033

doc: updated header text on behaviour structure

23 lines of code changed in 1 file:

sbu062 2017-08-29 16:27 Rev.: 5032

doc: fix header text

3 lines of code changed in 1 file:

sbu062 2017-08-29 16:19 Rev.: 5031

doc: fix names of behaviours

4749 lines of code changed in 3 files:

sbu062 2017-08-29 16:11 Rev.: 5030

doc: include behaviour construction diagram

3 lines of code changed in 1 file:

sbu062 2017-08-29 16:07 Rev.: 5029

doc: behaviour class diagram

18691 lines of code changed in 3 files:

sbu062 2017-08-29 15:01

doc: updated header doc on behaviour

12 lines of code changed in 2 files:

sbu062 2017-08-29 14:50 Rev.: 5026

doc: rewrote intro doc to behaviour class

31 lines of code changed in 1 file:

sbu062 2017-08-29 14:32 Rev.: 5025

doc: fix tite

1 lines of code changed in 1 file:

sbu062 2017-08-29 14:28 Rev.: 5024

doc: delete noninformative warnings

0 lines of code changed in 1 file:

sbu062 2017-08-29 14:25 Rev.: 5023

(behaviour_do_go_up): done, with public interface

29 lines of code changed in 1 file:

sbu062 2017-08-29 14:25 Rev.: 5022

(behaviour_do_go_down): done, with public interface

35 lines of code changed in 1 file:

sbu062 2017-08-29 14:25 Rev.: 5021

(behaviour_do_migrate): ready now

14 lines of code changed in 1 file:

sbu062 2017-08-29 09:20 Rev.: 5020

doc: title obsolete

0 lines of code changed in 1 file:

sbu062 2017-08-29 09:17 Rev.: 5019

doc: fix tag was broken

1 lines of code changed in 1 file:

sbu062 2017-08-29 09:16 Rev.: 5018

(behaviour_do_migrate): initial skeleton; fix doc on (behaviour_do_approach)

14 lines of code changed in 1 file:

sbu062 2017-08-29 09:09 Rev.: 5017

(behaviour_do_approach) fix doc levels

10 lines of code changed in 1 file:

sbu062 2017-08-29 09:00 Rev.: 5016

(behaviour_do_approach) docs done, procedure is now finished

24 lines of code changed in 1 file:

cje012 2017-08-29 08:33 Rev.: 5015

Added mean calculations for environment and mortality data given length and mortality type for individual mortality plots for those cases when there is no change in length from a timestep to the next, as it ruins the plots.

12 lines of code changed in 1 file:

cje012 2017-08-29 07:40 Rev.: 5014

Changed length_max to forward_length_max in forward. This was done to avoid weird behaciours when the individuals are close to reaching max length.

6 lines of code changed in 1 file:

cje012 2017-08-29 07:38 Rev.: 5013

Added new parameter forward_length_max to be able to run backward longer than forward to avoid weird behaviours when they are close to max length. Also changed the parameter values, to reflect what we have discovered to be the best parameter values for now.

7 lines of code changed in 1 file:

sbu062 2017-08-28 20:14 Rev.: 5012

default offset equals tolerance high

2 lines of code changed in 1 file:

sbu062 2017-08-28 20:09 Rev.: 5011

(behaviour_do_approach) named block

4 lines of code changed in 1 file:

sbu062 2017-08-28 20:04 Rev.: 5010

(behaviour_do_approach) continue skeleton

61 lines of code changed in 1 file:

sbu062 2017-08-28 20:04 Rev.: 5009

(approach_do_execute): bug fix, target object is mandatory, not optional

1 lines of code changed in 1 file:

sbu062 2017-08-28 20:04 Rev.: 5008

(behaviour_do_approach) initial skeleton

18 lines of code changed in 1 file:

sbu062 2017-08-28 19:23 Rev.: 5007

doc: small fix

0 lines of code changed in 1 file:

sbu062 2017-08-28 19:23 Rev.: 5006

(behaviour_do_escape_dart): notes, procedure mainly ready

11 lines of code changed in 1 file:

sbu062 2017-08-28 18:54 Rev.: 5005

doc: links one subsection

3 lines of code changed in 1 file:

sbu062 2017-08-28 18:43 Rev.: 5004

doc: small fix

4 lines of code changed in 1 file:

sbu062 2017-08-28 14:54 Rev.: 5003

(behaviour_do_escape_dart): skeleton

28 lines of code changed in 1 file:

sbu062 2017-08-28 14:42 Rev.: 5002

(behaviour_do_freeze): done

15 lines of code changed in 1 file:

sbu062 2017-08-28 14:42 Rev.: 5001

(behaviour_do_freeze): initial skeleton

10 lines of code changed in 1 file:

sbu062 2017-08-28 14:13 Rev.: 5000

deleted unused var

1 lines of code changed in 1 file:

sbu062 2017-08-28 14:13 Rev.: 4999

(behaviour_do_walk): the (execute) method for random walk ready now, small doc fixes

41 lines of code changed in 1 file:

sbu062 2017-08-28 14:13 Rev.: 4998

(do_walk): add to skeleton

15 lines of code changed in 1 file:

sbu062 2017-08-28 14:13 Rev.: 4997

doc: small addition

6 lines of code changed in 1 file:

sbu062 2017-08-28 14:13 Rev.: 4996

(do_walk) skeleton

5 lines of code changed in 1 file:

sbu062 2017-08-28 14:13 Rev.: 4995

renamed (do_eat_food_item), all behaviours execute methods should start from 'do_'

6 lines of code changed in 1 file:

cje012 2017-08-28 12:58 Rev.: 4994

R_categories and reserves_max is now saved as they were in the begynning of the first timestep in forward. Because of this reserves_max is now calculated before reserves in the initial calculations for the individuals in forwards.

15 lines of code changed in 1 file:

sbu062 2017-08-28 12:58 Rev.: 4993

doc: small fix

2 lines of code changed in 1 file:

sbu062 2017-08-28 12:42 Rev.: 4992

doc: small fix

2 lines of code changed in 1 file:

sbu062 2017-08-28 12:38 Rev.: 4991

doc. small fix

13 lines of code changed in 1 file:

sbu062 2017-08-28 12:28 Rev.: 4990

if block names

7 lines of code changed in 1 file:

sbu062 2017-08-28 12:28 Rev.: 4989

doc: small change

5 lines of code changed in 1 file:

sbu062 2017-08-28 11:48 Rev.: 4988

(walk_random_do_this): predator risk for long walks based on hope function

100 lines of code changed in 1 file:

sbu062 2017-08-28 11:48 Rev.: 4987

review zero: use high tolerance value instead of zero in (walk_random_do_this)

9 lines of code changed in 1 file:

sbu062 2017-08-27 13:23 Rev.: 4986

tests: test for .approx.

51 lines of code changed in 1 file:

sbu062 2017-08-27 08:29 Rev.: 4985

logged value

1 lines of code changed in 1 file:

sbu062 2017-08-27 08:23 Rev.: 4984

tolerance logged

3 lines of code changed in 1 file:

sbu062 2017-08-27 08:18 Rev.: 4983

doc: small fix

5 lines of code changed in 1 file:

sbu062 2017-08-27 08:13 Rev.: 4982

doc: on tolerance/epsilon

25 lines of code changed in 1 file:

sbu062 2017-08-27 08:12 Rev.: 4981

now use the standard defined TOLERANCE_HIGH_DEF in formulas not local constant

3 lines of code changed in 1 file:

sbu062 2017-08-27 08:12 Rev.: 4980

separate high tolerance tolerance_high_def for low precision, standard epsilon

18 lines of code changed in 1 file:

sbu062 2017-08-27 08:12 Rev.: 4979

tolerance_def now tolerance_low parameters, need separate high tolerance tolerance_high_def

21 lines of code changed in 1 file:

sbu062 2017-08-26 11:55

doc: more cleanups

4 lines of code changed in 2 files:

sbu062 2017-08-26 11:45

doc: more cleanups

3 lines of code changed in 2 files:

sbu062 2017-08-26 11:39

doc: more cleanups

10 lines of code changed in 2 files:

sbu062 2017-08-26 11:34 Rev.: 4972

doc: more cleanups

5 lines of code changed in 1 file:

sbu062 2017-08-26 11:27

doc: more cleanups

27 lines of code changed in 3 files:

sbu062 2017-08-26 11:18

doc: more cleanups

26 lines of code changed in 2 files:

sbu062 2017-08-26 11:11 Rev.: 4966

doc: more cleanups, markdown subtitles don't render well

12 lines of code changed in 1 file:

sbu062 2017-08-26 11:07 Rev.: 4965

doc: more cleanups

29 lines of code changed in 1 file:

sbu062 2017-08-26 10:57 Rev.: 4964

cleanup visual range backend: fixed constan precision, use .req. operator

60 lines of code changed in 1 file:

sbu062 2017-08-26 10:11 Rev.: 4963

.appr. still confusing, better .approx.

12 lines of code changed in 1 file:

sbu062 2017-08-25 23:42 Rev.: 4962

tag prefix for error, small fix note

3 lines of code changed in 1 file:

sbu062 2017-08-25 22:46 Rev.: 4961

(srgetr): more formal computation of tolerance

2 lines of code changed in 1 file:

sbu062 2017-08-25 22:30 Rev.: 4960

doc: small fix

2 lines of code changed in 1 file:

sbu062 2017-08-25 22:20 Rev.: 4959

rename shorter

12 lines of code changed in 1 file:

sbu062 2017-08-25 22:10 Rev.: 4958

added approximate equality operator

90 lines of code changed in 1 file:

sbu062 2017-08-25 13:48 Rev.: 4957

doc: small fix

1 lines of code changed in 1 file:

sbu062 2017-08-25 13:36 Rev.: 4956

debug: debug code for (consp_select)

25 lines of code changed in 1 file:

cje012 2017-08-25 11:44 Rev.: 4955

Added different calculations for dR before the part of the code that calculates the change of reaching max length, to fit the different interpolation types for reserves.

16 lines of code changed in 1 file:

sbu062 2017-08-25 11:41 Rev.: 4954

debug: debug code for (join)/(unjoin) deleted

0 lines of code changed in 1 file:

sbu062 2017-08-25 11:41 Rev.: 4953

tests: small change

3 lines of code changed in 1 file:

sbu062 2017-08-25 11:41 Rev.: 4952

debug: disabled all csv writing in debug code

11 lines of code changed in 1 file:

sbu062 2017-08-25 11:41 Rev.: 4951

doc: small

1 lines of code changed in 1 file:

sbu062 2017-08-25 09:21 Rev.: 4950

doc: small

1 lines of code changed in 1 file:

sbu062 2017-08-25 08:04 Rev.: 4949

doc: more notes on global habitats array

6 lines of code changed in 1 file:

sbu062 2017-08-25 07:58 Rev.: 4948

doc: small fix

1 lines of code changed in 1 file:

sbu062 2017-08-25 07:54 Rev.: 4947

doc: added intro text on environment stucture

5 lines of code changed in 1 file:

sbu062 2017-08-25 07:47 Rev.: 4946

doc: added ref to debug mode, the tag is @ref intro_debug_mode

71 lines of code changed in 1 file:

sbu062 2017-08-25 07:25 Rev.: 4945

doc: added intro text on environment stucture

8 lines of code changed in 1 file:

sbu062 2017-08-25 07:04 Rev.: 4944

tests: separated list-based and array-based tests for (join) and (unjoin)

266 lines of code changed in 1 file:

sbu062 2017-08-24 22:53

doc: small fixes

6 lines of code changed in 2 files:

sbu062 2017-08-24 22:45 Rev.: 4941

doc: small fixes

13 lines of code changed in 1 file:

sbu062 2017-08-24 22:45 Rev.: 4940

doc: code example from unit tests for Global_Habitats_Available, comments on debug code

31 lines of code changed in 1 file:

sbu062 2017-08-24 22:30 Rev.: 4939

debug code: assemble, join, unjoin, disassemble procedures in a row, tests ok with gnu and intel, including parallel

1 lines of code changed in 1 file:

sbu062 2017-08-24 22:30 Rev.: 4938

debug code: added call to assemble procedure

3 lines of code changed in 1 file:

sbu062 2017-08-24 22:29 Rev.: 4937

fix debug code, Global_Habitats_Available with four elements

14 lines of code changed in 1 file:

sbu062 2017-08-24 22:04 Rev.: 4936

tests: deleted all explicit tests altogether, from now on only a single global array of habitat objects Global_Habitats_Available can be used

1 lines of code changed in 1 file:

sbu062 2017-08-24 22:04 Rev.: 4935

IMPORTANT: deleted all explicit habitat array; segmentation faults seem difficult to overcom with multiple huge arrays and optional parameter transfers, give up so far; safer to use old lists of habitats/food resource objects; Global_Habitats_Available is the only global array: implicit procedures retained as global public object doesn't cause segmentation faults; implicit tests passed

62 lines of code changed in 2 files:

sbu062 2017-08-24 21:26 Rev.: 4934

tests: fix array size

4 lines of code changed in 1 file:

sbu062 2017-08-24 21:19 Rev.: 4933

tests: disable explicit tests

44 lines of code changed in 1 file:

sbu062 2017-08-24 21:19 Rev.: 4932

deleted unused vars

3 lines of code changed in 1 file:

sbu062 2017-08-24 21:19 Rev.: 4931

tests: join unjoin implicit only, explicit disabled

13 lines of code changed in 1 file:

sbu062 2017-08-24 21:19 Rev.: 4930

(global_habitats_disassemble_implicit) habitats intent out; debug code deleted in explicit; (global_habitats_assemble) habitats intent in

23 lines of code changed in 1 file:

sbu062 2017-08-24 21:19 Rev.: 4929

(food_resources_update_back_global_object_explicit): use %number_food_items rather than size intrinsic

1 lines of code changed in 1 file:

sbu062 2017-08-24 21:19 Rev.: 4928

(disassemble): added explicit and implicit versions separately

302 lines of code changed in 1 file:

sbu062 2017-08-24 21:18 Rev.: 4927

debug code for (join) and (unjoin) directly from the unit tests

124 lines of code changed in 1 file:

sbu062 2017-08-24 21:18 Rev.: 4926

(food_resources_collapse_global_object_explicit): fixed the COPY_FOODS loop in explicit (join) procedure, added inner loop: ifort does not breake now; debug code for explicit global array

13 lines of code changed in 1 file:

sbu062 2017-08-24 21:18 Rev.: 4925

(food_resources_collapse_global_object_implicit): small cleanup

1 lines of code changed in 1 file:

sbu062 2017-08-24 21:18 Rev.: 4924

(food_resources_collapse_global_object_implicit): fixed segmentation fault with ifort, it does not seem to work filling a huge array piecewise with multiple subarray slices, gfortran wasnt broken. debug code deleted

10 lines of code changed in 1 file:

sbu062 2017-08-24 21:18 Rev.: 4923

(food_resources_collapse_global_object_implicit): ifort does not accept array slices in COPY_FOODS loop, but works with an extra inner loop: this is a transitory drbug commit

16 lines of code changed in 1 file:

sbu062 2017-08-24 13:44 Rev.: 4922

reimplemented both implicit and explicit versions to (join)

34 lines of code changed in 1 file:

sbu062 2017-08-24 13:44 Rev.: 4921

tests: test implicit join unjoin; explicit does not pass tests, disabled

63 lines of code changed in 1 file:

sbu062 2017-08-24 13:44 Rev.: 4920

skeleton for a separate implicit (join) procedure

126 lines of code changed in 1 file:

sbu062 2017-08-24 13:44 Rev.: 4919

debug code adapted for testing implicit (unjoin)

5 lines of code changed in 1 file:

sbu062 2017-08-24 13:44 Rev.: 4918

(unjoin) procedure: reformat code for both explicit and implicit versions

12 lines of code changed in 1 file:

sbu062 2017-08-24 13:44 Rev.: 4917

had to implement two components of (unjoin) method as huge local allocatable copies of optional arrays cannot be passed back resulting in segmentation fault and "double free or corruption (!prev)" with ifort, probably memory allocation issue, ulimit unlimited didn't solve this

114 lines of code changed in 1 file:

sbu062 2017-08-24 13:44 Rev.: 4916

fix allocation of temporary arrays in (food_resources_collapse_global_object) and (food_resources_update_back_global_object); added user-defined source array in (global_habitats_disassemble); debug code

59 lines of code changed in 1 file:

sbu062 2017-08-23 16:09 Rev.: 4915

sall change

1 lines of code changed in 1 file:

sbu062 2017-08-23 15:19 Rev.: 4914

(global_habitats_disassemble_loc): obsolete

0 lines of code changed in 1 file:

sbu062 2017-08-23 15:19 Rev.: 4913

doc: obsolete comment

6 lines of code changed in 1 file:

sbu062 2017-08-23 13:26 Rev.: 4912

tests: added tests for unjoining, failed so far waiting for (unjoin) method

25 lines of code changed in 1 file:

sbu062 2017-08-23 13:26 Rev.: 4911

tests: raised timeouts

1 lines of code changed in 1 file:

sbu062 2017-08-23 13:26 Rev.: 4910

doc: added doc for interfaces to (assemble) and (disassemble)

18 lines of code changed in 1 file:

sbu062 2017-08-23 13:26 Rev.: 4909

(assemble) method for the global array of habitat objects

318 lines of code changed in 1 file:

sbu062 2017-08-23 13:26 Rev.: 4908

(disassemble) method for the global array of habitat objects

277 lines of code changed in 1 file:

sbu062 2017-08-23 10:51 Rev.: 4907

tests: initial tests skeleton for unjoining, now just copy of jpining code

273 lines of code changed in 1 file:

sbu062 2017-08-23 10:51 Rev.: 4906

global interface (unjoin)

4 lines of code changed in 1 file:

sbu062 2017-08-23 10:43 Rev.: 4905

(food_resources_update_back_global_object): loops transformed to parallel computation with do concurrent

2 lines of code changed in 1 file:

sbu062 2017-08-23 10:43 Rev.: 4904

(food_resources_update_back_global_object): reformat long line

3 lines of code changed in 1 file:

sbu062 2017-08-23 10:43 Rev.: 4903

(food_resources_update_back_global_object): the sum of all previous resource sizes in the array now calculated inline with implied loop and sum over array

5 lines of code changed in 1 file:

sbu062 2017-08-23 10:43 Rev.: 4902

(food_resources_update_back_global_object): fix wrong index

1 lines of code changed in 1 file:

sbu062 2017-08-23 10:43 Rev.: 4901

(food_resources_update_back_global_object): globally calculated index, non-incremental, will be safe for parallel calculations

8 lines of code changed in 1 file:

sbu062 2017-08-23 09:44 Rev.: 4900

(food_resources_update_back_global_object): fix wrong index

1 lines of code changed in 1 file:

sbu062 2017-08-23 09:44 Rev.: 4899

(food_resources_update_back_global_object): optional resources_in

22 lines of code changed in 1 file:

sbu062 2017-08-23 09:44 Rev.: 4898

ignore errors in makefiles due to non-essential and possibly unavailable pfunit unit tests frmwrk

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sbu062 2017-08-23 09:44 Rev.: 4897

(food_resources_update_back_global_object): initial implementation of unjoin method for array-based global object

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sbu062 2017-08-23 08:12 Rev.: 4896

added delete temp files in pfunit, small changes

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sbu062 2017-08-22 21:54 Rev.: 4895

doc fix example code

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sbu062 2017-08-22 21:49 Rev.: 4894

doc: forgot tags

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sbu062 2017-08-22 21:44 Rev.: 4893

added unit tests target

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sbu062 2017-08-22 21:27 Rev.: 4892

tests: fixed and completed tests for joining food resources procs

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sbu062 2017-08-22 21:27 Rev.: 4891

tests: initial tests for subarrays for joining food resources procs

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sbu062 2017-08-22 17:46 Rev.: 4890

tests: rearranges unit tests, individual test suites for each module

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sbu062 2017-08-22 17:46 Rev.: 4889

test: join food resources

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sbu062 2017-08-22 13:29

test: unit tests for joining food resources

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sbu062 2017-08-22 12:35 Rev.: 4886

(food_resources_collapse_global_boject): interface name (join)

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sbu062 2017-08-22 12:28 Rev.: 4885

(food_resources_collapse_global_boject): implemented food resource arrays procedure not using the .cat. operators

69 lines of code changed in 1 file:

sbu062 2017-08-22 12:28 Rev.: 4884

automatic allocation and reallocation of objects arrays does not work in gfortran 4.8.4, internal compiler error report here

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sbu062 2017-08-22 09:57 Rev.: 4883

implemented array concatenation procedures and operators .cat. for intrinsic types, spatial and spatial_moving; also .catloc. to concatenate location component only for spatial class objects; (food_resource_locate_3d) is pure. (food_resources_collapse_global_boject): skeleton - WARNING: does not build due to compiler bug in gfortran 4.8.4

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cje012 2017-08-21 13:26 Rev.: 4882

Removed unused code and comments. Wrote som functions to avoid equal plotting scripts and added plots for everything against length

79 lines of code changed in 1 file:

cje012 2017-08-18 14:15 Rev.: 4881

Fixed how the growth groups are assigned, Now uses tidyverse.

45 lines of code changed in 1 file:

tla051 2017-08-18 06:20 Rev.: 4880

natural mortality included

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cje012 2017-08-17 07:26 Rev.: 4879

Minor correction to in mortality plot function; base_size=16

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tla051 2017-08-17 06:09 Rev.: 4878

compare qsw0 with NASA model output

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tla051 2017-08-17 06:08 Rev.: 4877

plot zoom on a short time frame with hourly resolution

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tla051 2017-08-17 06:08 Rev.: 4876

updated with a switch to log plots

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tla051 2017-08-17 06:07 Rev.: 4875

plots the forward part of the models

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tla051 2017-08-17 06:06 Rev.: 4874

adopted to accept 4d arrays

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tla051 2017-08-17 06:05 Rev.: 4873

qsw0() fully re-integrated, code cleaned

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sbu062 2017-08-17 04:48 Rev.: 4872

doc: fixed broken vertical text (convert to curve); added source odg files for gos and attention

12739 lines of code changed in 4 files:

cje012 2017-08-16 13:41 Rev.: 4871

Big update with many changes: title.forward is no longer the title of the forward plots but is a small ID-tag on the top of each plot. Added limits for R_cat. Corrected error where NA ended up as a character. Changes one of the plots for hormonelevels with length and reserves, and hormonelevel as a colour. Big changes in the mortality plots; it now plots the mean for all individuals, for the different growth_speed groups and for chosen individuals.

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sbu062 2017-08-16 13:25 Rev.: 4870

doc: small change

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doc: small change comment on zero

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doc: small addition

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sbu062 2017-08-16 11:07 Rev.: 4864

EPSILON_LOC sets the tolerance limit for the default .feq. operator

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sbu062 2017-08-16 07:05 Rev.: 4863

merged from dev

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sbu062 2017-08-15 18:05 Rev.: 4862

larger tolerance values checking non-zero CVs

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sbu062 2017-08-15 17:53 Rev.: 4861

doc: small change

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doc: small addition, long integer

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doc: example values computed on x86_64.

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sbu062 2017-08-15 17:37 Rev.: 4858

doc: fix zero param

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sbu062 2017-08-15 16:41 Rev.: 4857

doc: subsubsubsections

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sbu062 2017-08-15 15:43 Rev.: 4856

doc: more notes on tolerance

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doc: typo

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doc: example parameters showing order of magnitude

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sbu062 2017-08-15 15:21 Rev.: 4853

added long

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print basic constants to log at init startup

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sbu062 2017-08-15 15:20 Rev.: 4851

test: epsilon is big

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doc: more notes

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test: small change

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doc: notes on tiny value and tolerance

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sbu062 2017-08-15 14:38 Rev.: 4847

TINY_HRP precision model fixed

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sbu062 2017-08-15 14:38 Rev.: 4846

test: renamed tiny param avoid conflict with global

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sbu062 2017-08-15 14:38 Rev.: 4845

(float_equal): redefined default safe tolerance value using global parameters

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(is_near_zero): redefined default safe tolerance value usinf global parameters; fix (is_maxval)

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sbu062 2017-08-15 14:37 Rev.: 4843

(is_maxval): redefined tolerance calc; added tiny parameter

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sbu062 2017-08-15 14:37 Rev.: 4842

(is_maxval): use global default tolerance parameter

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sbu062 2017-08-15 14:37 Rev.: 4841

added default tolerance parameter; fixed TINY_FACTOR precision; use the same tolerance in (is_maxval)

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sbu062 2017-08-15 12:33 Rev.: 4840

doc: typo

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sbu062 2017-08-15 11:52 Rev.: 4838

doc: added general computational notes

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doc: typo

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doc: added general computational notes

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doc: added general computational notes

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sbu062 2017-08-15 11:27 Rev.: 4834

doc: started adding general computational notes

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sbu062 2017-08-15 00:44 Rev.: 4833

tests: add error output

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tests: parameter more flexible for error output

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sbu062 2017-08-15 00:33 Rev.: 4831

tests: unit tests for float point approximate equality routines

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sbu062 2017-08-14 23:40

doc:small fixes

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sbu062 2017-08-14 23:36 Rev.: 4828

separated parameters render better in doxy

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sbu062 2017-08-14 23:29 Rev.: 4827

doc:small fixes

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sbu062 2017-08-14 23:24 Rev.: 4826

doc: more comments on arbitrary epsilon tolerance for float equality

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sbu062 2017-08-14 23:14 Rev.: 4825

doc: doxy cleanup, verbatim tag to code tag, in some cases

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sbu062 2017-08-14 22:34 Rev.: 4824

single interface operator for srp and hrp

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sbu062 2017-08-14 22:26 Rev.: 4823

deleted obsolete unused variables

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sbu062 2017-08-14 22:09 Rev.: 4822

doc: small comment fix

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sbu062 2017-08-14 22:09 Rev.: 4821

now use float point approximate equality operator .feq. for real equality in a few other cases; fix comments

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sbu062 2017-08-14 20:19 Rev.: 4820

now use float point approximate equality operator .feq. for real equality in some cases (these cases equate float with preassigned MISSING value code and not really important although safer); reformatted some reals leading zeros

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sbu062 2017-08-14 20:19 Rev.: 4819

rename operator to float equal .feq., seems a more logical name

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sbu062 2017-08-14 20:02 Rev.: 4818

temporarily disable generic patterns for HEDTOOLS as building with ifort got broken under Code:Blocks for some reason, RANDOM does not seem to make/use include

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sbu062 2017-08-14 20:02 Rev.: 4817

added makedile as prerequisite

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sbu062 2017-08-14 18:45 Rev.: 4816

implemented all procedures and generic interfaces and interface operators for real/float comparisons

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sbu062 2017-08-14 15:54 Rev.: 4815

tests: more tests for evaluation

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sbu062 2017-08-14 15:54 Rev.: 4814

tests: increased timeout

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sbu062 2017-08-14 15:54 Rev.: 4813

(is_near_zero): func to check if near-zero

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cje012 2017-08-11 09:29 Rev.: 4812

Changed the staching order of the area plot for the individual mortality facors.

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cje012 2017-08-10 12:22 Rev.: 4811

Fixed error that messed up the y-axis in the mortality plots.

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cje012 2017-08-10 11:29 Rev.: 4810

Minor change.

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cje012 2017-08-10 11:24 Rev.: 4809

Fixed error in the last commit, regarding the environmental line that was added to the mortality plots.

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cje012 2017-08-10 10:24 Rev.: 4808

Added a line for environment to the mortality plots.

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cje012 2017-08-10 09:03 Rev.: 4807

Fixed small error/spelling mistake that caused some figures to fail.

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cje012 2017-08-10 08:33 Rev.: 4806

Added new comments that explain the use of m1 and m2.

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cje012 2017-08-09 11:46 Rev.: 4805

Added histograms for dead individuals with length and timestep when they died. Added mortalityplots for single individuals. Commented out summarys as they take to long when running all at once. Also added length and hormone limits to the top of the script for more consistent plots for different simulations.

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sbu062 2017-08-08 09:47 Rev.: 4804

merge readme changes from dev branch

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cje012 2017-08-07 13:10 Rev.: 4803

Added call to fixed seed in the start of the forward simulation again, as well as before the backwards calculations. To ensure that you get the same result if you choose to only run forward.

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sbu062 2017-08-06 11:50 Rev.: 4802

web: update ifort builds, download links

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sbu062 2017-08-05 10:39 Rev.: 4801

web: reformat

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sbu062 2017-08-05 05:49 Rev.: 4800

doc: template

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sbu062 2017-08-05 05:44 Rev.: 4799

doc: link to binary builds

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sbu062 2017-08-05 05:39 Rev.: 4798

web: added tag

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sbu062 2017-08-05 05:30

web: updated ifort builds windows

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sbu062 2017-08-05 05:10 Rev.: 4795

testing only

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sbu062 2017-08-05 05:00 Rev.: 4794

merged latest changes from dev

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sbu062 2017-08-05 04:57 Rev.: 4793

update templates

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sbu062 2017-08-05 04:46 Rev.: 4792

merged latest changes from dev

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sbu062 2017-08-05 04:30 Rev.: 4791

web: update links to latest libhedutils bilds ifort on windows

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sbu062 2017-08-04 18:31 Rev.: 4790

doc: fix link

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doc: fix readme, build details

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doc: readme, build details

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doc: note on segmentation and stack size on non-windows platforms

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doc: loop fix

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doc: fix note on fixing stack overflow with ifort

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doc: note on fixing stack overflow with ifort

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sbu062 2017-08-04 07:02 Rev.: 4782

notes on PROCESSOR_ARCHITEW6432 on Windows WOW64

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sbu062 2017-08-04 07:02 Rev.: 4781

link to msdn

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sbu062 2017-08-03 22:22 Rev.: 4780

determine platform and hardware type for zip file

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sbu062 2017-08-03 22:03 Rev.: 4779

new binary versions of HEDTOOLS

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sbu062 2017-08-03 20:54 Rev.: 4778

adjustable 'del' command on Windows, platform uname note

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sbu062 2017-08-03 20:54 Rev.: 4777

fixed OBJ for multiple sources, generic pattern rules, autogenerate list of modules, user-adjustable command for rm on windows

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sbu062 2017-08-03 20:54 Rev.: 4776

autogenerate obj's, pdb enable

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doc: typo

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doc: list all deps

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doc: small change

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cje012 2017-08-03 13:09 Rev.: 4771

Added if statements for different kinds of calculations of dR before interpolation in forward.

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cje012 2017-08-03 13:09 Rev.: 4770

Added option for different kinds of calculations of intR before interpolation in forward.

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cje012 2017-08-03 13:07 Rev.: 4769

Added new simple plots (base R) for hormone levels against reserves, reserve categories and length.

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sbu062 2017-08-03 11:57

doc: small change

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doc: static doxy links in readme, dynamic don't render in bitbucket

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doc: readme added

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doc: title

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doc: shorter project name

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doc: project name, not coincide with top level section

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doc: title shoule nor coincide with doxy project name

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doc: global name and brief

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doc: getting started

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doc: refs

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doc: Makefile in readme

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sbu062 2017-08-02 17:08 Rev.: 4738

updated from latest HEDG2

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doc: no filters, add c style doxy tags

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doc: input filters only for makefile

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doc: disable input filters for makefile

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doc: enable input filters for makefile

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sbu062 2017-08-02 14:35 Rev.: 4733

doc: added main Makefile to doxygen documentation

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cje012 2017-08-02 13:54 Rev.: 4732

Fixed small error where the code said 0 this is now changed to 0._RP

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cje012 2017-08-02 11:09 Rev.: 4731

Fixed another error.

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cje012 2017-08-02 11:06 Rev.: 4730

Fixed small error, introduced in last version.

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doc: more info

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doc: lowercase

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doc: version is top level section

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sbu062 2017-08-02 10:45

small reformat

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cje012 2017-08-02 10:40 Rev.: 4724

Made it so individuals die if reserves is <= 0 not only when reserves < 0

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sbu062 2017-08-01 19:46 Rev.: 4723

delete pdb debugging files on Windows on distclean

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sbu062 2017-08-01 19:42 Rev.: 4722

huge stack size on the Windows platform, stack overflow resolved; added extended note

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sbu062 2017-08-01 19:23 Rev.: 4721

windows debug build opts, stack size increased

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windows debug build opts

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more notes

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more notes

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user-adjustable command for file delete on Windows: native 'del' may not work due to Cygwin

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all .mod files also deleted at distclean: the_evolution is not in autogenerated list

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autogenerate the list of modules by grepping source; autogenerate list of hedtools object fies; lowercase function

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cje012 2017-08-01 12:32 Rev.: 4714

Fixed small error.

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cje012 2017-08-01 12:31 Rev.: 4713

Added fixed random seed before backward part of code, and minor changes to comments.

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cje012 2017-08-01 12:21 Rev.: 4712

Commented out max_intake, added variable for fixed seed for random number generation.

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nzlcj 2017-08-01 11:57 Rev.: 4711

Coded together. Changed how strategies are looked up in forward part - now using next lowest reserves category to determine strategy. Removed extra intake constraint.

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cje012 2017-08-01 09:34 Rev.: 4710

Removed code that is not in use any more.

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sbu062 2017-08-01 00:32 Rev.: 4709

generic pattern rules for building HEDTOOLS

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July 2017 »

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