October 2017 Commit Log

Number of Commits:
427
Number of Active Developers:
2
sbu062 2017-10-31 15:22 Rev.: 6093

(generations_loop_gs): deleted obsolete code SAVE_FOOD_PRE SAVE_FOOD_POST

0 lines of code changed in 1 file:

sbu062 2017-10-31 15:19 Rev.: 6092

run: normal lifecycle, popsize unchanged

2 lines of code changed in 1 file:

sbu062 2017-10-31 15:05 Rev.: 6091

run: run EATONLY with normal population POPSIZE 10000

2 lines of code changed in 1 file:

sbu062 2017-10-31 14:31 Rev.: 6090

output cpuinfo from bio linux host

0 lines of code changed in 1 file:

sbu062 2017-10-31 14:15 Rev.: 6089

rudimentary text

7 lines of code changed in 1 file:

sbu062 2017-10-31 14:12 Rev.: 6088

doc file with description

0 lines of code changed in 1 file:

sbu062 2017-10-31 14:11 Rev.: 6087

benchmarking

0 lines of code changed in 10 files:

sbu062 2017-10-31 08:09

small addition

5 lines of code changed in 2 files:

sbu062 2017-10-31 07:56 Rev.: 6084

doc: small fixes

12 lines of code changed in 1 file:

sbu062 2017-10-31 07:45 Rev.: 6083

doc: small fixes

4 lines of code changed in 1 file:

sbu062 2017-10-30 20:06 Rev.: 6082

documented the environment variable that was added AHA_ZIP_FILES

10 lines of code changed in 2 files:

sbu062 2017-10-30 18:38 Rev.: 6081

delete gzipped data on cleandata

1 lines of code changed in 1 file:

sbu062 2017-10-30 18:38 Rev.: 6080

run: normal popsize 10000

1 lines of code changed in 1 file:

sbu062 2017-10-30 18:36 Rev.: 6079

(system_init): check if data compression is working

52 lines of code changed in 1 file:

sbu062 2017-10-30 18:36 Rev.: 6078

(system_init): environment var AHA_ZIP_FILES now determines if output file compression is enabled

26 lines of code changed in 1 file:

sbu062 2017-10-30 18:36 Rev.: 6077

aded option to compress output csv data files

88 lines of code changed in 1 file:

sbu062 2017-10-30 15:59 Rev.: 6076

run: small popsize 1000

1 lines of code changed in 1 file:

sbu062 2017-10-30 15:59 Rev.: 6075

(population_ga_mutation_rate_adaptive): adaptive mutation rate is now based on number of grown instead of just alive

11 lines of code changed in 1 file:

sbu062 2017-10-30 15:59 Rev.: 6074

(population_ga_mutation_rate_adaptive): renamed n_alive to n_base_point, as different criteria could be used

7 lines of code changed in 1 file:

sbu062 2017-10-30 15:59 Rev.: 6073

(population_ga_mutation_rate_adaptive): more commentson n_alive

7 lines of code changed in 1 file:

sbu062 2017-10-30 15:13 Rev.: 6072

build: added optimization reports for intel

3 lines of code changed in 1 file:

sbu062 2017-10-30 15:13 Rev.: 6071

build: delete intel annotations also in txt on neat

1 lines of code changed in 1 file:

sbu062 2017-10-30 15:13 Rev.: 6070

build: delete html intel annotations at distclean

2 lines of code changed in 1 file:

sbu062 2017-10-30 15:13 Rev.: 6069

build: set machine architecture to native in GNU

1 lines of code changed in 1 file:

sbu062 2017-10-30 15:12 Rev.: 6068

build: vectorization reports on Intel

1 lines of code changed in 1 file:

sbu062 2017-10-30 15:12 Rev.: 6067

build: add annotate for intel, compiler optimisation report in html

2 lines of code changed in 1 file:

sbu062 2017-10-30 08:57 Rev.: 6066

run: normal run with big popsize 10000

3 lines of code changed in 1 file:

sbu062 2017-10-30 08:36 Rev.: 6065

(preevol_steps_adaptive): adaptive steps with progressively reducing complexity, eatonly so far retained

6 lines of code changed in 1 file:

sbu062 2017-10-29 11:47 Rev.: 6064

run: run EATONLY with small population POPSIZE 1000

3 lines of code changed in 1 file:

sbu062 2017-10-29 11:37 Rev.: 6063

added call to (lifecycle_eatonly) for debug, disabled

2 lines of code changed in 1 file:

sbu062 2017-10-29 11:31 Rev.: 6062

doc: fix comments on public interface

4 lines of code changed in 1 file:

sbu062 2017-10-29 11:31 Rev.: 6061

(population_lifecycle_step_eatonly_preevol): generic interface

7 lines of code changed in 1 file:

sbu062 2017-10-29 11:31 Rev.: 6060

(population_lifecycle_step_eatonly_preevol): implemented eat-only procedure

17 lines of code changed in 1 file:

sbu062 2017-10-29 11:31

renamed debug procedure

3 lines of code changed in 2 files:

sbu062 2017-10-29 11:31 Rev.: 6057

(population_lifecycle_step_eatonly_preevol): started implementing eat-only lifecycle, copied base procedure so far

191 lines of code changed in 1 file:

sbu062 2017-10-27 14:06 Rev.: 6056

fix link

1 lines of code changed in 1 file:

sbu062 2017-10-27 14:03 Rev.: 6055

updated links

3 lines of code changed in 1 file:

sbu062 2017-10-27 13:50 Rev.: 6054

use svn

2 lines of code changed in 1 file:

sbu062 2017-10-27 12:57 Rev.: 6053

expliciut links better in pdf

4 lines of code changed in 1 file:

sbu062 2017-10-27 10:24 Rev.: 6052

small fix

5 lines of code changed in 1 file:

sbu062 2017-10-27 09:45

small fix

5 lines of code changed in 2 files:

sbu062 2017-10-27 09:44 Rev.: 6049

different precision benchmark

35 lines of code changed in 1 file:

sbu062 2017-10-27 09:13 Rev.: 6048

run: increased POPSIZE to 10,000

1 lines of code changed in 1 file:

sbu062 2017-10-27 08:44 Rev.: 6047

doc: updated doc comments

9 lines of code changed in 1 file:

sbu062 2017-10-27 08:22 Rev.: 6046

(population_ga_reproduce_max): more stringent criterion for fitness selection, only growing

5 lines of code changed in 1 file:

sbu062 2017-10-27 06:37

small fix

3 lines of code changed in 2 files:

sbu062 2017-10-27 06:36 Rev.: 6043

small fix title

1 lines of code changed in 1 file:

sbu062 2017-10-27 05:20 Rev.: 6042

(population_ga_reproduce_max): strengthened and reduced fitness in selection criterion to eating

2 lines of code changed in 1 file:

sbu062 2017-10-26 21:04 Rev.: 6041

pdf name

1 lines of code changed in 1 file:

sbu062 2017-10-26 20:56

small fix

3 lines of code changed in 2 files:

sbu062 2017-10-26 20:51 Rev.: 6038

add links

5 lines of code changed in 1 file:

sbu062 2017-10-26 20:48 Rev.: 6037

small fix

9 lines of code changed in 1 file:

sbu062 2017-10-26 19:50 Rev.: 6036

typo

1 lines of code changed in 1 file:

sbu062 2017-10-26 19:45 Rev.: 6035

doc: collapse tables

20 lines of code changed in 1 file:

sbu062 2017-10-26 19:37 Rev.: 6034

add numbered TOC to pandoc command

1 lines of code changed in 1 file:

sbu062 2017-10-26 19:32 Rev.: 6033

deleted code, obsolete

0 lines of code changed in 1 file:

sbu062 2017-10-26 19:29 Rev.: 6032

make pdf doc with pandoc

3 lines of code changed in 1 file:

sbu062 2017-10-26 19:11 Rev.: 6031

small fix

1 lines of code changed in 1 file:

sbu062 2017-10-26 18:57 Rev.: 6030

small fixes

3 lines of code changed in 1 file:

sbu062 2017-10-26 18:47 Rev.: 6029

makefile from tests, doesn't include driver

77 lines of code changed in 1 file:

sbu062 2017-10-26 18:41 Rev.: 6028

added csv benchmark

2397 lines of code changed in 3 files:

sbu062 2017-10-26 13:21 Rev.: 6027

get rid of the warning 'target conspecific is undefined', removed to debug messages

6 lines of code changed in 1 file:

sbu062 2017-10-26 12:26 Rev.: 6026

run: increased POPSIZE 6000

1 lines of code changed in 1 file:

sbu062 2017-10-26 12:23 Rev.: 6025

nonrun: reduced proportion reproducing GA_REPRODUCE_PR to 0.05. 0.15 seem to include too many poor guys

2 lines of code changed in 1 file:

sbu062 2017-10-26 11:42 Rev.: 6024

run: increased POPSIZE 6000

1 lines of code changed in 1 file:

sbu062 2017-10-26 11:40 Rev.: 6023

(generation_stats_record_write): fixed extra field in data table

0 lines of code changed in 1 file:

sbu062 2017-10-26 10:21 Rev.: 6022

(generation_stats_record_write): renumbered

102 lines of code changed in 1 file:

sbu062 2017-10-26 10:21 Rev.: 6021

(generation_stats_record_write): added number that were growing

5 lines of code changed in 1 file:

sbu062 2017-10-26 10:06 Rev.: 6020

(generation_stats_record_write): renumbered

104 lines of code changed in 1 file:

sbu062 2017-10-26 10:06 Rev.: 6019

(generation_stats_record_write): added adaptive number of reproducing agents

5 lines of code changed in 1 file:

sbu062 2017-10-26 09:44 Rev.: 6018

doc: small reformat code only

5 lines of code changed in 1 file:

sbu062 2017-10-26 04:29 Rev.: 6017

(fitness_mass_incr_ratio): fix poor items adjustment, should subtract

1 lines of code changed in 1 file:

sbu062 2017-10-25 19:51 Rev.: 6016

(fitness_mass_incr_ratio): add n eaten to fitness in unsuccess agents, they go first when sorted then and contribute to GA elite

1 lines of code changed in 1 file:

sbu062 2017-10-25 19:43 Rev.: 6015

(selection): separate variable for 'ga_reproduce' for readability, also avoids multiple calls to (ga_reproduce_max)

9 lines of code changed in 1 file:

sbu062 2017-10-25 19:43 Rev.: 6014

doc: continued doc for (population_ga_mutation_rate_adaptive)

3 lines of code changed in 1 file:

sbu062 2017-10-25 12:46 Rev.: 6013

added global parameters for adaptive GA

13 lines of code changed in 1 file:

sbu062 2017-10-25 12:32 Rev.: 6012

(population_ga_reproduce_max): smaller minimum elite group

1 lines of code changed in 1 file:

sbu062 2017-10-25 12:16 Rev.: 6011

doc: smaller plot

2882 lines of code changed in 1 file:

sbu062 2017-10-25 12:09 Rev.: 6010

doc: small change

1 lines of code changed in 1 file:

sbu062 2017-10-25 12:09 Rev.: 6009

doc: invoked add adaptive mutation rate plot in doc

6 lines of code changed in 1 file:

sbu062 2017-10-25 12:09 Rev.: 6008

add adaptive mutation rate plot from debug data

3299 lines of code changed in 4 files:

sbu062 2017-10-25 10:44 Rev.: 6007

minor reformat

0 lines of code changed in 1 file:

sbu062 2017-10-25 10:43 Rev.: 6006

(population_ga_mutation_rate_adaptive): fixed wrong order interpolation ordinate array

2 lines of code changed in 1 file:

sbu062 2017-10-25 10:34 Rev.: 6005

(population_ga_mutation_rate_adaptive): debug plot reformat code

2 lines of code changed in 1 file:

sbu062 2017-10-25 10:11 Rev.: 6004

(population_ga_mutation_rate_adaptive): debug plot

14 lines of code changed in 1 file:

sbu062 2017-10-25 10:05 Rev.: 6003

(population_ga_mutation_rate_adaptive): fix wrong pop size, need alive only

5 lines of code changed in 1 file:

sbu062 2017-10-25 09:58 Rev.: 6002

(mate_reproduce): more logging

2 lines of code changed in 1 file:

sbu062 2017-10-25 09:55 Rev.: 6001

(mate_reproduce): refactor adaptive mutation rate; log it

11 lines of code changed in 1 file:

sbu062 2017-10-25 09:15 Rev.: 6000

(generation_stats_record_write): renumber

106 lines of code changed in 1 file:

sbu062 2017-10-25 09:15 Rev.: 5999

(generation_stats_record_write): save adaptive mutation rate

12 lines of code changed in 1 file:

sbu062 2017-10-25 09:01 Rev.: 5998

GENERATIONS_PREEVOL: avoid cycling the main loop if everyone had died

3 lines of code changed in 1 file:

sbu062 2017-10-25 04:37 Rev.: 5997

fix GENERATIONS_PREEVOL stopping rule

1 lines of code changed in 1 file:

sbu062 2017-10-24 18:48 Rev.: 5996

(individual_preevol_fitness_calc): fix fitness code for dead

1 lines of code changed in 1 file:

sbu062 2017-10-24 18:37 Rev.: 5995

(fitness_mass_incr_ratio): fix multiplier

1 lines of code changed in 1 file:

sbu062 2017-10-24 18:06 Rev.: 5994

(fitness_mass_incr_ratio): fix division by zero

1 lines of code changed in 1 file:

sbu062 2017-10-24 18:03 Rev.: 5993

(fitness_mass_incr_ratio): fix multiplier

1 lines of code changed in 1 file:

sbu062 2017-10-24 17:45 Rev.: 5992

(fitness_mass_incr_ratio): restrict fitness to only mass exceeding the birth mass

5 lines of code changed in 1 file:

sbu062 2017-10-24 14:56 Rev.: 5991

SWIMMING_SPEED_COST_BURST: reduced cost of swimming

1 lines of code changed in 1 file:

sbu062 2017-10-24 14:56 Rev.: 5990

(individual_preevol_fitness_calc): fitness function based on mass increment ratio

17 lines of code changed in 1 file:

sbu062 2017-10-24 14:56 Rev.: 5989

Revert svn 5986: fitness based on foodmass rate does not make sense because the whole generation has the same n of steps, and comparison ranking is within the same generation

8 lines of code changed in 1 file:

sbu062 2017-10-24 11:05 Rev.: 5988

added steps parameter to fitness calc calls

11 lines of code changed in 1 file:

sbu062 2017-10-24 10:36 Rev.: 5987

(individual_preevol_fitness_calc): fitness function based on food mass rate per step

35 lines of code changed in 1 file:

sbu062 2017-10-23 23:19 Rev.: 5986

(mate_reproduce): invoked adaptive mutation rate

3 lines of code changed in 1 file:

sbu062 2017-10-23 23:11 Rev.: 5985

(ga_mutat_adaptive): add plot code

1 lines of code changed in 1 file:

sbu062 2017-10-23 23:11 Rev.: 5984

(ga_mutat_adaptive): small fix

1 lines of code changed in 1 file:

sbu062 2017-10-23 23:11 Rev.: 5983

(ga_mutat_adaptive): generic interface for nonparametric adaptive mutation rate: also fix type

11 lines of code changed in 1 file:

sbu062 2017-10-23 23:11 Rev.: 5982

(mutation_rate_adaptive): implements nonparametric adaptive mutation rate

30 lines of code changed in 1 file:

sbu062 2017-10-23 17:00 Rev.: 5981

(individual_preevol_fitness_calc): fitness is switched to stomach mass abs

23 lines of code changed in 1 file:

sbu062 2017-10-23 14:59 Rev.: 5980

(population_save_data_all_agents_csv): renumber

18 lines of code changed in 1 file:

sbu062 2017-10-23 14:59 Rev.: 5979

(population_save_data_all_agents_csv): added cumulative mass of food items eaten

2 lines of code changed in 1 file:

sbu062 2017-10-23 14:49 Rev.: 5978

(generations_loop_preevol): adapted stopping rule for fitness in GENERATIONS_PREEVOL

1 lines of code changed in 1 file:

sbu062 2017-10-23 14:26 Rev.: 5977

(individual_preevol_fitness_calc): fitness is switched to cumulative food mass eaten

20 lines of code changed in 1 file:

sbu062 2017-10-23 14:26 Rev.: 5976

(generations_loop_preevol): renumber after addition of two vars

64 lines of code changed in 1 file:

sbu062 2017-10-23 14:26 Rev.: 5975

added cumulative food mass eatento indicators, save data generation-wise file

28 lines of code changed in 1 file:

sbu062 2017-10-23 10:26 Rev.: 5974

get rid of multiple asterisks, they don't rende in doxygen well

9 lines of code changed in 1 file:

sbu062 2017-10-23 10:13 Rev.: 5973

zipdata file name as macro, print name for possible easy manual operation

5 lines of code changed in 1 file:

sbu062 2017-10-23 09:51 Rev.: 5972

(generations_loop_preevol): adapted stopping rule for fitness in GENERATIONS_PREEVOL

1 lines of code changed in 1 file:

sbu062 2017-10-23 09:48 Rev.: 5971

(individual_preevol_fitness_calc): fitness is switched to stomach ratio, small fixes avoiding division by zero

8 lines of code changed in 1 file:

sbu062 2017-10-23 09:21 Rev.: 5970

(individual_preevol_fitness_calc): now modular fitness function; added fitness based on stomach mass ratio

61 lines of code changed in 1 file:

sbu062 2017-10-22 11:42 Rev.: 5969

doc: deleted unneeeded comment

1 lines of code changed in 1 file:

sbu062 2017-10-22 11:42 Rev.: 5968

made SVN_Version protected, MMDD allocatable, no need to trim mmdd now

28 lines of code changed in 1 file:

sbu062 2017-10-21 18:30 Rev.: 5967

add svn version tag to file names, after mmdd

19 lines of code changed in 1 file:

sbu062 2017-10-21 12:18 Rev.: 5966

(individual_preevol_fitness_calc): increased weights

2 lines of code changed in 1 file:

sbu062 2017-10-21 09:16 Rev.: 5965

target to delete any compressed data

5 lines of code changed in 1 file:

sbu062 2017-10-21 09:07 Rev.: 5964

(individual_preevol_fitness_calc): added weighting by n of foods eaten, to facilitate independent feeding rather than initial birth energy selection

21 lines of code changed in 1 file:

sbu062 2017-10-20 12:52 Rev.: 5963

adapt fig to any specific REPRODUCT_BODY_MASS_OFFSPR_ABSCISSA

802 lines of code changed in 2 files:

sbu062 2017-10-20 12:12 Rev.: 5962

REPRODUCT_BODY_MASS_OFFSPR_ABSCISSA reduced greatly, make reproduction easier

1 lines of code changed in 1 file:

sbu062 2017-10-19 17:23 Rev.: 5961

(lifecycle_preevol): fix forgotten array indexes

6 lines of code changed in 1 file:

sbu062 2017-10-19 15:22 Rev.: 5960

(lifecycle_preevol): doc heads/notes added

6 lines of code changed in 1 file:

sbu062 2017-10-19 15:17 Rev.: 5959

(lifecycle_preevol): init count data to unknown

5 lines of code changed in 1 file:

sbu062 2017-10-19 15:11 Rev.: 5958

(lifecycle_preevol): time-step-wise stats, doc notes added

15 lines of code changed in 1 file:

sbu062 2017-10-19 15:11 Rev.: 5957

(lifecycle_preevol): time-step-wise stats for habitats, save data: procedures ready

34 lines of code changed in 1 file:

sbu062 2017-10-19 15:11 Rev.: 5956

(lifecycle_preevol): time-step-wise stats for habitats

38 lines of code changed in 1 file:

sbu062 2017-10-19 15:11 Rev.: 5955

(lifecycle_preevol): time-step-wise stats for agents

44 lines of code changed in 1 file:

sbu062 2017-10-19 15:11 Rev.: 5954

STATS: new tag for time-step based statistics

1 lines of code changed in 1 file:

sbu062 2017-10-19 13:52 Rev.: 5953

(generations_loop_ga): log mean and sd grid values for birth mortality

13 lines of code changed in 1 file:

sbu062 2017-10-19 12:35 Rev.: 5952

(generations_loop_ga): now use statistical parameters for (mortality_birth) in calculations, parameters lost 'save' attribute

18 lines of code changed in 1 file:

sbu062 2017-10-19 12:35 Rev.: 5951

(generations_loop_ga): defined variables to keep (mortality_birth) parameters from the initial generation

11 lines of code changed in 1 file:

sbu062 2017-10-19 12:09 Rev.: 5950

(lifecycle_preevol): more comments

3 lines of code changed in 1 file:

sbu062 2017-10-19 12:09 Rev.: 5949

(lifecycle_preevol): Forced fixed mean and sd values from generation 1 data

3 lines of code changed in 1 file:

sbu062 2017-10-19 12:09 Rev.: 5948

(population_birth_mortality_init): fix grid arrays

2 lines of code changed in 1 file:

sbu062 2017-10-19 12:09 Rev.: 5947

(population_birth_mortality_init): additional doc notes

41 lines of code changed in 1 file:

sbu062 2017-10-19 10:46 Rev.: 5946

(lifecycle_preevol): now use the (migrate_food_vertical) procedure that works directly on the global array 'Global_Habitats_Available' and doesn't need potentially slow syncing with the habitat objects

11 lines of code changed in 1 file:

sbu062 2017-10-19 10:39 Rev.: 5945

(migrate_vertical) for global array renamed to (migrate_food_vertical); additional notes and examples

54 lines of code changed in 2 files:

sbu062 2017-10-19 09:33 Rev.: 5944

tests: tests for (migrate_vertical)

167 lines of code changed in 1 file:

sbu062 2017-10-19 09:33 Rev.: 5943

(migrate_vertical): implemented procedure that works directly on the global array Global_Habitats_Available

44 lines of code changed in 1 file:

sbu062 2017-10-19 09:33 Rev.: 5942

(lifecycle_preevol): have to add (disassemble) and (assemble) pre post migration to update food resource objects and global array

2 lines of code changed in 1 file:

sbu062 2017-10-19 09:33 Rev.: 5941

(population_birth_mortality_init): added interpolation plots

20 lines of code changed in 1 file:

sbu062 2017-10-19 06:56 Rev.: 5940

(population_birth_mortality_init): implemented optional mean and sd to enforce

25 lines of code changed in 1 file:

sbu062 2017-10-19 06:55 Rev.: 5939

additional pattern

1 lines of code changed in 1 file:

sbu062 2017-10-18 19:02 Rev.: 5938

(population_birth_mortality_init): htintrpl plot command

1 lines of code changed in 1 file:

sbu062 2017-10-18 19:02 Rev.: 5937

now call the population-based selective mortality (mortality_birth) in (lifecycle_preevol)

5 lines of code changed in 1 file:

sbu062 2017-10-18 19:02 Rev.: 5936

(population_birth_mortality_init): small reformat

2 lines of code changed in 1 file:

sbu062 2017-10-18 19:02 Rev.: 5935

(condition_init_genotype): deleted call to individual debug (mortality_birth) method

0 lines of code changed in 1 file:

sbu062 2017-10-18 19:02 Rev.: 5934

(population_birth_mortality_init): birth mortality based on statistical properties methof for population, initial implementation

40 lines of code changed in 1 file:

sbu062 2017-10-18 16:04

doc: fix tags

5 lines of code changed in 2 files:

sbu062 2017-10-18 15:56

doc: fix latex formula tags

3 lines of code changed in 2 files:

sbu062 2017-10-18 15:51 Rev.: 5929

tests: tests for (std_dev) and (average)

29 lines of code changed in 1 file:

sbu062 2017-10-18 15:51 Rev.: 5928

(std_dev): to calculate standard deviation

68 lines of code changed in 1 file:

sbu062 2017-10-18 14:42 Rev.: 5927

doc. small fix

1 lines of code changed in 1 file:

sbu062 2017-10-18 14:41 Rev.: 5926

(birth_mortality_enforce_init_fixed_debug): implements an initial version of fixed birth mortality, nonlinear nonparametric

37 lines of code changed in 1 file:

sbu062 2017-10-18 13:49 Rev.: 5925

(condition_init_genotype): erroneous agents die at start

4 lines of code changed in 1 file:

sbu062 2017-10-18 13:34 Rev.: 5924

(population_save_data_all_agents_csv): added energy at birth

66 lines of code changed in 1 file:

sbu062 2017-10-18 13:21 Rev.: 5923

(generation_stats_record_write): renumbered

84 lines of code changed in 1 file:

sbu062 2017-10-18 13:21 Rev.: 5922

(generation_stats_record_write): added energy at birth

8 lines of code changed in 1 file:

sbu062 2017-10-18 13:21 Rev.: 5921

added energy_birth attribute at CONDITION, init and accessor

19 lines of code changed in 1 file:

sbu062 2017-10-18 12:59 Rev.: 5920

(generation_stats_record_write): renumber

86 lines of code changed in 1 file:

sbu062 2017-10-18 12:59 Rev.: 5919

(generation_stats_record_write): added birth mass and length

14 lines of code changed in 1 file:

sbu062 2017-10-18 12:33 Rev.: 5918

(approach_conspecifics_do_this): tag is now warning

2 lines of code changed in 1 file:

sbu062 2017-10-18 11:02 Rev.: 5917

add zipdata target to compress all the data outputs

6 lines of code changed in 1 file:

sbu062 2017-10-18 10:43 Rev.: 5916

(lifecycle_preevol): disable debug saving of food resource data each time step, too huge data writing

40 lines of code changed in 1 file:

sbu062 2017-10-18 10:43 Rev.: 5915

(generations_loop_ga): fixed data save blocks; SAVE_DATA_FOOD_POST saves food resources data after each generation

22 lines of code changed in 1 file:

sbu062 2017-10-18 10:20 Rev.: 5914

debug: restore is_debug check (lifecycle_preevol), food data saved after each step only in DEBUG mode

2 lines of code changed in 1 file:

sbu062 2017-10-18 10:17 Rev.: 5913

debug: disable is_debug check (lifecycle_preevol) to enable saving food resource data

2 lines of code changed in 1 file:

sbu062 2017-10-18 10:12 Rev.: 5912

minor reformat

2 lines of code changed in 1 file:

sbu062 2017-10-18 09:32 Rev.: 5911

(lifecycle_preevol): fix debug saving of food resource data, save also post step

28 lines of code changed in 1 file:

sbu062 2017-10-18 09:17 Rev.: 5910

(lifecycle_preevol): added a call to (disassemble) to update food resources from global array

7 lines of code changed in 1 file:

sbu062 2017-10-18 09:17 Rev.: 5909

debug: applied patch hg3683 with (disassemble) global habitats array

4 lines of code changed in 1 file:

sbu062 2017-10-18 05:08 Rev.: 5908

code reformat only

20 lines of code changed in 1 file:

sbu062 2017-10-18 05:03 Rev.: 5907

debug: debug code DISABLED, temporarily enabled IS_DEBUG, protect back

1 lines of code changed in 1 file:

sbu062 2017-10-18 05:03 Rev.: 5906

(population_save_data_all_agents_csv): fix nonexisting environment 0 in dead agents after they are nullified

7 lines of code changed in 1 file:

sbu062 2017-10-18 05:03 Rev.: 5905

debug: fix debug code, save food resources after

7 lines of code changed in 1 file:

sbu062 2017-10-18 05:03 Rev.: 5904

debug: debug code only, temporarily enabled IS_DEBUG, non-protect

11 lines of code changed in 1 file:

sbu062 2017-10-18 05:02 Rev.: 5903

debug: (life_cycles_debug_test) check for dead agent in WALKS_BEH

6 lines of code changed in 1 file:

sbu062 2017-10-18 05:02 Rev.: 5902

(eat_food_item_do_execute): fix debugging logs

8 lines of code changed in 1 file:

sbu062 2017-10-17 19:37 Rev.: 5901

doc: small fix

2 lines of code changed in 1 file:

sbu062 2017-10-17 19:33 Rev.: 5900

doc: added small note

6 lines of code changed in 1 file:

sbu062 2017-10-17 19:32 Rev.: 5899

reformat code only

4 lines of code changed in 1 file:

sbu062 2017-10-17 19:32 Rev.: 5898

(trait_init_linear) and (trait_set_linear): generic interfaces

20 lines of code changed in 1 file:

sbu062 2017-10-17 19:32 Rev.: 5897

(trait_init_linear_sum_additive_comps_2genes_r): implemented fully; (trait_set_linear_sum_additive_comps_2genes_r): with intent in

105 lines of code changed in 1 file:

sbu062 2017-10-17 15:15 Rev.: 5896

(trait_init_linear_sum_additive_comps_r): initial skeleton og fixed genotype top phenotype (init) method

105 lines of code changed in 1 file:

sbu062 2017-10-17 12:59 Rev.: 5895

ATTENTION_WEIGHT_ : doc: fix table

14 lines of code changed in 1 file:

sbu062 2017-10-17 12:53 Rev.: 5894

ATTENTION_WEIGHT_ : doc: fix table

14 lines of code changed in 1 file:

sbu062 2017-10-17 12:45 Rev.: 5893

ATTENTION_WEIGHT_ : doc: overall pattern matrix table

19 lines of code changed in 1 file:

sbu062 2017-10-17 12:18 Rev.: 5892

ATTENTION_WEIGHT_ : limit baseline attention weights to create fixed bundles, small fix

1 lines of code changed in 1 file:

sbu062 2017-10-17 12:16 Rev.: 5891

ATTENTION_WEIGHT_ : limit baseline attention weights to create fixed bundles

26 lines of code changed in 1 file:

sbu062 2017-10-17 10:47 Rev.: 5890

(population_ga_reproduce_max): small note on MIN_GA_REPRODUCE

2 lines of code changed in 1 file:

sbu062 2017-10-17 10:47 Rev.: 5889

(population_ga_reproduce_max): reduced minimum limit

1 lines of code changed in 1 file:

sbu062 2017-10-17 09:53 Rev.: 5888

(logger_init): small note on ifort

4 lines of code changed in 1 file:

sbu062 2017-10-17 09:32 Rev.: 5887

(logger_init): hostname reporting disabled so far due to non-standard and not portable code

4 lines of code changed in 1 file:

sbu062 2017-10-17 09:32 Rev.: 5886

(logger_init): report hostname

27 lines of code changed in 1 file:

sbu062 2017-10-17 04:49 Rev.: 5885

doc: added note

3 lines of code changed in 1 file:

sbu062 2017-10-17 04:49 Rev.: 5884

(repfac_perception_get_object): refactor to use (reproductive_factor)

5 lines of code changed in 1 file:

sbu062 2017-10-17 04:49 Rev.: 5883

(generation_stats_record_write): use (reproductive_factor) in generation-wise output

2 lines of code changed in 1 file:

sbu062 2017-10-17 04:49 Rev.: 5882

(reproductive_factor): method to calculate the reproductive factor

26 lines of code changed in 1 file:

sbu062 2017-10-16 19:23 Rev.: 5881

doc: typo fix

1 lines of code changed in 1 file:

sbu062 2017-10-16 18:09 Rev.: 5880

doc: fix note span

3 lines of code changed in 1 file:

sbu062 2017-10-16 18:01 Rev.: 5879

(generation_stats_record_write): doc: long names

48 lines of code changed in 1 file:

sbu062 2017-10-16 12:48 Rev.: 5878

(generations_loop_ga): renumbered

30 lines of code changed in 1 file:

cje012 2017-10-16 12:41 Rev.: 5877

Added new plots: mortality ~ O2_used/O2max_THF, SMR_std&SMR_THF~THF, O2max_THF&O2_used~THF, growth~GHF, conversion_costs~GHF, foraging~OXF, foraging_cost~OXF and intake~OXF.

99 lines of code changed in 1 file:

sbu062 2017-10-16 12:36 Rev.: 5876

(generations_loop_ga): added n of food items available to generation-wise stats output file

9 lines of code changed in 1 file:

sbu062 2017-10-16 11:54 Rev.: 5875

adjusted perception and motivation history size to HISTORY_SIZE_SPATIAL

2 lines of code changed in 1 file:

sbu062 2017-10-14 12:29 Rev.: 5874

(generation_stats_record_write): delete white space only

0 lines of code changed in 1 file:

sbu062 2017-10-14 12:29 Rev.: 5873

(generation_stats_record_write): added number alive in safe and dangerous habitats to generation-wise outputs

16 lines of code changed in 1 file:

sbu062 2017-10-14 12:29 Rev.: 5872

(generation_stats_record_write): small note

2 lines of code changed in 1 file:

sbu062 2017-10-14 12:07 Rev.: 5871

(individual_create_zero): avoid using genome objects, this should be a full empty / missing value constructor

23 lines of code changed in 1 file:

sbu062 2017-10-14 10:45 Rev.: 5870

(generation_stats_record_write): renumbered

88 lines of code changed in 1 file:

sbu062 2017-10-14 10:45 Rev.: 5869

(generation_stats_record_write): added preevol_steps to generation-wise stats output

6 lines of code changed in 1 file:

sbu062 2017-10-14 10:45 Rev.: 5868

implemented (dies) method for 'appraisal', overriding 'individual_genome'; added lists in each override doc

55 lines of code changed in 1 file:

sbu062 2017-10-14 10:45 Rev.: 5867

additional note on (dies)

3 lines of code changed in 1 file:

sbu062 2017-10-14 10:45 Rev.: 5866

implemented (dies) method for 'gos_global', overriding 'individual_genome'; added lists in each override doc

69 lines of code changed in 1 file:

sbu062 2017-10-14 10:45 Rev.: 5865

implemented (dies) method for 'individual_agent', overriding 'individual_genome'

35 lines of code changed in 1 file:

sbu062 2017-10-14 08:48 Rev.: 5864

(generation_stats_record_write): added foods eaten to outputs for alive

24 lines of code changed in 1 file:

sbu062 2017-10-14 07:49 Rev.: 5863

(generation_stats_record_write): added probability of reproduction output with separate loop

17 lines of code changed in 1 file:

sbu062 2017-10-14 07:49 Rev.: 5862

(generation_stats_record_write): blocks alive by sexes, reproductive factor output

16 lines of code changed in 1 file:

sbu062 2017-10-14 07:49 Rev.: 5861

(generation_stats_record_write): initial addition of alive values, simple ALIVE block

53 lines of code changed in 1 file:

sbu062 2017-10-14 07:49 Rev.: 5860

(generation_stats_record_write): small change prepare for big alive data block

4 lines of code changed in 1 file:

sbu062 2017-10-14 07:48 Rev.: 5859

(generation_stats_record_write): added fitness in all, should separate all values for alive

15 lines of code changed in 1 file:

sbu062 2017-10-13 18:04 Rev.: 5858

doc: small fix

2 lines of code changed in 1 file:

sbu062 2017-10-13 17:53

doc: small fix

7 lines of code changed in 2 files:

sbu062 2017-10-13 17:47 Rev.: 5855

doc: accessibility note file_io

2 lines of code changed in 1 file:

sbu062 2017-10-13 17:39 Rev.: 5854

doc: note on (tag_mmdd), reformat code

71 lines of code changed in 1 file:

sbu062 2017-10-13 17:39 Rev.: 5853

revised access rights to objects in commondata; access rights policy enabled

64 lines of code changed in 1 file:

cje012 2017-10-13 14:21 Rev.: 5852

Made new plots with mortality~hormones.

88 lines of code changed in 1 file:

cje012 2017-10-13 14:20

Made sure no calculations are down with a mixture of integers and reals, by going through the whole code and adding real(), nint(), and ._RP etc.

39 lines of code changed in 2 files:

cje012 2017-10-13 14:16 Rev.: 5849

Changed idnint() inti nint().

4 lines of code changed in 1 file:

sbu062 2017-10-13 10:30 Rev.: 5848

revised access rights to objects in commondata, deleted calls to tag_mmdd(), use MMDD variable

33 lines of code changed in 1 file:

sbu062 2017-10-13 08:22 Rev.: 5847

tests: added file status assert

5 lines of code changed in 1 file:

sbu062 2017-10-13 08:22 Rev.: 5846

tests: array-based visual range test, for range of outputs

35 lines of code changed in 1 file:

sbu062 2017-10-13 08:22

tests: small fixes

8 lines of code changed in 2 files:

sbu062 2017-10-13 08:22 Rev.: 5843

tests: added test for visual range (elemental)

33 lines of code changed in 2 files:

sbu062 2017-10-13 06:26 Rev.: 5842

doc: added note

3 lines of code changed in 1 file:

sbu062 2017-10-13 06:23 Rev.: 5841

(preevol_steps_adaptive): made adaptive time steps in GA monotonously accelerating / increasing: two point linear broken line pattern sresults in overlearning and reduction of survival in svn.5827

7 lines of code changed in 1 file:

sbu062 2017-10-13 05:54 Rev.: 5840

(generation_stats_record_write): renumbered

48 lines of code changed in 1 file:

sbu062 2017-10-13 05:54 Rev.: 5839

(generation_stats_record_write): added control unselected trait

5 lines of code changed in 1 file:

sbu062 2017-10-12 14:21 Rev.: 5838

tests: added more trivial tests for commondata

129 lines of code changed in 1 file:

sbu062 2017-10-12 12:52 Rev.: 5837

doc: svg with 700

10543 lines of code changed in 1 file:

sbu062 2017-10-12 12:48 Rev.: 5836

filled diamond for population

2731 lines of code changed in 3 files:

sbu062 2017-10-12 11:28 Rev.: 5835

tests: renamed shorter

1034 lines of code changed in 3 files:

sbu062 2017-10-12 10:38 Rev.: 5834

tests: small fix

5 lines of code changed in 1 file:

sbu062 2017-10-12 10:38 Rev.: 5833

(save_dynamics): label for readability

2 lines of code changed in 1 file:

sbu062 2017-10-12 10:26 Rev.: 5832

tests: test for save_dynamics

36 lines of code changed in 1 file:

sbu062 2017-10-12 10:26 Rev.: 5831

(save_dynamics): success indicator added

27 lines of code changed in 1 file:

sbu062 2017-10-12 09:22 Rev.: 5830

tests: test for init_steps csv

23 lines of code changed in 4 files:

sbu062 2017-10-12 09:22 Rev.: 5829

(preevol_steps_adaptive_save_csv): add success status

11 lines of code changed in 2 files:

sbu062 2017-10-12 09:21 Rev.: 5828

doc: small fix lnk

2 lines of code changed in 1 file:

sbu062 2017-10-11 15:56 Rev.: 5827

(generations_loop_ga): save time steps for adaptive GA at init

8 lines of code changed in 1 file:

sbu062 2017-10-11 15:56 Rev.: 5826

(preevol_steps_adaptive_save_csv): upper limit is GENERATIONS, not PREEVOL_TSTEPS

6 lines of code changed in 1 file:

sbu062 2017-10-11 15:56 Rev.: 5825

(preevol_steps_adaptive): in LINTERPOL grid arrays must strictly encompass the interpolation value, never be equal, hence upper bound array + 1

1 lines of code changed in 1 file:

sbu062 2017-10-11 14:41 Rev.: 5824

(preevol_steps_adaptive_save_csv): diagnostics proc to save adaptive time steps in GA

22 lines of code changed in 1 file:

sbu062 2017-10-11 14:10 Rev.: 5823

doc: fix/update comments

8 lines of code changed in 1 file:

sbu062 2017-10-11 12:31

doc: small reformat

2 lines of code changed in 2 files:

sbu062 2017-10-11 12:30 Rev.: 5820

doc: small reformat, note with plot code

4 lines of code changed in 1 file:

sbu062 2017-10-11 12:14 Rev.: 5819

(lifecycle_preevol): small changes, shorter indexing var name

6 lines of code changed in 1 file:

sbu062 2017-10-11 12:14 Rev.: 5818

(lifecycle_preevol): involke adaptive GA time steps algorithm, steps

12 lines of code changed in 1 file:

sbu062 2017-10-11 11:57 Rev.: 5817

(preevol_steps_adaptive): fully implemented, renamed from (preevol_cycles_adaptive)

46 lines of code changed in 1 file:

sbu062 2017-10-11 11:57 Rev.: 5816

(preevol_cycles_adaptive): function to calculate time steps for adaptive GA, so far skeleton

53 lines of code changed in 1 file:

sbu062 2017-10-11 06:52 Rev.: 5815

increase preevol life cycles PREEVOL_CYCLES to 545

1 lines of code changed in 1 file:

sbu062 2017-10-11 06:41 Rev.: 5814

set initial depth of agents INIT_AGENTS_DEPTH to initial average target depth of food items

2 lines of code changed in 1 file:

sbu062 2017-10-11 06:41 Rev.: 5813

(individual_create_zero): clean spatial positions

3 lines of code changed in 1 file:

sbu062 2017-10-11 06:40 Rev.: 5812

(individual_init_random): clean spatial positions

3 lines of code changed in 1 file:

sbu062 2017-10-11 06:06

small reformat

7 lines of code changed in 2 files:

sbu062 2017-10-10 18:49 Rev.: 5809

(generations_loop_ga): save behaviour history data calling (save_behaviour_csv)

6 lines of code changed in 1 file:

sbu062 2017-10-10 18:34 Rev.: 5808

doc: added (save_behaviour_csv) to list of output files

2 lines of code changed in 1 file:

sbu062 2017-10-10 18:25 Rev.: 5807

deleted obsolete local var

0 lines of code changed in 1 file:

sbu062 2017-10-10 18:16 Rev.: 5806

(behaviour_do_freeze): add call to (repeat_position)

9 lines of code changed in 1 file:

sbu062 2017-10-10 18:16 Rev.: 5805

(behaviour_do_reproduce): add call to (repeat_position), need to do this for all behaviours that do not involve movement

12 lines of code changed in 1 file:

sbu062 2017-10-10 17:49 Rev.: 5804

(repeat_position): procedure to fake update the history stack

16 lines of code changed in 1 file:

sbu062 2017-10-10 17:33 Rev.: 5803

(save_behaviour_csv): public interface

6 lines of code changed in 1 file:

sbu062 2017-10-10 16:45 Rev.: 5802

(population_save_data_behaviours): implemented, still needs audit

32 lines of code changed in 1 file:

sbu062 2017-10-10 16:45 Rev.: 5801

behaviour history stack uses separate parameter HISTORY_SIZE_BEHAVIOURS; (population_save_data_behaviours): procedure to save behaviours history stack , so far skeleton

84 lines of code changed in 1 file:

sbu062 2017-10-10 16:07 Rev.: 5800

BEHAVIOUR class: implemented history stack of behaviouir labels "history_behave", added code to update stack on each (do_) method.

70 lines of code changed in 1 file:

sbu062 2017-10-10 14:14 Rev.: 5799

merged devbranch

7 lines of code changed in 1 file:

sbu062 2017-10-10 14:12 Rev.: 5798

doc: link to intel docs, command line

7 lines of code changed in 1 file:

sbu062 2017-10-10 13:51 Rev.: 5797

doc: added (save_movements_csv) to list of output files

3 lines of code changed in 1 file:

sbu062 2017-10-10 13:51 Rev.: 5796

SAVE_DATA_INDS_GENERATION block: save latest movement history

6 lines of code changed in 1 file:

sbu062 2017-10-10 13:51 Rev.: 5795

(save_movements_csv): renemed public interface for consistency

1 lines of code changed in 1 file:

sbu062 2017-10-10 13:31 Rev.: 5794

(save_movements): implemented subroutine to save spatial moving history of agents (population_save_data_movements)

93 lines of code changed in 1 file:

sbu062 2017-10-10 13:31 Rev.: 5793

(population_save_data_movements): save movement history of agents, initial skeleton

31 lines of code changed in 1 file:

sbu062 2017-10-10 09:19 Rev.: 5791

rename link

1 lines of code changed in 1 file:

sbu062 2017-10-10 09:14 Rev.: 5790

merged from dev branch

1561 lines of code changed in 4 files:

sbu062 2017-10-10 09:07

small additiion

4 lines of code changed in 2 files:

sbu062 2017-10-10 09:00 Rev.: 5787

briefly on overloading

50 lines of code changed in 1 file:

sbu062 2017-10-09 19:31 Rev.: 5786

(generations_loop_ga): initial random uniform positionof 'proto_parents' within GENERATIONS_PREEVOL

11 lines of code changed in 1 file:

sbu062 2017-10-09 14:51 Rev.: 5785

(lifecycle_preevol): habitat-specific predation disabled

6 lines of code changed in 1 file:

sbu062 2017-10-09 14:51 Rev.: 5784

(selection): re-initialise parents from the elite group from their genome for each generation

10 lines of code changed in 1 file:

sbu062 2017-10-09 12:47 Rev.: 5783

doc: typo

1 lines of code changed in 1 file:

sbu062 2017-10-09 12:34 Rev.: 5782

(lifecycle_preevol): habitat-specific predation disabled so far

12 lines of code changed in 1 file:

sbu062 2017-10-09 12:34 Rev.: 5781

(lifecycle_preevol): added habitat-specific predation

17 lines of code changed in 1 file:

sbu062 2017-10-09 12:34 Rev.: 5780

set habitat-specific risks in habitat (make) calls

3 lines of code changed in 1 file:

sbu062 2017-10-09 12:34 Rev.: 5779

doc: separated comments

6 lines of code changed in 1 file:

sbu062 2017-10-09 12:34 Rev.: 5778

adjust predator number in habitats, reduce number of food items in habitats, set specific habitat-specific mortality risks

12 lines of code changed in 1 file:

sbu062 2017-10-09 12:34 Rev.: 5777

(population_subject_other_risks): deleted obsolete optional objects

1 lines of code changed in 1 file:

sbu062 2017-10-09 12:34 Rev.: 5776

(generations_loop_ga): distance between food items calculated in normal generation-wise stats now

2 lines of code changed in 1 file:

cje012 2017-10-09 11:22 Rev.: 5775

Added new plot that plots hormone levels according to length, reserve category and environment.

45 lines of code changed in 1 file:

sbu062 2017-10-08 10:56 Rev.: 5774

doc: small addition

5 lines of code changed in 1 file:

sbu062 2017-10-08 10:48 Rev.: 5773

class symbols moved to hedtools

0 lines of code changed in 3 files:

sbu062 2017-10-08 10:46 Rev.: 5772

added class diagram basics

858 lines of code changed in 4 files:

sbu062 2017-10-08 09:58

copy class diagram symbols

1469 lines of code changed in 2 files:

sbu062 2017-10-08 09:57 Rev.: 5769

copy class diagram symbols

0 lines of code changed in 1 file:

sbu062 2017-10-08 08:31 Rev.: 5768

renamed

0 lines of code changed in 6 files:

sbu062 2017-10-08 08:26 Rev.: 5767

three connectors

1089 lines of code changed in 3 files:

sbu062 2017-10-08 08:12 Rev.: 5766

add symbol plot for redme_nf

291 lines of code changed in 3 files:

sbu062 2017-10-08 07:56 Rev.: 5765

small change

1 lines of code changed in 1 file:

sbu062 2017-10-07 09:00 Rev.: 5764

doc: small addition

6 lines of code changed in 1 file:

sbu062 2017-10-07 08:51 Rev.: 5763

doc: link to new features

5 lines of code changed in 1 file:

sbu062 2017-10-07 08:19 Rev.: 5762

small fix

2 lines of code changed in 1 file:

sbu062 2017-10-07 08:07 Rev.: 5761

updated recent changes from dev branch

235 lines of code changed in 1 file:

sbu062 2017-10-07 08:04 Rev.: 5760

additional ref

2 lines of code changed in 1 file:

sbu062 2017-10-07 08:01 Rev.: 5759

added refs to oo

15 lines of code changed in 1 file:

sbu062 2017-10-06 22:02 Rev.: 5758

small addition

13 lines of code changed in 1 file:

sbu062 2017-10-06 20:29

doc: small fix

8 lines of code changed in 2 files:

sbu062 2017-10-06 20:18 Rev.: 5755

links to doxygen

18 lines of code changed in 1 file:

sbu062 2017-10-06 20:05 Rev.: 5754

small changes

5 lines of code changed in 1 file:

sbu062 2017-10-06 19:59 Rev.: 5753

updated on OO

1 lines of code changed in 1 file:

sbu062 2017-10-06 19:52

updated on OO

202 lines of code changed in 2 files:

sbu062 2017-10-06 19:49 Rev.: 5750

doc: writing brief doc on fortran features

7 lines of code changed in 1 file:

sbu062 2017-10-06 18:34 Rev.: 5749

doc: writing brief doc on fortran features

1 lines of code changed in 1 file:

sbu062 2017-10-06 18:27 Rev.: 5748

doc: writing brief doc on fortran features

2 lines of code changed in 1 file:

sbu062 2017-10-06 18:19

doc: writing brief doc on fortran features

16 lines of code changed in 2 files:

sbu062 2017-10-06 17:59 Rev.: 5745

doc: writing brief doc on fortran features

66 lines of code changed in 1 file:

sbu062 2017-10-06 15:52 Rev.: 5744

doc: writing brief doc on fortran features

2 lines of code changed in 1 file:

sbu062 2017-10-06 15:44

doc: writing brief doc on fortran features

9 lines of code changed in 2 files:

sbu062 2017-10-06 15:36

doc: writing brief doc on fortran features

7 lines of code changed in 2 files:

sbu062 2017-10-06 15:31 Rev.: 5739

doc: writing brief doc on fortran features

22 lines of code changed in 1 file:

sbu062 2017-10-06 15:24 Rev.: 5738

doc: writing brief doc on fortran features

48 lines of code changed in 1 file:

sbu062 2017-10-06 15:01 Rev.: 5737

doc: writing brief doc on fortran features

4 lines of code changed in 1 file:

sbu062 2017-10-06 14:53

doc: writing brief doc on fortran features

8 lines of code changed in 2 files:

sbu062 2017-10-06 14:47

doc: writing brief doc on fortran features

38 lines of code changed in 2 files:

sbu062 2017-10-06 14:41 Rev.: 5732

doc: writing brief doc on fortran features

4 lines of code changed in 1 file:

sbu062 2017-10-06 14:35

doc: writing brief doc on fortran features

75 lines of code changed in 2 files:

sbu062 2017-10-06 14:12 Rev.: 5729

doc: writing brief doc on fortran features

50 lines of code changed in 1 file:

sbu062 2017-10-06 14:05 Rev.: 5728

doc: writing brief doc on fortran features

14 lines of code changed in 1 file:

sbu062 2017-10-06 13:58

doc: writing brief doc on fortran features

91 lines of code changed in 2 files:

sbu062 2017-10-06 13:33 Rev.: 5725

doc: writing fortran features

9 lines of code changed in 1 file:

sbu062 2017-10-06 13:27 Rev.: 5724

renamed to change default alphabetic order in doxygen

19 lines of code changed in 2 files:

sbu062 2017-10-06 13:27 Rev.: 5723

doc: small addition

2 lines of code changed in 1 file:

sbu062 2017-10-06 13:23 Rev.: 5722

doc: add document on fortran features

0 lines of code changed in 1 file:

sbu062 2017-10-06 13:23 Rev.: 5721

doc: add title

1 lines of code changed in 1 file:

sbu062 2017-10-06 13:11 Rev.: 5720

doc: modules overview goes first

14 lines of code changed in 1 file:

sbu062 2017-10-06 13:02 Rev.: 5719

doc: small changes, links to hedtools

8 lines of code changed in 1 file:

sbu062 2017-10-06 12:58

doc: minor fix format

3 lines of code changed in 2 files:

sbu062 2017-10-06 12:51 Rev.: 5716

doc: small changes, links to hedtools

6 lines of code changed in 1 file:

sbu062 2017-10-06 12:45 Rev.: 5715

doc: small changes

5 lines of code changed in 1 file:

sbu062 2017-10-06 12:41 Rev.: 5714

doc: try to fix link

1 lines of code changed in 1 file:

sbu062 2017-10-06 12:38 Rev.: 5713

doc: info on file outputs

38 lines of code changed in 1 file:

sbu062 2017-10-06 12:01 Rev.: 5712

(generation_stats_record_write): additional comments

4 lines of code changed in 1 file:

sbu062 2017-10-06 11:58 Rev.: 5711

(population_save_data_all_agents_csv): renumbered cols, reformat

82 lines of code changed in 1 file:

sbu062 2017-10-06 11:58 Rev.: 5710

(population_save_data_all_agents_csv): reformatting column names

44 lines of code changed in 1 file:

sbu062 2017-10-06 11:58 Rev.: 5709

(population_save_data_all_agents_csv): add body length at birth to data save

7 lines of code changed in 1 file:

sbu062 2017-10-06 11:58 Rev.: 5708

added body length at birth to 'CONDITION' class, so far only for records

21 lines of code changed in 1 file:

sbu062 2017-10-06 09:42 Rev.: 5707

(generation_stats_record_write): added n of males and females

86 lines of code changed in 1 file:

sbu062 2017-10-05 14:48 Rev.: 5706

(generation_stats_record_write): average fitness only in those who are alive

6 lines of code changed in 1 file:

sbu062 2017-10-05 14:47 Rev.: 5705

(generation_stats_record_write): added minimum fitness

7 lines of code changed in 1 file:

sbu062 2017-10-05 14:47 Rev.: 5704

(generation_stats_record_write): added average fitness

11 lines of code changed in 1 file:

sbu062 2017-10-05 14:25 Rev.: 5703

(generation_stats_record_write): fix initialisation, p_repr obsolete

3 lines of code changed in 1 file:

sbu062 2017-10-05 14:24 Rev.: 5702

(generation_stats_record_write): forgot initialise arrays

4 lines of code changed in 1 file:

sbu062 2017-10-05 14:24 Rev.: 5701

(generation_stats_record_write): added perceprion in safe and dangerous habitats

44 lines of code changed in 1 file:

sbu062 2017-10-05 13:43 Rev.: 5700

(generations_loop_ga): average distance between food items reported only in debug mode, normally is in generations_ csv file

10 lines of code changed in 1 file:

sbu062 2017-10-05 13:43 Rev.: 5699

(generation_stats_record_write): added mean distance between food items

12 lines of code changed in 1 file:

sbu062 2017-10-05 13:43 Rev.: 5698

(generation_stats_record_write): added average depth of agents

8 lines of code changed in 1 file:

sbu062 2017-10-05 13:14 Rev.: 5697

delete lock file on neat

1 lines of code changed in 1 file:

sbu062 2017-10-05 13:14 Rev.: 5696

check lock file at startup, halt if exists

53 lines of code changed in 1 file:

sbu062 2017-10-05 12:20 Rev.: 5695

more comments on lock file

9 lines of code changed in 1 file:

sbu062 2017-10-05 12:12 Rev.: 5694

comments on lock file

18 lines of code changed in 1 file:

sbu062 2017-10-05 12:12 Rev.: 5693

implemented lock file

63 lines of code changed in 1 file:

sbu062 2017-10-05 12:12 Rev.: 5692

(generations_loop_ga): close generation-wise stats file, more notes

9 lines of code changed in 1 file:

sbu062 2017-10-04 20:01 Rev.: 5691

doc: updated and fixed doc for the (generation_loop_ga)

27 lines of code changed in 1 file:

sbu062 2017-10-04 18:38 Rev.: 5690

(generation_stats_record_write): small fix docs

4 lines of code changed in 1 file:

sbu062 2017-10-04 18:37 Rev.: 5689

(generation_stats_save): renamed to (generation_stats_record_write)

3 lines of code changed in 1 file:

sbu062 2017-10-04 18:35 Rev.: 5688

(generation_stats_save): call (record_write) method to write the record

6 lines of code changed in 1 file:

sbu062 2017-10-04 18:29 Rev.: 5687

(generation_stats_save): procedure done, block SAVE_GENERATION_STATS deleted

105 lines of code changed in 1 file:

sbu062 2017-10-04 18:29 Rev.: 5686

SAVE_GENERATION_STATS block isolated to subroutine (generation_stats_save): skeleton

106 lines of code changed in 1 file:

sbu062 2017-10-04 18:05 Rev.: 5685

(generations_loop_ga): block is now done

49 lines of code changed in 1 file:

sbu062 2017-10-04 13:57 Rev.: 5684

(generations_loop_ga): continue code to save generation-wise statistics

2 lines of code changed in 1 file:

sbu062 2017-10-04 13:47 Rev.: 5683

(generations_loop_ga): continue code to save generation-wise statistics

3 lines of code changed in 1 file:

sbu062 2017-10-04 13:47 Rev.: 5682

(generations_loop_ga): continue code to save generation-wise statistics: average p_reproduction in an implied loop

4 lines of code changed in 1 file:

sbu062 2017-10-04 13:32 Rev.: 5681

(generations_loop_ga): continue code to save generation-wise statistics

71 lines of code changed in 1 file:

sbu062 2017-10-04 13:32 Rev.: 5680

(generations_loop_ga): started code to save generation-wise statistics

87 lines of code changed in 1 file:

cje012 2017-10-04 12:12 Rev.: 5679

Added ordering of growth speed groups from fast to dead for better plots. Changed from hist() to ggplot with geom_histogram(). Added survival and growth speed group to individual mortality plots. As well as some minor fixes.

45 lines of code changed in 1 file:

sbu062 2017-10-03 19:27 Rev.: 5678

(generations_loop_ga): save memory stacks on each generation.

8 lines of code changed in 1 file:

sbu062 2017-10-03 19:27 Rev.: 5677

smaller number of additive components

1 lines of code changed in 1 file:

sbu062 2017-10-03 17:12 Rev.: 5676

small fix link

1 lines of code changed in 1 file:

sbu062 2017-10-03 15:45 Rev.: 5675

(population_save_data_all_genomes): fix doc comments

13 lines of code changed in 1 file:

sbu062 2017-10-03 15:39 Rev.: 5674

debug: delete debug code

0 lines of code changed in 1 file:

sbu062 2017-10-03 15:39 Rev.: 5673

(population_save_data_memory): docs and reformat, fully done

50 lines of code changed in 1 file:

sbu062 2017-10-03 14:57 Rev.: 5672

(population_save_data_memory): writing data values done, debug code

1 lines of code changed in 1 file:

sbu062 2017-10-03 14:57 Rev.: 5671

(population_save_data_memory): writing data values done

72 lines of code changed in 1 file:

sbu062 2017-10-03 14:57 Rev.: 5670

(population_save_data_memory): continue, starting data values

16 lines of code changed in 1 file:

sbu062 2017-10-03 14:57 Rev.: 5669

(population_save_data_memory): build column names done

14 lines of code changed in 1 file:

sbu062 2017-10-03 14:57 Rev.: 5668

(population_save_data_memory): build column names

27 lines of code changed in 1 file:

sbu062 2017-10-03 14:57 Rev.: 5667

(population_save_data_memory): starting skeleton

97 lines of code changed in 1 file:

sbu062 2017-10-03 14:56 Rev.: 5666

rename block for consistency

2 lines of code changed in 1 file:

sbu062 2017-10-03 11:54 Rev.: 5665

save genome data on each time step

10 lines of code changed in 1 file:

sbu062 2017-10-03 11:40 Rev.: 5664

(genome_mutate_wrapper): chromosomal mutations are again disabled

16 lines of code changed in 1 file:

sbu062 2017-10-03 11:40 Rev.: 5663

reformat code

18 lines of code changed in 1 file:

sbu062 2017-10-03 11:40 Rev.: 5662

(genome_mutate_wrapper): chromosomal mutations are again disabled

14 lines of code changed in 1 file:

sbu062 2017-10-03 11:40 Rev.: 5661

(genome_mutate_wrapper): optional mutation parameters

42 lines of code changed in 1 file:

sbu062 2017-10-03 11:22 Rev.: 5660

(chromosome_mutate_relocate_shift_random): optional mutation probability parameter

14 lines of code changed in 1 file:

sbu062 2017-10-03 11:22 Rev.: 5659

(chromosome_mutate_relocate_swap_random): optional mutation probability parameter

14 lines of code changed in 1 file:

sbu062 2017-10-03 11:22 Rev.: 5658

(allele_mutate_random_batch): optional mutation probability parameter

15 lines of code changed in 1 file:

sbu062 2017-10-03 11:22 Rev.: 5657

(allele_mutate_random): optional mutation probability parameter

16 lines of code changed in 1 file:

sbu062 2017-10-03 11:01 Rev.: 5656

debug: deleted debug code for (save_genomes_csv)

0 lines of code changed in 1 file:

sbu062 2017-10-03 10:54 Rev.: 5655

increase mutation rate for simple allale mutations (chromosome mutations disabled)

2 lines of code changed in 1 file:

sbu062 2017-10-03 10:54 Rev.: 5654

(population_save_data_all_genomes): final success param

2 lines of code changed in 1 file:

sbu062 2017-10-03 10:54 Rev.: 5653

(population_save_data_all_agents_csv): error checking code for file write

20 lines of code changed in 1 file:

sbu062 2017-10-02 15:29 Rev.: 5652

(population_save_data_all_genomes): done and tested

31 lines of code changed in 1 file:

sbu062 2017-10-02 14:27 Rev.: 5651

(population_save_data_all_genomes): contunue, almost ready, fixes and docs

67 lines of code changed in 1 file:

sbu062 2017-10-02 14:27 Rev.: 5650

(population_save_data_all_genomes): contunue, write data

21 lines of code changed in 1 file:

sbu062 2017-10-02 14:26 Rev.: 5649

(population_save_data_all_genomes): contunue, write first record column names

24 lines of code changed in 1 file:

sbu062 2017-10-02 14:26 Rev.: 5648

(population_save_data_all_genomes): built column names for genome data, allocatable

22 lines of code changed in 1 file:

sbu062 2017-10-02 14:26 Rev.: 5647

(population_save_data_all_genomes): built column names for genome data

32 lines of code changed in 1 file:

sbu062 2017-10-02 11:40 Rev.: 5646

(genome_mutate_wrapper): disable relocation mutations

11 lines of code changed in 1 file:

sbu062 2017-10-02 11:40 Rev.: 5645

(population_save_data_all_genomes): starting skeleton

39 lines of code changed in 1 file:

sbu062 2017-10-01 21:39 Rev.: 5644

doc: small fixes, deleted obsolete stage 2 proto_offspring tramnsitory evolution code in (generations_loop_ga)

8 lines of code changed in 1 file:

sbu062 2017-10-01 16:14 Rev.: 5643

(mate_reproduce): check sex, force mother female and father male

11 lines of code changed in 1 file:

sbu062 2017-10-01 11:47 Rev.: 5642

short PREEVOL_CYCLES; add tag to logger average distance between foods

11 lines of code changed in 1 file:

September 2017 »

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