July 2016 Commit Log

Number of Commits:
143
Number of Active Developers:
4
judyjinn 2016-07-28 21:52 Rev.: 1200

added back CommonSquirrel

22 lines of code changed in 1 file:

judyjinn 2016-07-28 21:52 Rev.: 1199

trying to fix conflict/out dated error in svn. copy pasted all the files again

0 lines of code changed in 1 file:

judyjinn 2016-07-28 21:51 Rev.: 1198

fixed error in stay_risk equation. Changed next_loc to curr_loc. Reduced bud replenish rate. changed stay risk beta from 20 to 10. Turned memory gene back on for foodmem decay

19 lines of code changed in 3 files:

sbu062 2016-07-28 08:35 Rev.: 1197

get mass and length standard functions

28 lines of code changed in 1 file:

sbu062 2016-07-28 08:31 Rev.: 1196

updated figs

92 lines of code changed in 2 files:

sbu062 2016-07-22 17:57 Rev.: 1195

chromosome labels + fix outdated comment-outs

2 lines of code changed in 1 file:

sbu062 2016-07-22 15:12 Rev.: 1194

fixed body mass growth increment , to Kleiber's 4/3 power

9 lines of code changed in 1 file:

sbu062 2016-07-22 12:22 Rev.: 1193

forgot to init age, + fix comments

32 lines of code changed in 1 file:

sbu062 2016-07-22 10:59 Rev.: 1192

Fixed all phenotypic labels

13 lines of code changed in 1 file:

sbu062 2016-07-22 10:45 Rev.: 1191

fixed label in trait_init_genotype

10 lines of code changed in 1 file:

sbu062 2016-07-22 10:34 Rev.: 1190

reorganised parameters

21 lines of code changed in 1 file:

sbu062 2016-07-22 09:03 Rev.: 1189

doxygen comments

18 lines of code changed in 1 file:

sbu062 2016-07-22 03:42 Rev.: 1188

implemented epsilon for zero parameter

8 lines of code changed in 1 file:

sbu062 2016-07-22 02:15 Rev.: 1187

fixed body mass smr function

16 lines of code changed in 1 file:

judyjinn 2016-07-21 23:46 Rev.: 1186

Changed weight gain to be at the end of every day instead of at the end of the simulation.

195 lines of code changed in 2 files:

sbu062 2016-07-21 13:30 Rev.: 1185

implemented growth functions (mass and length) + starvation death check

144 lines of code changed in 1 file:

sbu062 2016-07-21 09:46 Rev.: 1184

removed function do weight increment, fixed check starvation

6 lines of code changed in 1 file:

sbu062 2016-07-21 09:18 Rev.: 1183

initial implementation of body, length mass and smr. Fixed NaNs in gamma2gene

137 lines of code changed in 1 file:

sbu062 2016-07-15 11:45 Rev.: 1182

renamed to the body

3 lines of code changed in 1 file:

sbu062 2016-07-15 11:11 Rev.: 1181

function to get mass from length

28 lines of code changed in 1 file:

sbu062 2016-07-15 09:58 Rev.: 1180

added condition module to physical condition objects + genetic determination

187 lines of code changed in 1 file:

sbu062 2016-07-15 09:48 Rev.: 1179

updated class hierarchy fig

1515 lines of code changed in 2 files:

sbu062 2016-07-15 08:47 Rev.: 1178

added the condition module and initial type

39 lines of code changed in 1 file:

judyjinn 2016-07-15 02:34 Rev.: 1177

fixed the acorn_eff. Was too high at fisrst

4 lines of code changed in 1 file:

judyjinn 2016-07-15 02:14 Rev.: 1176

trying out removal of acorn replenishing

11 lines of code changed in 1 file:

judyjinn 2016-07-15 02:01 Rev.: 1175

changed replen rate for buds, forage success rate of acorns, kcals of buds. Squirrels only gain weight at the end of a day now. added a totkcals for acorns/buds in common squirrel. Change the calculation of final weight to be based on what weight squirrels had gained over 10 days

80 lines of code changed in 2 files:

judyjinn 2016-07-15 00:22 Rev.: 1174

Changing entire program to be 10 days long. Increased eating speed of acorns, decreased replenishing rate of buds to 0.005, changed acorn finding success rate

12 lines of code changed in 1 file:

sbu062 2016-07-14 13:44 Rev.: 1173

updated lower-order components for perception objects

21 lines of code changed in 1 file:

sbu062 2016-07-14 08:28 Rev.: 1172

added lower-order components for perception object

55 lines of code changed in 1 file:

sbu062 2016-07-13 08:31 Rev.: 1171

changes that did in bus

7 lines of code changed in 1 file:

sbu062 2016-07-13 08:26 Rev.: 1170

updated hierarchy of types for neurobio and individual agent

31 lines of code changed in 1 file:

sbu062 2016-07-13 06:37 Rev.: 1169

delted roadmap readme, it is no more actual

0 lines of code changed in 1 file:

sbu062 2016-07-12 17:45 Rev.: 1168

minor revisions, emotional subobjects - need testing access in higher order classes

13 lines of code changed in 1 file:

sbu062 2016-07-12 11:31 Rev.: 1167

REMOVED so far neural_response procedure neuro_bundle_signal_response from THE_NEUROBIO, we now have a general procedure to set any trait from the genome

1 lines of code changed in 1 file:

sbu062 2016-07-12 11:28 Rev.: 1166

added init parameters and procedure for SMR

62 lines of code changed in 1 file:

sbu062 2016-07-12 10:57 Rev.: 1165

minor formatting

15 lines of code changed in 1 file:

sbu062 2016-07-12 10:55 Rev.: 1164

hormone _init_genotype is now REMOVED, will use general procedure trait_init_genotype for all traits upwards in class hierarchy

0 lines of code changed in 1 file:

sbu062 2016-07-12 10:50 Rev.: 1163

added general trait init function at the individual genome level of class hierarchy, hormone init function will be removed. added body_mass parameters, added minimum zero for positive traits

171 lines of code changed in 1 file:

sbu062 2016-07-11 17:41 Rev.: 1162

more tips on subversion

33 lines of code changed in 1 file:

sbu062 2016-07-11 13:06 Rev.: 1161

STARTING NEUROBIO. Added general neural response function for neural bundles

86 lines of code changed in 1 file:

sbu062 2016-07-11 12:12 Rev.: 1160

comment on NaNs in alleleconv type 2

2 lines of code changed in 1 file:

sbu062 2016-07-11 11:42 Rev.: 1159

fixed gamma2gene function, gaussian perception

50 lines of code changed in 1 file:

sbu062 2016-07-11 09:21 Rev.: 1158

fix comments only

12 lines of code changed in 1 file:

sbu062 2016-07-11 05:07 Rev.: 1157

svnignore and hgignore added

90 lines of code changed in 2 files:

sbu062 2016-07-11 04:48 Rev.: 1156

comments only fix

10 lines of code changed in 1 file:

sbu062 2016-07-11 04:38 Rev.: 1155

ADDES alleleconv conversion in gamma2gene

14 lines of code changed in 1 file:

sbu062 2016-07-11 04:17 Rev.: 1154

gamma2gene_2 is now removed

3 lines of code changed in 1 file:

sbu062 2016-07-11 04:14 Rev.: 1153

fix comments only

42 lines of code changed in 1 file:

sbu062 2016-07-11 03:14 Rev.: 1152

previous alleleconv is now allelescale (elemental) + added alleleconv to convert normalised allele value to arbitrary alleleconv rescaled, new alleleconv not used yet though

26 lines of code changed in 1 file:

sbu062 2016-07-11 02:43 Rev.: 1151

added alleleconv function elemental, will convert previous alleleconv with generic interfaces to allelescale

29 lines of code changed in 1 file:

sbu062 2016-07-10 10:28 Rev.: 1150

updated svnignore

1 lines of code changed in 1 file:

sbu062 2016-07-10 07:54 Rev.: 1148

maintenance, deleted PDF doc, and updated svnignore properties

0 lines of code changed in 1 file:

sbu062 2016-07-10 07:52 Rev.: 1147

updated svnignore properties

28 lines of code changed in 1 file:

sbu062 2016-07-10 06:10 Rev.: 1146

fix pics

78 lines of code changed in 2 files:

sbu062 2016-07-10 05:37 Rev.: 1145

comments only fix

15 lines of code changed in 1 file:

sbu062 2016-07-10 05:10 Rev.: 1144

added on style of labels/var names

18 lines of code changed in 1 file:

sbu062 2016-07-09 09:53 Rev.: 1143

updated figs

175 lines of code changed in 2 files:

sbu062 2016-07-09 09:04 Rev.: 1142

added code style - uppercase and lowercase use rules

56 lines of code changed in 1 file:

sbu062 2016-07-09 08:09 Rev.: 1141

REMOVED hormone-specific initialisation functions, they are now served by a module-private universal function

12 lines of code changed in 1 file:

sbu062 2016-07-09 07:45 Rev.: 1140

implemented general hormone initialisation function, will remove specific next

126 lines of code changed in 1 file:

sbu062 2016-07-09 06:46 Rev.: 1139

started implementing UNIVERSAL hormone init code

2 lines of code changed in 1 file:

sbu062 2016-07-08 22:52 Rev.: 1138

disable sorting class objects alphabetically SORT_MEMBER_DOCS=NO

1 lines of code changed in 1 file:

sbu062 2016-07-08 22:32 Rev.: 1137

minor note on coding style at the top

2 lines of code changed in 1 file:

sbu062 2016-07-08 22:28 Rev.: 1136

estrogen init implemented + set functions for all hormones

136 lines of code changed in 1 file:

sbu062 2016-07-08 20:22 Rev.: 1135

added cortisol and testosterone

223 lines of code changed in 1 file:

sbu062 2016-07-08 18:35 Rev.: 1134

updated fig.

101 lines of code changed in 2 files:

sbu062 2016-07-08 14:54 Rev.: 1133

added adrenaline

78 lines of code changed in 1 file:

sbu062 2016-07-08 14:25 Rev.: 1132

updated pics for doc (UML diagrams)

677 lines of code changed in 2 files:

sbu062 2016-07-08 14:15 Rev.: 1131

added UML diagram for the individual

15 lines of code changed in 1 file:

sbu062 2016-07-08 14:03 Rev.: 1130

added pics for class hierarchy, UML diagram

2060 lines of code changed in 2 files:

sbu062 2016-07-08 11:10 Rev.: 1129

fix fig 2 gen. structure

9 lines of code changed in 2 files:

sbu062 2016-07-08 11:03 Rev.: 1128

added genetic structure pics

2848 lines of code changed in 3 files:

sbu062 2016-07-08 10:59 Rev.: 1127

added new AHA genetic structure schemes to the doc

28 lines of code changed in 1 file:

sbu062 2016-07-08 08:40

fix HeadURL

4 lines of code changed in 4 files:

sbu062 2016-07-08 08:40 Rev.: 1123

added HeadURL

1 lines of code changed in 1 file:

sbu062 2016-07-08 08:34

added keywords

9 lines of code changed in 2 files:

sbu062 2016-07-08 06:33 Rev.: 1120

hide private objects in docs, see EXTRACT_PRIVATE

1 lines of code changed in 1 file:

sbu062 2016-07-08 06:08 Rev.: 1119

fixed comments, @param, for doxygen

85 lines of code changed in 1 file:

sbu062 2016-07-08 05:27 Rev.: 1118

removed local-object alleleconf, it is redundant now

0 lines of code changed in 1 file:

sbu062 2016-07-08 05:21 Rev.: 1117

remove TODOs for array-based alleleconv, loop-based seems ok and speed overhead wouldn't be large

0 lines of code changed in 1 file:

sbu062 2016-07-08 05:01 Rev.: 1116

implemented gamma2gene for real parameters, it does not invoke alleleconv, + added to generic interface

87 lines of code changed in 1 file:

sbu062 2016-07-07 19:04 Rev.: 1115

amended comments on the code

30 lines of code changed in 1 file:

sbu062 2016-07-07 15:33 Rev.: 1114

implemented function get for thyroid hormone level

11 lines of code changed in 1 file:

sbu062 2016-07-07 15:23 Rev.: 1113

fixed global hormone init function name, it is not random

4 lines of code changed in 1 file:

sbu062 2016-07-07 15:20 Rev.: 1112

Set haploid warning for gamma2gene and thyroid hormone init function, haploid doesn't work and results in short-circuit

11 lines of code changed in 1 file:

sbu062 2016-07-07 15:06 Rev.: 1111

fixed random chromosome selection

2 lines of code changed in 1 file:

glj042 2016-07-07 14:59 Rev.: 1110

Gabbi - new comments only

27 lines of code changed in 1 file:

sbu062 2016-07-07 14:51 Rev.: 1109

fixed integer division in alleleconv

4 lines of code changed in 1 file:

sbu062 2016-07-07 14:30 Rev.: 1108

refactor gamma2gene and alleleconv functions, added generic interfaces, plus initial implementation of thyroid hormone init based on gamma2gene

270 lines of code changed in 1 file:

nzlcj 2016-07-07 12:57 Rev.: 1107

Coded together. Corrected some loops. Corrected and simplified writing of cumulative fitness to Ind array.

4 lines of code changed in 1 file:

glj042 2016-07-07 12:38 Rev.: 1106

gabbi

28 lines of code changed in 1 file:

nzlcj 2016-07-07 11:22 Rev.: 1105

Coded together. Changed some time references - think through what happens at the beginning and during a timestep.

14 lines of code changed in 1 file:

glj042 2016-07-07 07:07 Rev.: 1104

Gabbi questions - cumulative fitness

12 lines of code changed in 1 file:

sbu062 2016-07-06 23:28 Rev.: 1103

added the boolean genotype x phenotype matrices for all the hormones

102 lines of code changed in 1 file:

judyjinn 2016-07-06 22:46 Rev.: 1102

commit before changing from 10months to 1 week time frame

4 lines of code changed in 1 file:

judyjinn 2016-07-06 19:11 Rev.: 1101

messed up my branch, readding files and deleting misc

209 lines of code changed in 1 file:

sbu062 2016-07-06 18:17 Rev.: 1100

comment, minor further fix on reshape

5 lines of code changed in 1 file:

sbu062 2016-07-06 18:03 Rev.: 1099

fix reshape in COMMONDATA to fit the maximum number of alleles - construction of _GENOTYPE_PHENOTYPE boolean matrices

20 lines of code changed in 1 file:

sbu062 2016-07-06 15:19 Rev.: 1098

Removed the implementation of sex determination based on explicit SEXLOCUS_CHROMOSOME and SEXLOCUS_ALLELE. Now, it is based on GENOTYPE_PHENOTYPE matrix. Spee doverhead is negligible.

8 lines of code changed in 1 file:

sbu062 2016-07-06 14:59 Rev.: 1097

added implementation of sex determination based on G_P matrix, NOTE: this version includes both older implementation code based on explicit settings of the sex locus AND the new implementation based on the G_P matrix. Comparing speed of both did not reveal any serious differences

59 lines of code changed in 1 file:

glj042 2016-07-06 14:52 Rev.: 1096

Corrections by Gabbi in Forward simulation.

36 lines of code changed in 1 file:

sbu062 2016-07-06 12:16 Rev.: 1095

reformatted reshape array constructors comments for clear cisibility + added padding and reordering parameters

16 lines of code changed in 1 file:

sbu062 2016-07-06 11:49 Rev.: 1094

reformatted comments for genotype x phenotype arrays for better visibility

6 lines of code changed in 1 file:

sbu062 2016-07-06 11:43 Rev.: 1093

Implemented phenotype to genotype matrix for SEX and HORMONES, for SEX it's unused

84 lines of code changed in 1 file:

sbu062 2016-07-06 09:06 Rev.: 1092

Removed outdated implementation of ADDITIVE ALLELE COMPONENTS that was branched out previously: branches/budaev/HEDG2_01s2

0 lines of code changed in 1 file:

sbu062 2016-07-06 09:05 Rev.: 1091

LATEST VERSION OF OLD version of ADDITIVE COMPONENTS for alleles, this version is branched to ...01s2 branch and now DISCOURAGED -- reimplemented new in old continuing branch

0 lines of code changed in 2 files:

sbu062 2016-07-06 08:54 Rev.: 1090

Removed branches/christian

0 lines of code changed in 63 files:

sbu062 2016-07-06 08:52 Rev.: 1089

Removed branches/gabriella

0 lines of code changed in 1 file:

sbu062 2016-07-06 08:15 Rev.: 1088

small comment addition for allele_value

4 lines of code changed in 1 file:

glj042 2016-07-06 07:19 Rev.: 1087

Gabbi

1 lines of code changed in 1 file:

glj042 2016-07-05 16:03 Rev.: 1086

Questions by Gabbi

28 lines of code changed in 1 file:

sbu062 2016-07-05 14:23 Rev.: 1085

fixed multicomponent gamma2gene function

1 lines of code changed in 1 file:

sbu062 2016-07-05 14:19 Rev.: 1084

added multicomponent gamma2gene function

70 lines of code changed in 1 file:

sbu062 2016-07-05 13:14 Rev.: 1083

RE-IMPLEMENTED two-layer allele structure, with ADDITIVE_COMPS

65 lines of code changed in 1 file:

sbu062 2016-07-05 12:34 Rev.: 1082

minor fix + hormones

16 lines of code changed in 1 file:

nzlcj 2016-07-05 12:02 Rev.: 1081

Coded together. Changed mortality, costs, so they can vary seasonally. Removed some bugs.

56 lines of code changed in 1 file:

sbu062 2016-07-05 11:01 Rev.: 1080

fixed allele label creation to trim chromosom e label if too long

21 lines of code changed in 1 file:

sbu062 2016-07-04 17:54 Rev.: 1079

fixed genetic structure - removed two-layer sysyem for simplicity

71 lines of code changed in 1 file:

sbu062 2016-07-04 17:07 Rev.: 1078

moved - change name of older two-level genetic structure to a shorter

0 lines of code changed in 3 files:

sbu062 2016-07-04 15:51

adding other files

0 lines of code changed in 2 files:

sbu062 2016-07-04 15:49 Rev.: 1075

added older two-level genetic structure code to the dir

0 lines of code changed in 1 file:

sbu062 2016-07-04 14:37 Rev.: 1073

added a stub for finalisation procedure for individual object. Unfortunately final may not yet be implemenmted by compilers

24 lines of code changed in 1 file:

sbu062 2016-07-04 14:09 Rev.: 1072

made create zero functions for creating empty genetic objects, added alive attribute to the individual agent

217 lines of code changed in 1 file:

nzlcj 2016-07-04 12:39 Rev.: 1071

Coded together. Removed interpolation of state category in forward loop. Modified forward simulation to use first-year strategy only. Added spawning to figures.

60 lines of code changed in 1 file:

sbu062 2016-07-04 08:56 Rev.: 1070

more small changes made in bus

21 lines of code changed in 1 file:

sbu062 2016-07-04 07:02 Rev.: 1068

use custom makefile in c:b and smart svn tool

55 lines of code changed in 3 files:

sbu062 2016-07-04 07:00 Rev.: 1067

gaussian perception error in gamma2gene is now set from CV of error rather than raw variance parameter, that's more intuitive to set +sex initialise in population object + fully init new offspring

72 lines of code changed in 1 file:

sbu062 2016-07-01 21:00 Rev.: 1066

cleanup code: fixed mutationrate, fixed labels for sex

12 lines of code changed in 1 file:

sbu062 2016-07-01 17:42 Rev.: 1065

reorganised labels etc

10 lines of code changed in 1 file:

sbu062 2016-07-01 17:16 Rev.: 1064

Rearranged functions, removed reference to fish, now agents.

45 lines of code changed in 1 file:

sbu062 2016-07-01 15:58 Rev.: 1063

changed name of sex determination function as it is the sex init in fact, may need another for runtime sex determination from the genome, but maybe not

4 lines of code changed in 1 file:

sbu062 2016-07-01 15:53 Rev.: 1062

sex determination function implemented separately

54 lines of code changed in 1 file:

sbu062 2016-07-01 15:17 Rev.: 1061

Initial implementation of genetic sex determination

43 lines of code changed in 1 file:

glj042 2016-07-01 13:44 Rev.: 1060

16 lines of code changed in 1 file:

sbu062 2016-07-01 11:08 Rev.: 1059

initial implementation of diploid and polyploid genomes

15 lines of code changed in 1 file:

sbu062 2016-07-01 10:48 Rev.: 1058

changed male sex labels to more logical + use now genome_size, but fixed

15 lines of code changed in 1 file:

nzlcj 2016-07-01 10:35 Rev.: 1057

Coded together. Removed interpolation of reserve state when looking up strategy in forward part.

2 lines of code changed in 1 file:

nzlcj 2016-07-01 10:18 Rev.: 1056

After adding comments together.

12 lines of code changed in 1 file:

sbu062 2016-07-01 09:13 Rev.: 1055

fix outdated info about modules

15 lines of code changed in 1 file:

sbu062 2016-07-01 09:01 Rev.: 1054

added ezwinports to software - for make for windows

5 lines of code changed in 1 file:

glj042 2016-07-01 07:56 Rev.: 1053

1 lines of code changed in 1 file:

nzlcj 2016-07-01 07:20 Rev.: 1052

Coded together. Increased x categories to smooth interpolation. Added gradually subtracted migration costs for increased graph readability.

12 lines of code changed in 1 file:

sbu062 2016-07-01 07:02 Rev.: 1051

minor fix for ieee modules link

2 lines of code changed in 2 files:

June 2016 »

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