June 2022 Commit Log

Number of Commits:
108
Number of Active Developers:
4
hje044 2022-06-30 09:19 Rev.: 12648

Added functionality to saved the random seed in the ncdf file.

189 lines of code changed in 3 files:

sbu062 2022-06-28 13:25 Rev.: 12647

appetite at night is low

6 lines of code changed in 1 file:

sbu062 2022-06-28 13:00 Rev.: 12646

need crop

0 lines of code changed in 1 file:

sbu062 2022-06-28 12:55 Rev.: 12645

typo fix

1 lines of code changed in 1 file:

sbu062 2022-06-28 12:37 Rev.: 12644

added gui screenshot for fish object save/load function

4 lines of code changed in 2 files:

sbu062 2022-06-28 11:17 Rev.: 12643

typo

1 lines of code changed in 1 file:

sbu062 2022-06-28 11:09 Rev.: 12642

add screenshot for restart with fish object save load

6 lines of code changed in 4 files:

sbu062 2022-06-28 07:39 Rev.: 12641

doc: small rewording

1 lines of code changed in 1 file:

sbu062 2022-06-28 07:32 Rev.: 12640

doc: document fish object data functionality

49 lines of code changed in 4 files:

hje044 2022-06-27 12:50 Rev.: 12639

Model version 1.0 finally ready. Now includes better functionality for starting from a previous population, plots have been added to showcase starting values, and year 1 is now always saved in results regardless of WriteInterval.

380 lines of code changed in 4 files:

sbu062 2022-06-27 11:02 Rev.: 12638

some check stats
{{{
From: Sergey Budaev <sergey.budaev@uib.no>
To: Øyvind Johan Korsøen <oyvind.korsoen@bluegrove.com>
Subject: Re: Data
Date: Mon, 27 Jun 2022 12:58:07 +0200
Organization: Universitetet i Bergen

I have looked at the data. A couple of questions:

1. Am I right that these columns 1:24 is the fish density at
the depth 1:24 m? at the time defined by DateTime?

2. What is the valid range of the fish density? Is it within 0:1?
There are a few cases of very high values, e.g.

```
> summary(echodata_first_period$dens_max)
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.1826 0.2655 0.2774 0.3568 42.8144 1714
```

The maximum value of data row max'es is 42.8144. Is it a data error?

Then I need a data quality assurance checking for each data (a
script to check and remove/impute wring data).

Thanks!

Best wishes,

Sergey
}}}

12 lines of code changed in 1 file:

sbu062 2022-06-27 10:31 Rev.: 12637

fix, was density

3 lines of code changed in 1 file:

sbu062 2022-06-27 10:28 Rev.: 12636

get median depth as `depth_median`

13 lines of code changed in 1 file:

sbu062 2022-06-27 10:14 Rev.: 12635

basic data import for echodata 1

4 lines of code changed in 1 file:

sbu062 2022-06-27 10:10 Rev.: 12634

autogenerated rmd

29 lines of code changed in 1 file:

sbu062 2022-06-27 10:05 Rev.: 12633

fix file name

32221 lines of code changed in 2 files:

sbu062 2022-06-27 10:04 Rev.: 12632

cleanup: remove empty columns from excel bug

32221 lines of code changed in 1 file:

sbu062 2022-06-27 09:58 Rev.: 12631

project file

13 lines of code changed in 1 file:

sbu062 2022-06-27 09:53 Rev.: 12630

NF2Waste project setup
{{{
From: Øyvind Johan Korsøen <oyvind.korsoen@bluegrove.com>
To: Sergei Budaev <Sergey.Budaev@uib.no>
Cc: Floriana Lai <Floriana.Lai@uib.no>
Subject: Data
Date: Tue, 21 Jun 2022 12:55:52 +0200

Hei Sergey.
I send this file, but the data is preliminary and lacks the last period. So
new files will come, hopefully, next week. Also includes feeding
intensities, which we will have for higher resolution (5 or 10 minutes).

But you can have a look at the structure and we can have a meeting this
week to discuss it. Øyvind

Øyvind J. Korsøen
PhD
Customer Success Manager
(+47) 958 83 854
}}}

32221 lines of code changed in 1 file:

sbu062 2022-06-27 09:35 Rev.: 12629

nssm commands for gator

0 lines of code changed in 2 files:

sbu062 2022-06-24 20:38 Rev.: 12628

workaround fix gui plot rate, was nonzero at start

2 lines of code changed in 1 file:

sbu062 2022-06-24 20:12 Rev.: 12627

init all rate plot data arrays to zeroes

5 lines of code changed in 1 file:

sbu062 2022-06-24 19:46 Rev.: 12626

correct zoom x scale in all rate plots, propagate fix in r12625

7 lines of code changed in 1 file:

sbu062 2022-06-24 19:27 Rev.: 12625

correct zoom x scale in (do_plot_output_rate_ingested)
{{{
Zoom_Lower/HOUR+
}}}

2 lines of code changed in 1 file:

sbu062 2022-06-24 12:43 Rev.: 12624

propagate change r12623 to other time-plots, not rates

18 lines of code changed in 1 file:

sbu062 2022-06-24 11:46 Rev.: 12623

adjusted x time scale for zoomed plots, first in (do_plot_output_total_ingested)
{{{
! X axis array with rescaled increment:
x_init = real(Zoom_Lower, SRP)
x_end = real(Zoom_Upper, SRP)
}}}

9 lines of code changed in 1 file:

sbu062 2022-06-23 08:46 Rev.: 12622

string added for solomonoff

2251 lines of code changed in 1 file:

sbu062 2022-06-23 08:40 Rev.: 12621

pixelise p5

4854 lines of code changed in 1 file:

sbu062 2022-06-23 08:07 Rev.: 12620

tsotsos attention

10647 lines of code changed in 1 file:

sbu062 2022-06-22 19:33 Rev.: 12619

add tsotsos

16617 lines of code changed in 1 file:

sbu062 2022-06-22 19:04 Rev.: 12618

small changes

13247 lines of code changed in 1 file:

sbu062 2022-06-22 14:27 Rev.: 12617

Tinbergen + Marr joint scheme

176 lines of code changed in 2 files:

sbu062 2022-06-22 14:21 Rev.: 12616

figure p35 only

606 lines of code changed in 1 file:

sbu062 2022-06-22 14:14 Rev.: 12615

small adjustments, optimal E

10332 lines of code changed in 1 file:

sbu062 2022-06-22 14:04 Rev.: 12614

more or less complete

11449 lines of code changed in 1 file:

sbu062 2022-06-22 12:44 Rev.: 12613

nearly all

175812 lines of code changed in 1 file:

sbu062 2022-06-22 08:24 Rev.: 12612

save before svn meeting

8881 lines of code changed in 1 file:

sbu062 2022-06-22 07:57 Rev.: 12611

morning, first edits

2810 lines of code changed in 1 file:

sbu062 2022-06-21 23:00 Rev.: 12610

late changes

7003 lines of code changed in 1 file:

sbu062 2022-06-21 22:37 Rev.: 12609

before going to sleep

34296 lines of code changed in 1 file:

sbu062 2022-06-21 21:46 Rev.: 12608

done many

38384 lines of code changed in 1 file:

sbu062 2022-06-21 16:17 Rev.: 12607

bayes, dyno and cod

5264 lines of code changed in 1 file:

sbu062 2022-06-21 16:02 Rev.: 12606

bayes

759 lines of code changed in 1 file:

sbu062 2022-06-21 12:46 Rev.: 12605

so far 10

11450 lines of code changed in 1 file:

sbu062 2022-06-21 10:17 Rev.: 12604

done outline

306 lines of code changed in 1 file:

sbu062 2022-06-21 09:09 Rev.: 12603

template for seminar

"Philosophical foundations of animal decision-making and
cognition"

I will write a better talk description later, but the idea was to (1) point
to the stimulus-response dogma (SR) and how it is rooted 17-18 century
empiricist philosophy, "associationism," behaviorism, early ethology
and modern behavioural ecology; (2) outline a framework for complexity
(vs. simplicity), show that the intuitive understanding of complexity and
the notion of complexity implicit in empiricist philosophy can be naive (it
could reflect human evolved cognitive traits) and misleading; (3) point that
the SR dogma of "simple association" as the "null hypothesis" is wrong; (4)
briefly describe the foundations of Solomonoff's theory of universal induction
(math of Occam's razor), and algorithmic complexity (Kolmogorov-Chaitin). (5)
outline an alternative framework that integrates
- Tinbergen's 4 questions
- Marr's levels of analysis for computational system
(6) Integrating causal inference with fitness provides a pathway for the
study of the evolution of animal decision-making and cognition.

With this framework, some problems (e.g. penotypic gambit) can be easily
solved, interesting questions (e.g. baseline/spontaneous activity) largely
ignored in the SR dogma can be studied, while some intriguing things like
innovation, creativity and consciousness can be (better) approached.

2179 lines of code changed in 1 file:

sbu062 2022-06-16 19:40 Rev.: 12602

delete obsolete debug code

0 lines of code changed in 1 file:

sbu062 2022-06-15 21:46 Rev.: 12601

white space only

1 lines of code changed in 1 file:

sbu062 2022-06-15 14:42 Rev.: 12600

(do_plot_output_rate_waste_ingested) now zoom interval function works, fixed also weird crashes

29 lines of code changed in 1 file:

sbu062 2022-06-15 11:53 Rev.: 12599

GUI implements ingestion rate for waste, ingested/provided

45 lines of code changed in 1 file:

sbu062 2022-06-15 11:09 Rev.: 12598

(get_ingestion_ratio_waste) function to get an array of ingested/provided for instantaneous waste

47 lines of code changed in 1 file:

sbu062 2022-06-14 21:05 Rev.: 12597

declare impurity

1 lines of code changed in 1 file:

sbu062 2022-06-14 20:15 Rev.: 12596

fix use pointer assignment operator
ifore was error:
{{{
Attempt to use pointer when it is not associated with a target
}}}

1 lines of code changed in 1 file:

sbu062 2022-06-14 20:02 Rev.: 12595

(do_plot_schedule_total_provided) in GUI mode for planning food provisioning schedule

74 lines of code changed in 1 file:

sbu062 2022-06-14 19:24 Rev.: 12594

(init_provisioning) isolates food provisioning arrays init code, for reuse

41 lines of code changed in 1 file:

sbu062 2022-06-14 18:30 Rev.: 12593

(get_food_schedule_display) get emulate food provisioning schedule for display and planning

23 lines of code changed in 1 file:

sbu062 2022-06-14 12:38 Rev.: 12592

fix bug confounding array name `is_day` and function (is_day) same name
This caused the feeding pattern code to produce night al the time

4 lines of code changed in 1 file:

sbu062 2022-06-14 10:47 Rev.: 12591

move food provisioning data to `dat` directory, must be CSV

87463 lines of code changed in 5 files:

sbu062 2022-06-14 10:38 Rev.: 12590

need consistent debug message

1 lines of code changed in 1 file:

sbu062 2022-06-14 10:30 Rev.: 12589

better GUI error reporting and diagnostics

29 lines of code changed in 1 file:

sbu062 2022-06-14 09:51 Rev.: 12588

fix dialog error message in (do_load_food_provision_file)

2 lines of code changed in 1 file:

sbu062 2022-06-14 09:48 Rev.: 12587

chek if provisioning file exists in (do_load_food_provision_file)

9 lines of code changed in 1 file:

sbu062 2022-06-14 09:38 Rev.: 12586

need report file problems in (do_load_food_provision_file)

6 lines of code changed in 1 file:

sbu062 2022-06-14 09:08 Rev.: 12585

`|` can substitute CRLF in dislin code

1 lines of code changed in 1 file:

sbu062 2022-06-14 09:02 Rev.: 12584

need confirm loading provision file in GUI

2 lines of code changed in 1 file:

sbu062 2022-06-13 22:13 Rev.: 12583

implemented fish object load functionality in GUI mode

60 lines of code changed in 1 file:

sbu062 2022-06-13 14:21 Rev.: 12582

implemented save binary fish object data in GUI mode

60 lines of code changed in 1 file:

sbu062 2022-06-13 09:13 Rev.: 12581

ieee module call is obsolete

0 lines of code changed in 2 files:

sbu062 2022-06-13 09:09 Rev.: 12580

add include files for gfortran and Intel fortran to respectively gf and if dirs

21 lines of code changed in 3 files:

sbu062 2022-06-12 21:39 Rev.: 12579

rw option for Hanif branch

4 lines of code changed in 1 file:

sbu062 2022-06-12 09:45 Rev.: 12577

implemented fish data object load functionality in CMD mode

37 lines of code changed in 1 file:

sbu062 2022-06-11 06:38 Rev.: 12576

(test_run) optional `is_get_fish_agent_file` can be TRUE or FALSE explicitly

9 lines of code changed in 1 file:

sbu062 2022-06-11 06:28 Rev.: 12575

(test_run) can get FISH object data saved from file if `is_get_fish_agent_file` option is set TRUE

19 lines of code changed in 1 file:

sbu062 2022-06-11 06:07 Rev.: 12574

(test_run) more intuitive output parameter `fish_agent_out`

5 lines of code changed in 3 files:

sbu062 2022-06-10 22:12 Rev.: 12573

set `fish_object_file` parameter in CMD mode

19 lines of code changed in 1 file:

sbu062 2022-06-10 21:49 Rev.: 12572

CMD mode, command `save fish_object_data` calls (fish_save_object_state)

9 lines of code changed in 1 file:

sbu062 2022-06-10 21:32 Rev.: 12571

invocation of (test_run) in both CMD and GUI return the full `FISH` object data that can be saved; saving not done yet

8 lines of code changed in 2 files:

sbu062 2022-06-10 21:08 Rev.: 12570

white space only

1 lines of code changed in 1 file:

sbu062 2022-06-10 21:06 Rev.: 12569

(test_run): caller procedure can get output `fish_agent_get` parameter
This is needed to be able to use (fish_save_object_state) with data from the current simulation

8 lines of code changed in 1 file:

sbu062 2022-06-10 20:41 Rev.: 12568

compare two conforming arrays to check equality

4 lines of code changed in 1 file:

sbu062 2022-06-10 19:17 Rev.: 12567

set FISH object binary file name from `fish_object_file` configuration parameter

3 lines of code changed in 1 file:

sbu062 2022-06-10 19:12 Rev.: 12566

define FISH object file name

11 lines of code changed in 1 file:

sbu062 2022-06-10 18:11 Rev.: 12565

procedure to get FISH object from plaftorm-specific binary file

31 lines of code changed in 1 file:

sbu062 2022-06-10 17:59 Rev.: 12564

function to save FISH object in a platform-specific binary file

26 lines of code changed in 1 file:

sbu062 2022-06-10 12:11 Rev.: 12563

test file save and read derived type data structure

44 lines of code changed in 1 file:

sbu062 2022-06-09 14:05

no need obsolete file

0 lines of code changed in 2 files:

sbu062 2022-06-08 10:59 Rev.: 12560

simulation for `midgut_michaelis_k`

5 lines of code changed in 1 file:

sbu062 2022-06-08 10:12 Rev.: 12559

reset `midgut_michaelis_r_max`

5 lines of code changed in 1 file:

sbu062 2022-06-08 10:06 Rev.: 12558

fix input file name

1 lines of code changed in 1 file:

sbu062 2022-06-08 10:00 Rev.: 12557

copied worksheet for data r12551

201 lines of code changed in 1 file:

sbu062 2022-06-08 09:49 Rev.: 12556

data from simulation r12551 `midgut_michaelis_r_max`

657 lines of code changed in 1 file:

ksc046 2022-06-07 12:58 Rev.: 12555

test

1 lines of code changed in 1 file:

sbu062 2022-06-07 12:56 Rev.: 12554

add user to rw

1 lines of code changed in 1 file:

nzlcj 2022-06-07 12:21 Rev.: 12553

Testing Kims subversion.

1 lines of code changed in 1 file:

sbu062 2022-06-07 11:55 Rev.: 12552

better style

9 lines of code changed in 2 files:

sbu062 2022-06-07 10:00 Rev.: 12551

run simulation check `midgut_michaelis_r_max`
do also revert `svn merge -r HEAD:12532 .`

8 lines of code changed in 1 file:

sbu062 2022-06-03 20:15 Rev.: 12550

main configuration file can be set using the environment variable: `FFA_MODEL_PARAMETER_FILE`

51 lines of code changed in 7 files:

sbu062 2022-06-03 05:04 Rev.: 12549

version sent to Marc

9 lines of code changed in 1 file:

sbu062 2022-06-02 12:19 Rev.: 12548

changes today

263 lines of code changed in 1 file:

sbu062 2022-06-01 20:52 Rev.: 12547

doc: documented `day_starts_hour`

8 lines of code changed in 1 file:

sbu062 2022-06-01 17:39 Rev.: 12546

set and report `Global_Day_Starts_Hour` in GUI mode

103 lines of code changed in 1 file:

sbu062 2022-06-01 16:28 Rev.: 12545

set and report `Global_Day_Starts_Hour` in CMD mode

15 lines of code changed in 2 files:

sbu062 2022-06-01 16:10 Rev.: 12544

added `Global_Day_Starts_Hour` parameter for day start offset in (is_day)

18 lines of code changed in 4 files:

sbu062 2022-06-01 11:24 Rev.: 12543

add comments for gnuplot-based plotting for parameter optimisation

8 lines of code changed in 1 file:

sbu062 2022-06-01 11:12 Rev.: 12542

get back to zero `DAY_STARTS_HOUR` for compatibility with earlier models

1 lines of code changed in 1 file:

sbu062 2022-06-01 11:11 Rev.: 12541

add comment on adjustment for `DAY_STARTS_HOUR`

17 lines of code changed in 1 file:

sbu062 2022-06-01 11:00 Rev.: 12540

in (is_day) function, day-night schedule can now follow calendar pattern with `DAY_STARTS_HOUR` parameter, not light-dark pattern starting from light.
TODO: need adding `DAY_STARTS_HOUR` to global model parameters

9 lines of code changed in 1 file:

sbu062 2022-06-01 09:06 Rev.: 12539

use the (is_day) function not duplicate code

1 lines of code changed in 1 file:

May 2022 »

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