Directory branches/henrik/ecoevo_ibm/

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Most Recent Commits

hje044 2022-06-30 09:19 Rev.: 12648

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

13 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+13 -6)

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.

170 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: main.f90 (+167 -79), svnignore.txt (+3 -1)

hje044 2022-04-06 08:36 Rev.: 12345

Now also saves cumulative fecundity for plotting purposes.

45 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+45 -20)

hje044 2022-03-15 12:29 Rev.: 12223

R script can now handle NA values, allowing me to load in runs that crashed prior to finishing

11 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+11 -7)

hje044 2022-03-11 08:09 Rev.: 12220

Added option for increasing temperature over the years, and generalised parameters for stochastic deviance in inheritance and phenotypic plasticity.

80 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+80 -59)

hje044 2022-02-02 09:41 Rev.: 12148

Includes better plotting functionality in R using interactive Plotly plots ans Esquisser() function built facet plots.

6 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+6 -6)

hje044 2022-01-26 09:48 Rev.: 12015

Added diminishing returns to Appetite-energy, and moved Appetite onto energy intake rather than energy availability. Full rundown in OneNote 2022-2 and 2022-3.

44 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+44 -37)

hje044 2021-12-08 11:12 Rev.: 11861

Moved density dependance to energy rather than appetite, testing out deminishing returns on appetite

14 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+14 -10)

hje044 2021-11-29 11:54 Rev.: 11836

Makefile updated to be OS-agnostic. NetCDF libraries now pulled based on operating system

13 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: main.f90 (+5 -5), makefile (+8)

hje044 2021-11-11 14:29 Rev.: 11797

Saved large runs after 10K years to reach equilibrium both fished and unfished

5 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+5 -3)

hje044 2021-11-09 09:16 Rev.: 11771

New plots for wholly unfished population as well, use in meeting tomorrow

5 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+5 -4)

hje044 2021-11-03 11:25 Rev.: 11734

Now plots evolution of maturation-related measures for all runs.

12 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: main.f90 (+11 -3), makefile (+1 -1)

hje044 2021-11-02 13:43 Rev.: 11725

Model now also capable of saving heritabilities. R-script updated to also pull in several runs heritabilities, and plotting these.

69 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+69 -13)

hje044 2021-10-25 13:09 Rev.: 11694

Fixed a bug which added negative growth to smaller individuals, eventually leading to crashing the population

30 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+30 -29)

hje044 2021-10-20 10:19 Rev.: 11644

Added biomass plot to R-script

1 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+1 -1)

hje044 2021-10-18 11:44 Rev.: 11625

R loads parameters too, and now plots several runs alongside each other. Saved results include evolving traits, which R now plots over the years.

40 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: main.f90 (+39 -29), makefile (+1 -1)

hje044 2021-10-14 09:59 Rev.: 11581

Fixed bug in calculating skipspawnthreshold, number of spawn skippers now much more realistic, and no more negative gonad growth. Also added R functionality to read data when only a single run was made.

36 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: main.f90 (+33 -18), makefile (+3 -2)

hje044 2021-10-12 10:02 Rev.: 11568

R now capable of importing and combining multiple .nc files

1 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+1 -1)

hje044 2021-10-11 17:15 Rev.: 11567

Now saves standard deviation, and avoids overwriting previous runs

95 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: main.f90 (+94 -55), makefile (+1 -1)

hje044 2021-10-06 11:08 Rev.: 11560

Cleaned up remnants of csv saving paradigm, and added legend to netCDF file. Also included new function to calculate standard deviation to be implemented in saving the results.

83 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: main.f90 (+76 -101), makefile (+7 -2)

hje044 2021-10-05 15:15 Rev.: 11555

netCDF file now also contains the parameters used in the saved run

58 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+58 -54)

hje044 2021-10-05 14:46 Rev.: 11553

Added netCDF saving functionality to the fortran script, and rewrote R-script to load 3d netCDF data instead

97 lines of code changed in 3 files:

• branches/henrik/ecoevo_ibm: ecoevo_ibm.Rproj (+15 -13), main.f90 (+65 -6), makefile (+17 -5)

hje044 2021-09-27 15:58 Rev.: 11519

Improved efficiency in writing results, and added a makefile

58 lines of code changed in 3 files:

• branches/henrik/ecoevo_ibm: ecoevo_ibm.Rproj (+13 -13), main.f90 (+18 -15), makefile (new 27)

hje044 2021-08-31 10:58 Rev.: 11416

Model now saves files with years run in the filename to avoid overwriting when continuing population from earlier

94 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+94 -70)

hje044 2021-08-30 11:08 Rev.: 11396

Added density dependant food environment, as well as saving results for these, and R plotting

36 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: main.f90 (+36 -21), recursive_testing.f90 (del)

hje044 2021-08-23 11:55 Rev.: 11350

144 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: recursive_testing.f90 (new 144)

hje044 2021-08-23 11:53 Rev.: 11349

Model now includes a recursive function for pulling random parents, which increase efficiency significantly. In addition, the model prints updates every few years, more stochasticity is included, and more comments have been added to increase readability.

125 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+125 -65)

hje044 2021-08-17 10:56 Rev.: 11327

Added minimum energy for migrating, several types of stochastisticity, and most importantly: inheritance based on values from weighted random parent selection

80 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+80 -24)

hje044 2021-08-05 11:34 Rev.: 11322

Added pop-size switch, included mixed fishing as GearType and tested random_normal() function.

104 lines of code changed in 3 files:

• branches/henrik/ecoevo_ibm: m_random.f90 (+2 -2), main.f90 (+101 -35), svnignore.txt (+1)

hje044 2021-05-18 10:55 Rev.: 11172

Added many comments for readability, and now scales recruitment to TargetInd (tentatively)

1653 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: m_random.f90 (+1594 -52), main.f90 (+59 -25)

hje044 2021-03-31 11:19 Rev.: 10969

Fisheries mortality implemented. Calculated for Trawl, Gillnet and Unselective. R script now generates plots for population dynamics by year.

28 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm: main.f90 (+28 -21)

hje044 2021-03-24 12:03 Rev.: 10845

Finally figured out how to properly set ignore for subfolders for all unversioned files.

16 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: ecoevo_ibm.Rproj (new 13), svnignore.txt (+3 -4)

hje044 2021-03-24 11:47 Rev.: 10842

Attempting to clean up files and ignores

76 lines of code changed in 6 files:

• branches/henrik/ecoevo_ibm: a.out (changed), base_utils.mod (del), csv_io.mod (del), m_random.f90 (new 53), m_zrand.f90 (new 10), svnignore.txt (new 13)

hje044 2021-03-24 11:17 Rev.: 10840

Starting out using svn properly, hopefully

406 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm: a.out (changed), main.f90 (+406 -139)

hje044 2020-03-09 09:20 Rev.: 9499

Attempting to add the first version, which contains initialization, dummy growth, recruitment and age/removal

11206 lines of code changed in 6 files:

• branches/henrik/ecoevo_ibm: a.out (new), base_utils.f90 (new 5774), base_utils.mod (new), csv_io.mod (new), m_csv_io.f90 (new 5120), main.f90 (new 312)