Directory branches/henrik/ecoevo_ibm/R/

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

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

176 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm/R: for_risk_paper.R (new 175), time_series_plots.R (+1 -1)

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.

210 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm/R: initial_pop_plots.R (new 144), time_series_plots.R (+66 -84)

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

Now also saves cumulative fecundity for plotting purposes.

46 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+46 -13)

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

2 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+2)

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.

193 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+193 -143)

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

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

198 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+198 -55)

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.

41 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+41 -26)

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

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

29 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+29 -4)

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

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

29 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+29 -8)

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

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

24 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+24 -18)

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

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

11 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+11 -11)

hje044 2021-11-09 08:28 Rev.: 11768

Saves additional evolution plot, now including growth

51 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+51 -3)

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

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

45 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+45 -10)

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.

43 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+43 -6)

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

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

5 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+5)

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

Added biomass plot to R-script

16 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+16)

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.

83 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+83 -18)

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.

31 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+31 -26)

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

R now capable of importing and combining multiple .nc files

63 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+63 -25)

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.

1 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+1)

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

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

1 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+1 -1)

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

34 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+34 -3)

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

Improved efficiency in writing results, and added a makefile

10 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+10 -1)

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

1 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+1 -1)

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

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

27 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+27 -5)

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.

27 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+27 -16)

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

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

5 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+5)

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.

17 lines of code changed in 1 file:

• branches/henrik/ecoevo_ibm/R: time_series_plots.R (+17 -1)

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

Attempting to clean up files and ignores

186 lines of code changed in 2 files:

• branches/henrik/ecoevo_ibm/R: final_pop_plots.R (new 125), time_series_plots.R (new 61)