This repository contains the code and data files for the unpublished content of my PhD thesis.
(Note on file extensions: .py and .pyx = python; .R and .rmd = R)
(Note: plot and function files are located in the Chapter 4 folder; files from the publication are located in the dedicated repository)
relationship_encountered_stones_to_depositions_sim_data.R:
numerical simulation for the discussion of Figure 3 in Franks and Deneubourg (1997)
run_large_sim:
simulations with all models (template-only, template + feedback, gradual model) across stone density values (runs sims, extracts results, and makes figures; funcs are in wall_funcs.py)
SA.pyx:
runs and analyses results from the sensitivity analysis (all models)
analyseData.R:
combines brood data and building event data files and calculates per-min building rate
Activity analysis - overall variables - best models selection.rmd (output: Activity-analysis-by-ROI---best-models-selection.pdf):
regression-model evaluation and comparison
best_starting_values_HMMs.R:
fits HMM regressions across a range of starting parameter values to ensure best fit is the global optimum
rates.csv:
processed data (used for model fit)
Column legend:
D = per-min deposition rate calculated over a 15 min interval
stone_dens = stone_dens value (averaged across interval)
n_ants = n of ants in the brood cluster (averaged across interval)
distance = distance between building site and brood cluster centroid, averaged across buildig sites (averaged across interval)
timepoints = time since start of building activity in the colony (min)
ID = colony ID
for data-processing replication/: folder contains raw data used to generate rates and covariates
Deposition_data-colonies_R54-R34-R29-R5.csv: raw building event data
Colony = colony ID
ROI = building site (numbered 1-3 in each colony)
x,y = building site coordinates in video (in pixel)
event = type of building event
behaviour_type = subtype of building event
time_in_video = time from video start at which the event takes place (hh:mm:ss format)
cut_video_start = lenght of cut from original video
time = time from original video start at which the event takes place
time_s, cut_from_video_start_s, cut_video_start_s = convertion to seconds of previous three columns
n_stones = n of stones at building site when event starts (i.e., not including effect of current event or of other events occurring simultaneously)
pixel/mm = n of pixels per mm in video
radius_mm = building site radius converted to mm
stone_density = n stones/mm at building site when event starts
brood_measurements - colonies_R34-R54-R29-R5 - anonymous measurers.xlsx: brood measurement data taken at 15 min time intervals
standardised_n_ants_in_cluster_1.5-ant = n of ants in cluster standardised within colony
X_centroid_1.5-ant, Y_centroid_1.5-ant = coordinates of brood cluster centroid (in pixels)
cluster_density_1.5-ant = density of brood cluster (ants/mm^2)
measurer = measurer ID
all_building_data - colonies_R54-R34-R29-R5.csv: combines above files
normalised time = time of event (s) from first building event in colony
ROI_coordinates.xlsx: pixel coordinates of the centre of each ROI
ind_var_sim.pyx:
epigenetic individual variation file (runs sims and extracts results; funcs are in wall_funcs.py)
make_plots.R:
makes all plots from building simulations (Chapter 2 and Chapter 4)
patrilines_sim.pyx:
patriline-specific individual variation file (runs sims and extracts results; funcs are in wall_funcs.py)
Rq_sweep.pyx:
mutation-in-germline file (runs sims and extracts results; funcs are in wall_funcs.py)
wall_funcs.py:
contains all wall-building simulation functions