Imitial commit, Gary and Nick's code edited time period and made hypnorum focal species
test commit
now contains bombus only filter for calculating 'LL'
uses a grep to subset bombus records out, then has some new plotting functions for means and credible intervals
LL all bees for comparison, date and time now in filename
produced equivalent plots for bombus and all bee list lengths (with list length as covariate) and histograms of list length distributions for all bees and Bombus
saves output with date in the filename, improved plotting function
plotting functions for 'Arco' model which treats LL a a factor with 3 levels
started work on assessment of gradients in LCM to inform creation of factors for SDM
LCM PCA, subset now works more efficiently; PCA runs and gives plots of gradients this is temporary hiatus while I work on:

Dynamic model, recoded 'Arco' model so that: occupancy depends on previous state, a global persistence prob and a colonisation prob coded over year. Random site effect removed. Strong prior for occupancy in 2000 to be effectively 0
Implemented dynamic model and incresed run to 50000 (nt = 2, burn in = 5000), all parameters converge
Merge branch 'master' of https://github.com/LPCrowther/dynamic_occ_mods