Initial MSc code

Code for MSc on capture recapture analysis. Currently contains
population matrix simulators, capture matrix simulators and some
functions to calculate estimators.
Various fixes

Separated simulation of population and capture matrices. Can now run
several capture simulations on same population. Began adding function
for Jolly Seber estimator.
JS estimator start

Started implementing Jolly Seber estimator. Various functions to
calculate statistics. Currently using old code's variable names - FIX.
Code tidy

Deleted unnecessary code for capture matrices and useless stat code.
Began putting new stat code in for JS that takes capture matrix as
input.
Calculate marked function

Can now calculate number of previously marked animals in final sample of
capture matrix.
JS estimator

Finished JS estimator. Fixed bugs in analysis of CR Robust estimator.
Note that JS estimator is consistently low for early time - check that
statistics calculated correctly (haven't checked Z properly yet).
Added mean, mse and var

Added loop to main for open pop sim to calculate mean, mean squared
error and variance. Still need to work out how to implement bias.
Trout cod analysis

Added code for analysis of trout cod data. Values used in thesis tables.
Fix bugs JS function

Fixed bug in JS function. Number of released previously set to m, total
marked captured at i. Should be set to n, total captured at i.
Fixed bug in calcZ function. k should be calculated outside loop.
Bug fix and bias adjusted JS`

Fixed bug when only one animal is captured for a particular sampling
occasion. Also converted JS estimator to the bias adjusted version.
Lists for open sim

Open sim now uses lists to house estimators and statistics for different
methods. Capture matrix functions renamed
Create  testOpenSim function

Put all open simulation analysis into function
Comments

Commenting out next recapture year table code. Need to figure out how to
implement (maybe plyr?)
ggplot switch

Melted data and switched to using ggplot for plots
Plot change

Reordered method factor levels and changed plot title
Tidy code

Deleted some crap
Tidy up TC
TC dates for estimators.

Added date values and occasion for JS abundity estimates for TC data.
Munges data to tidy form and also now uses ggplot.
CR estimator for TC

Added CR estimator for TC. Also includes loop to investigate window
width impact and then plots.
Switched CR plot type for TC

Using geom_point instead of line now