I have gone through all tests @clorton and updated associated calc/est funcs and plotting code. All tests should run now, and all pass except for the spatial hazard. This commit has updated test script: 868979e

These are the only two loose ends to look into:

• Appears that the $\pi_{ij}$ matrix is transposed when it does not need to be (possible this is the source of the spatial hazard item)
• Spatial hazard calculation