For Herse et al. 'A demographic model to support customary management of a culturally important waterfowl species'

This analysis includes three R script files. Analysis should follow the order below. 

Refer to the annotations with the script files for more details.

1. Cygnet_survival.R
2. Back_calculate_SHY.R
3. Final_matrix_models.R

File descriptions/metadata:

readme.txt
  Short note on the R workflow

copy_data_Adult_aerial_counts_Waihora.csv
  Year
  Obs (observers)
  Survey (i.e., 1st or 2nd count)
  Adults
  Cygnets

copy_data_CygnetEncounters.csv
  Date
  Ordinal (date)
  Frequency (VHF radio)
  Colony_brood (colony where cygnet hatched from and was tagged)
  Cygnet_no (cygnet number, beginning with 1)
  Brood (brood ID, to account for some cygnets coming from the same brood)
  NZTM_east
  NZTM_north
  Encounter (captured, heard (but not seen), seen (alive), found depredated/scavenged, not detected)
  Type (either Aerial or Ground, i.e. from the airplane on the ground)
  Comments

data_for_cygnet_survival.csv
  ID (VHF frequency)
  time (follow up time, see 'survival' R package)
  time2 (ending time of the interval, i.e. censore time, see 'survival' R package)
  status (0 = alive, 1 = dead)
  site (nesting colony where the cygnet originated from; 1 = Ataahua, 2 = Kaituna, 3 = Yarrs)
  brood (brood number)

newnestdata_for_backcalc_SHY.csv
  Nest.ID 
  Recruitment.attempt1 (number of eggs hatched from the first nesting attempt)
  Colony (AT = Ataahua, KA = Kaituna, YA = Yarrs)
  Eggs.removed (egg harvest treatment: 0, 2, 4, or ALL eggs)
  Camera.initial (indicates where a camera was installed at the onset of nest monitoring, Y/N)

Cygnet_survival.R
  R script for modelling cygnet survival, as a first step for back-calculating hatch-year survival (SHY) to use in the final population
  model. Script also includes code for relevant figures.

Back_calculate_SHY.R
  R script for back-calculating hatch-year survival (SHY) to use in the final population model. Script also includes code for relevant
  figures.

Final_matrix_models.r
  R sript for developing the final population harvest model and plotting relevant figures.

transientdynamics_DavidFletcher.R
  R script for assessing potential transient population dynamics.