Update ProjectNotes

ProjectNotes

@@ -1,14 +1,30 @@
 Next steps for eSeal Data Analysis
 
 1. Plot Data through time for each age class and for each site.  ALSO plot total for all sites.
-1. For COWS, use the largest count of the year and correct for count (date adjusted) using the data in appendix of Condit et al 2021.
-1. For all other age classes, just use largest count of year.
+2. For COWS, use the largest count of the year and correct for count (date adjusted) using the data in appendix of Condit et al 2021.
+3. For all other age classes, just use largest count of year.
 
-## New 2021-06/01
+## New 2021-06-01
 
 1. EPUP should be grouped with PUP.  
-1. please make the plots as we discussed, but we will likely only do statistical analysis on:
+2. please make the plots as we discussed, but we will likely only do statistical analysis on:
   - COWS
   - PUPS combined with WEANERS on the same day for a maximum annual count.
-1. Note that YEAR is tricky since the surveys often start in december of the previous year and continue through the winter of the current year.  
-1. So surveys from December should be included with JAN, FEB, MARCH, APRIL, etc. of the current year.
+3. Note that YEAR is tricky since the surveys often start in december of the previous year and continue through the winter of the current year.  
+4. So surveys from December should be included with JAN, FEB, MARCH, APRIL, etc. of the current year.
+
+
+## 2021-06-09
+
+Silas has coded plotting functions.
+Next steps:
+
+1. Think about population trend analyses for the tree sites and population as whole.
+  A. FIRST BASIC
+    i. Simple linear regression on log(counts) for cows and pups/weaners at the three sites and as a whole. 
+    ii. Could also do generalized linear model with counts as poisson distributed.
+  B. THEN ADVANCED
+    i. Use either the ATSAR package or the MARSS package to build multivariate state-space models of the three sites to get population trajectories
+    ii. ATSAR: https://nwfsc-timeseries.github.io/atsa-labs/
+      chapters 7, 8, 13, 
+