hatchery-analysis.RmdThis analysis provides the proportion_hatchery,
hatchery_allocation and
natural_adult_removal_rate inputs to the springRunDSM.
Temporal Range: 2010 - 2012
Most data were obtained from CWT (coded wire tag) analyses with limited data in 2010 from CVPIA ChinookProd Database Version 2, September 22, 2017. Data from these sources were compiled in a csv called hatchery_fish_fate2010_2012.csv.
Adjustment to Feather and Yuba Rivers:
Feather and Yuba Rivers do not separate spring and fall run in totals. Here, we apply the proportion of spring hatchery return adults to adjust the totals for 2010 - 2012. Data used for Feather and Yuba adjustment were from GrandTab 2017 version.
The data table below shows the prepped data for analysis.
(No_hatch_returns corresponds to the number of hatchery
fish returning, Hatch_flag describes if fish are
hatchery(1) or not hatchery(0))
The proportion_hatchery for each tributary is calculated
below. To find the proportion_hatchery, we grouped our data
by tributary and summarized to find the mean percentage of hatchery fish
for each tributary.
The number of hatch_adults is determined in the
model.R script through a multinominal distribution, with
the probability equal to the hatchery_allocation calculated
below.
To find the hatchery_allocation we calculated the
proportion of hatchery fish allocated to each tributary in each year,
grouped our data by tributary and Run, and summarized to find the mean
percentage of hatchery fish for each tributary.
We assign lowest proportion of Spring Run hatchery fish spawning in our observed dataset to these tributaries and we renormalize the values so that they all sum to 1.
natural_adult_removal_rate is used in the springRunDSM
by the get_spawning_adults() function. The number of
natural_adults_by_month is determined by the binomial
distribution with the probability equal to the
1 - natural_adult_removal_rate.
We calculated the natural adult removal rate for each tributary by estimating the proportion of naturally produced fish used in a hatchery (i.e., they did not spawn).
For Spring Run natural_adult_removal_rate, there is 1
tributary where fish is removed for use in hatcheries.