Projects for kalman filter: 
15 of
5
shown (2 visible only to FishBox members, 1 visible only to project members).



DARTER (Diffusion Approximation Tools for Extinction Risk Estimation)
by brice.semmens, last updated 8/23/07, sharing set to public
This program allows one to walk through the steps required to conduct a population viability analysis, or PVA, using a population time time series. The model outputs probabilities of extinction as a function of time steps into the future, and importantly, gives confidence intervals for these probabilities.This tool has two major advantages over traditional PVA techniques:
1) It uses a statespace Kalman filter that allows for both process and nonprocess error.
So what's the big deal? Functionally it filters the data, and allows a more accurate fit for population parameters of interest.2) It uses a Bayesian samplingimportanceresampling algorithm to fully address uncertainty in the parameter estimates given the data.Rather than developing a single function that describes the probability of population extinction through time, we can use the uncertainty in parameter estimates to develop 'probabilities of probabilities', or, the uncertainty surrounding the probability of extinction through time.

Estimating heritability from time series
by mdscheuerell, last updated 1/5/11, sharing set to public
We use a multivariate statespace model and a time series of yearly migration dates for sockeye salmon to estimate the heritability coef from the classic breeder's equation.
The 2 files below are the dataset and the R script.

MARSS Dev Site
by e2holmes, last updated 9/30/14, sharing set to public
MARSS is an R package to fit mulitvariate autoregressive statespace (MARSS) models with Gaussian errors to multivariate time series data. Developers: Eli Holmes, Eric Ward, Mark Scheuerell and Kellie Wills. This is the DEVELOPMENT site for the MARSS. For the current MARSS release go to CRAN or download straight from the R GUI using "Install Packages" menu. To see what's coming in the next version, click NEWS in the files.
To install patchessource("patchfile.r") #replace with actual file name
To install the development version
library(R.utils) #install if needed
#replace patch_fun with function name in patchfile.r
reassignInPackage("patch_fun", pkgName="MARSS", patch_fun)library(devtools)
install_url("https://fishbox.nwfsc.noaa.gov/zip/e2holmes/MARSS%20Dev%20Site/MARSS_source.zip") 
PVA estimation code
by e2holmes, last updated 11/9/07, sharing set to public
A series of modules for estimation of PVA parameters from time series data. Uses kalman filters, REML, and slope methods. 
Teaching code for Statespace models
by e2holmes, last updated 5/31/07, sharing set to public
This is some matlab labs for teaching basic concepts about stochastic population trajectories and estimation for those trajectories.
Projects for kalman filter: 
15 of
5
shown (2 visible only to FishBox members, 1 visible only to project members).

