Sightability model definition

Primary Investigator: Althea ArchMiller

Collaborators: J. Fieberg, B. Dorazio, K. St. Clair

Description This JAGS model takes the detection/non-detection data from the sightability trials (2005 to 2007) and fits the sightability model (i.e., logistic regression between observation (binary) and visual obstruciton (0 to 1))

Preamble

# Documentation-related
library(devtools)
library(knitr)
library(ezknitr)

JAGS Model Definition

Sightabilty model

model.tilde <- function(){
  #### PRIORS

  # Detection model
  b0g ~ dnorm(0,0.1)
  b1g ~ dnorm(0,0.1)

  # PA data
  for(i in 1:R){ # each sightability trial
    logitg[i] <- b0g + b1g*x.tilde[i]
    g.tilde[i] <- exp(logitg[i])/(1+exp(logitg[i]))
    z.tilde[i] ~ dbern(g.tilde[i])
  }
}

Footer

Session Information

devtools::session_info()

## Session info --------------------------------------------------------------

##  setting  value                       
##  version  R version 3.3.2 (2016-10-31)
##  system   x86_64, darwin13.4.0        
##  ui       RStudio (1.0.136)           
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  tz       America/Chicago             
##  date     2017-03-29

## Packages ------------------------------------------------------------------

##  package     * version date       source        
##  devtools    * 1.12.0  2016-06-24 CRAN (R 3.3.0)
##  digest        0.6.12  2017-01-27 CRAN (R 3.3.2)
##  evaluate      0.10    2016-10-11 CRAN (R 3.3.0)
##  ezknitr     * 0.6     2016-09-16 CRAN (R 3.3.0)
##  knitr       * 1.15.1  2016-11-22 CRAN (R 3.3.2)
##  magrittr      1.5     2014-11-22 CRAN (R 3.3.0)
##  markdown      0.7.7   2015-04-22 CRAN (R 3.3.0)
##  memoise       1.0.0   2016-01-29 CRAN (R 3.3.0)
##  R.methodsS3   1.7.1   2016-02-16 CRAN (R 3.3.0)
##  R.oo          1.21.0  2016-11-01 CRAN (R 3.3.0)
##  R.utils       2.5.0   2016-11-07 CRAN (R 3.3.0)
##  rstudioapi    0.6     2016-06-27 CRAN (R 3.3.0)
##  stringi       1.1.2   2016-10-01 CRAN (R 3.3.0)
##  stringr       1.1.0   2016-08-19 CRAN (R 3.3.0)
##  withr         1.0.2   2016-06-20 CRAN (R 3.3.0)

spun with: ezknitr::ezspin(“programs/ms_programs/a_define_sightability_model.R”, out_dir = “output”, fig_dir = “figures”, keep_md = F)