Devin Johnson dsjohnson
dsjohnson
/ stpp_rsf_helper.R
Created
December 11, 2013 21:17
Helper functions for analyzing animal telemetry data with point process models from Devin S. Johnson, Mevin B. Hooten, and Carey E. Kuhn (2013) Estimating animal resource selection from telemetry data using point process models. Journal of Animal Ecology 82:1155--1164.
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| ## Spatio-temporal point process RSF helper functions | |
| ### | |
| ### Create spatial polygons object from a SpatialPoints object | |
| ### | |
| voronoiPoly <- function(layer){ | |
| require(deldir) | |
| require(sp) | |
| crds <- layer@coords | |
| z <- deldir(crds[,1], crds[,2], rw=as.vector(t(bbox(layer)))) |
dsjohnson
/ run_nfs_analysis_pop_INLA.R
Created
December 11, 2013 21:26
Fur seal analysis from Devin S. Johnson, Mevin B. Hooten, and Carey E. Kuhn (2013) Estimating animal resource selection from telemetry data using point process models. Journal of Animal Ecology 82:1155--1164.
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| library(sp) | |
| library(rgdal) | |
| library(RColorBrewer) | |
| library(spdep) | |
| library(INLA) | |
| library(grid) | |
| library(gridExtra) | |
| Greys <- colorRampPalette(brewer.pal(9,"Greys")) | |
| #source("stpp_rsf_helper.R") | |
| load("nfs_analysis/JAE_analysis_data_spatial.RData") |
dsjohnson
/ run_nfs_analysis_indiv.R
Last active
December 31, 2015 02:09
Individual space-time analysis of fur seal data from : Devin S. Johnson, Mevin B. Hooten, and Carey E. Kuhn (2013) Estimating animal resource selection from telemetry data using point process models. Journal of Animal Ecology 82:1155--1164
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| library(sp) | |
| library(rgdal) | |
| library(raster) | |
| library(gstat) | |
| library(rgeos) | |
| library(automap) | |
| library(mgcv) | |
| source("stpp_rsf_helper.R") | |
| load("nfs_analysis/JAE_analysis_data_st.RData") | |
| # load("stQuadList_countVersion.RData") |
dsjohnson
/ run_nfs_data_assimilation.R
Created
December 11, 2013 21:30
Building data for fur seal analysis in: Devin S. Johnson, Mevin B. Hooten, and Carey E. Kuhn (2013) Estimating animal resource selection from telemetry data using point process models. Journal of Animal Ecology 82:1155--1164
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| library(sp) | |
| library(rgdal) | |
| library(raster) | |
| library(gstat) | |
| library(rgeos) | |
| library(automap) | |
| library(adehabitatHR) | |
| source("stpp_rsf_helper.R") | |
| # Read in telemtry |
dsjohnson
/ NFS_CR_simulation.R
Last active
January 2, 2016 20:39
Simulation of a Northern fur seal CR data set
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| library("marked") | |
| #### Some preliminaries ### | |
| ilogit = function(x){log(x/(1-x))} | |
| min.adult.age=5 | |
| additional.resight=3 | |
| adult.age="stable" | |
| set.seed(111) | |
| n.rel.pup=c(138,57,38,250,rep(100,4)) |
dsjohnson
/ R symlinks
Last active
August 29, 2015 14:00
Symliks to add for R 3.1.0 (Mavericks version) to run and compile packages
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| After you have installed gfortran from homebrew using | |
| $ brew install gfortran | |
| After installing R... add the following lines to ~/.R/Makevars | |
| FC = /usr/local/bin/gfortran | |
| F77 = /usr/local/bin/gfortran | |
| FLIBS = -L/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9 -lgfortran -lquadmath -lm | |
| and openblas using | |
| $ brew install openblas |
dsjohnson
/ logistic_funcs.R
Last active
November 9, 2015 19:46
Fit logistic growth model like "nlsList" but allow user to specify a design matrix for each parameter
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| ### New growth function | |
| logistic_growth = function(x, phi1, phi2, phi3){ | |
| phi1/(1 + exp(-(x-phi2)/phi3)) | |
| } | |
| ll_logistic = function(par, y, xvar, phi1_dm, phi2_dm, phi3_dm, sigma_dm, sigma=1, predict=FALSE, scale=-2){ | |
| n1 = ncol(phi1_dm) | |
| n2 = ncol(phi2_dm) | |
| n3 = ncol(phi3_dm) | |
| if(!missing(sigma_dm)) n4 = ncol(sigma_dm) |
dsjohnson
/ logistic_analysis_stan.R
Last active
November 10, 2015 01:26
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| library(rstan) | |
| devtools::source_gist("8f675b9aa74ab9900fb4") | |
| load("Sig_test_DJ.RData") | |
| data = all_model | |
| data$Year = factor(data$Year) | |
| data = droplevels(data) | |
| ### Add beach variables | |
| data$Beach4 = ifelse(data$Beach=="4", 1, 0) | |
| data$Beach7 = ifelse(data$Beach=="7", 1, 0) |
dsjohnson
/ logistic_analysis_stan_summary.R
Created
November 13, 2015 19:18
Summary of logistic growth MCMC output from stan
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| library(cowplot) | |
| library(coda) | |
| load("Sig_test_DJ.RData") | |
| data = all_model | |
| data$Year = factor(data$Year) | |
| data = droplevels(data) | |
| ### Add beach variables | |
| data$Beach4 = ifelse(data$Beach=="4", 1, 0) | |
| data$Beach7 = ifelse(data$Beach=="7", 1, 0) |
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| ### Load packages ### | |
| # Must have 'marked' v >= 1.1.8 | |
| library(marked) | |
| # The splines package is only necessary for fitting b-spline curves used in the paper | |
| # It is not required for the multivate models in the marked package | |
| library(splines) | |
| ### Import and process data ### |
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