hierarchicalDS: Functions For Performing Hierarchical Analysis of Distance Sampling Data

Functions for performing hierarchical analysis of distance sampling data, with ability to use an areal spatial ICAR model on top of user supplied covariates to get at variation in abundance intensity. The detection model can be specified as a function of observer and individual covariates, where a parametric model is supposed for the population level distribution of covariate values. The model uses data augmentation and a reversible jump MCMC algorithm to sample animals that were never observed. Also included is the ability to include point independence (increasing correlation multiple observer's observations as a function of distance, with independence assumed for distance=0 or first distance bin), as well as the ability to model species misclassification rates using a multinomial logit formulation on data from double observers. New in version 2.1 is the ability to include zero inflation, but this is only recommended for cases where sample sizes and spatial coverage of the survey are high.

AuthorP.B. Conn \email{paul.conn@@noaa.gov}
Date of publication2014-11-26 08:09:54
MaintainerPaul B Conn <paul.conn@noaa.gov>
LicenseUnlimited
Version2.9

View on CRAN

Man pages

calc_linex_a: estimate optimal 'a' parameter for linex loss function

convert.HDS.to.mcmc: function to convert HierarchicalDS MCMC list vector (used in...

generate_inits: generate initial values for MCMC chain if not already...

generate_inits_misID: generate initial values for misID model if not already...

get_confusion_array: Fill confusion array - one confusion matrix for each...

get_confusion_mat: Fill a list with confusion matrices for each record

get_mod_matrix: function to produce a design matrix given a dataset and...

hierarchical_DS: Primary function for hierarchical, areal analysis of distance...

linear_adj: Produce an adjacency matrix for a vector

log_lambda_gradient: compute the first derivative of log_lambda likelihood...

log_lambda_log_likelihood: compute the likelihood for nu parameters

mcmc_ds: Function for MCMC analysis

plot_N_map: function to plot a map of abundance. this was developed for...

plot_obs_pred: plot 'observed' versus predicted values for abundance of each...

post_loss: function to calculate posterior predictive loss given the...

probit.fct: Mrds probit detection and related functions

rect_adj: Produce an RW1 adjacency matrix for a rectangular grid for...

rect_adj_RW2: Produce an RW2 Adjacency matrix for a rectangular grid for...

rrw: SIMULATE AN ICAR PROCESS

simdata: MCMC output from running example in Hierarchical DS

sim_out: MCMC output from running example in Hierarchical DS

simulate_data: function to simulate double observer spatial distance...

square_adj: Produce an adjacency matrix for a square grid

stack_data: function to stack data (going from three dimensional array to...

stack_data_misID: function to stack data for midID updates (going from four...

summary_N: calculate parameter estimates and confidence intervals for...

switch_pdf: function to calculate the joint pdf for a sample of values...

switch_sample: function to sample from a specified probability density...

switch_sample_prior: function to sample from hyperpriors of a specified...

table.mcmc: function to export posterior summaries from an mcmc object to...

Files in this package

hierarchicalDS
hierarchicalDS/inst
hierarchicalDS/inst/cache
hierarchicalDS/inst/cache/cache-example11_dec9ea02145bf8c1095cf437a7785a4c.rdx
hierarchicalDS/inst/cache/cache-example7_1640587fd6f8e638b98c524b7123ab4b.RData
hierarchicalDS/inst/cache/cache-example8_d1e3bea60985f9d4426852c68af6d816.RData
hierarchicalDS/inst/cache/cache-example10_522be745bfde15eff1594dca0074fd64.RData
hierarchicalDS/inst/cache/cache-example4_b43fe5abd76a24257f2f78e4bc001b2b.RData
hierarchicalDS/inst/cache/cache-example6_88ab8a01ed70b5e42b8b3dd01ef497ee.rdx
hierarchicalDS/inst/cache/cache-example20_6f7447e99b705f65de93e63e193f819f.RData
hierarchicalDS/inst/cache/cache-example14_6700128c3164be34d9c445284c7ce74e.rdb
hierarchicalDS/inst/cache/cache-example21_ce2624066512c74c285f03af2512a639.rdb
hierarchicalDS/inst/cache/cache-install2_ad7f9b4fa93b009394879a017973668b.rdx
hierarchicalDS/inst/cache/cache-example13_042a549245272ed844ac6b568a2a2cb5.rdx
hierarchicalDS/inst/cache/cache-example10_522be745bfde15eff1594dca0074fd64.rdx
hierarchicalDS/inst/cache/cache-example16_dce2cf83f0ab177834e256535325e427.rdb
hierarchicalDS/inst/cache/cache-example15_86d12bb607e1490926b5e0f1d0649b3e.rdb
hierarchicalDS/inst/cache/cache-example21_ce2624066512c74c285f03af2512a639.rdx
hierarchicalDS/inst/cache/cache-example5_08fd60505630e091a5ab43cdd20103f2.RData
hierarchicalDS/inst/cache/cache-example12_6e95c814fb486629588b6c7248a9631b.RData
hierarchicalDS/inst/cache/cache-example15_86d12bb607e1490926b5e0f1d0649b3e.rdx
hierarchicalDS/inst/cache/cache-example13_042a549245272ed844ac6b568a2a2cb5.rdb
hierarchicalDS/inst/cache/cache-example3_1a5d77ae6c4e263618c484339a31040c.rdb
hierarchicalDS/inst/cache/cache-example13_042a549245272ed844ac6b568a2a2cb5.RData
hierarchicalDS/inst/cache/cache-example17_5dea3befa2f5a8c4ff414568f703d3ef.rdx
hierarchicalDS/inst/cache/cache-install1_495d4a18e95bbe663768664c96919772.RData
hierarchicalDS/inst/cache/cache-example11_dec9ea02145bf8c1095cf437a7785a4c.RData
hierarchicalDS/inst/cache/cache-example5_08fd60505630e091a5ab43cdd20103f2.rdx
hierarchicalDS/inst/cache/cache-example4_b43fe5abd76a24257f2f78e4bc001b2b.rdb
hierarchicalDS/inst/cache/cache-example8_d1e3bea60985f9d4426852c68af6d816.rdb
hierarchicalDS/inst/cache/cache-example20_6f7447e99b705f65de93e63e193f819f.rdx
hierarchicalDS/inst/cache/cache-example2_1843aba5a766a84a0a6d376186282424.rdb
hierarchicalDS/inst/cache/cache-example14_6700128c3164be34d9c445284c7ce74e.RData
hierarchicalDS/inst/cache/cache-example18_35bc47a2091aebf483f6a43b0fd9d253.rdb
hierarchicalDS/inst/cache/cache-example17_5dea3befa2f5a8c4ff414568f703d3ef.rdb
hierarchicalDS/inst/cache/cache-example6_88ab8a01ed70b5e42b8b3dd01ef497ee.rdb
hierarchicalDS/inst/cache/cache-example3_1a5d77ae6c4e263618c484339a31040c.rdx
hierarchicalDS/inst/cache/cache-example5_08fd60505630e091a5ab43cdd20103f2.rdb
hierarchicalDS/inst/cache/cache-example18_35bc47a2091aebf483f6a43b0fd9d253.rdx
hierarchicalDS/inst/cache/cache-install2_ad7f9b4fa93b009394879a017973668b.RData
hierarchicalDS/inst/cache/cache-example10_522be745bfde15eff1594dca0074fd64.rdb
hierarchicalDS/inst/cache/cache-example22_26009984fc3c8c17d6aea2fcf9799aa0.rdx
hierarchicalDS/inst/cache/cache-example2_1843aba5a766a84a0a6d376186282424.RData
hierarchicalDS/inst/cache/cache-install1_495d4a18e95bbe663768664c96919772.rdx
hierarchicalDS/inst/cache/cache-example16_dce2cf83f0ab177834e256535325e427.rdx
hierarchicalDS/inst/cache/cache-example19_e27b6f11e2391ff1df05057eac8c0fa5.rdb
hierarchicalDS/inst/cache/cache-example1_82a67210abcd15ccfdb62ae5d45a6c9d.rdb
hierarchicalDS/inst/cache/cache-example17_5dea3befa2f5a8c4ff414568f703d3ef.RData
hierarchicalDS/inst/cache/cache-example7_1640587fd6f8e638b98c524b7123ab4b.rdb
hierarchicalDS/inst/cache/cache-example19_e27b6f11e2391ff1df05057eac8c0fa5.rdx
hierarchicalDS/inst/cache/cache-example11_dec9ea02145bf8c1095cf437a7785a4c.rdb
hierarchicalDS/inst/cache/cache-example2_1843aba5a766a84a0a6d376186282424.rdx
hierarchicalDS/inst/cache/cache-example12_6e95c814fb486629588b6c7248a9631b.rdx
hierarchicalDS/inst/cache/cache-example9_dd16693b1903f69e47e937a065112f2d.RData
hierarchicalDS/inst/cache/cache-example1_82a67210abcd15ccfdb62ae5d45a6c9d.RData
hierarchicalDS/inst/cache/cache-example18_35bc47a2091aebf483f6a43b0fd9d253.RData
hierarchicalDS/inst/cache/cache-example9_dd16693b1903f69e47e937a065112f2d.rdb
hierarchicalDS/inst/cache/cache-example9_dd16693b1903f69e47e937a065112f2d.rdx
hierarchicalDS/inst/cache/cache-example20_6f7447e99b705f65de93e63e193f819f.rdb
hierarchicalDS/inst/cache/cache-example7_1640587fd6f8e638b98c524b7123ab4b.rdx
hierarchicalDS/inst/cache/cache-example15_86d12bb607e1490926b5e0f1d0649b3e.RData
hierarchicalDS/inst/cache/cache-install1_495d4a18e95bbe663768664c96919772.rdb
hierarchicalDS/inst/cache/cache-example16_dce2cf83f0ab177834e256535325e427.RData
hierarchicalDS/inst/cache/cache-example19_e27b6f11e2391ff1df05057eac8c0fa5.RData
hierarchicalDS/inst/cache/cache-example4_b43fe5abd76a24257f2f78e4bc001b2b.rdx
hierarchicalDS/inst/cache/cache-example12_6e95c814fb486629588b6c7248a9631b.rdb
hierarchicalDS/inst/cache/cache-__packages
hierarchicalDS/inst/cache/cache-example3_1a5d77ae6c4e263618c484339a31040c.RData
hierarchicalDS/inst/cache/cache-example22_26009984fc3c8c17d6aea2fcf9799aa0.RData
hierarchicalDS/inst/cache/cache-example6_88ab8a01ed70b5e42b8b3dd01ef497ee.RData
hierarchicalDS/inst/cache/cache-example21_ce2624066512c74c285f03af2512a639.RData
hierarchicalDS/inst/cache/cache-example1_82a67210abcd15ccfdb62ae5d45a6c9d.rdx
hierarchicalDS/inst/cache/cache-example8_d1e3bea60985f9d4426852c68af6d816.rdx
hierarchicalDS/inst/cache/cache-example14_6700128c3164be34d9c445284c7ce74e.rdx
hierarchicalDS/inst/cache/cache-example22_26009984fc3c8c17d6aea2fcf9799aa0.rdb
hierarchicalDS/inst/cache/cache-install2_ad7f9b4fa93b009394879a017973668b.rdb
hierarchicalDS/inst/HierarchicalDS_vignette.Rnw
hierarchicalDS/inst/HierarchicalDS_vignette.tex
hierarchicalDS/inst/HierarchicalDS_vignette.toc
hierarchicalDS/inst/NEWS.txt
hierarchicalDS/inst/figure
hierarchicalDS/inst/figure/graphics-example22.png
hierarchicalDS/inst/HierarchicalDS_vignette.pdf
hierarchicalDS/inst/HierarchicalDS_vignette.log
hierarchicalDS/inst/simulate_data_overd.R
hierarchicalDS/NAMESPACE
hierarchicalDS/data
hierarchicalDS/data/simdata.rda
hierarchicalDS/data/sim_out.rda
hierarchicalDS/data/datalist
hierarchicalDS/data/simdata.rdata
hierarchicalDS/R
hierarchicalDS/R/simulate_data.R hierarchicalDS/R/spat_funcs.R hierarchicalDS/R/mcmc_ds.R hierarchicalDS/R/hierarchical_DS.R
hierarchicalDS/MD5
hierarchicalDS/DESCRIPTION
hierarchicalDS/man
hierarchicalDS/man/plot_obs_pred.Rd hierarchicalDS/man/rect_adj.Rd hierarchicalDS/man/square_adj.Rd hierarchicalDS/man/rrw.Rd hierarchicalDS/man/post_loss.Rd hierarchicalDS/man/hierarchical_DS.Rd hierarchicalDS/man/switch_sample_prior.Rd hierarchicalDS/man/get_mod_matrix.Rd hierarchicalDS/man/linear_adj.Rd hierarchicalDS/man/sim_out.Rd hierarchicalDS/man/generate_inits_misID.Rd hierarchicalDS/man/stack_data_misID.Rd hierarchicalDS/man/log_lambda_gradient.Rd hierarchicalDS/man/log_lambda_log_likelihood.Rd hierarchicalDS/man/convert.HDS.to.mcmc.Rd hierarchicalDS/man/get_confusion_array.Rd hierarchicalDS/man/switch_pdf.Rd hierarchicalDS/man/switch_sample.Rd hierarchicalDS/man/calc_linex_a.Rd hierarchicalDS/man/probit.fct.Rd hierarchicalDS/man/rect_adj_RW2.Rd hierarchicalDS/man/simdata.Rd hierarchicalDS/man/stack_data.Rd hierarchicalDS/man/generate_inits.Rd hierarchicalDS/man/simulate_data.Rd hierarchicalDS/man/get_confusion_mat.Rd hierarchicalDS/man/table.mcmc.Rd hierarchicalDS/man/summary_N.Rd hierarchicalDS/man/mcmc_ds.Rd hierarchicalDS/man/plot_N_map.Rd

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