Package: SightabilityModel 1.5.5

Schwarz Carl James

SightabilityModel: Wildlife Sightability Modeling

Uses logistic regression to model the probability of detection as a function of covariates. This model is then used with observational survey data to estimate population size, while accounting for uncertain detection. See Steinhorst and Samuel (1989).

Authors:Fieberg John [aut], Schwarz Carl James [aut, cre]

SightabilityModel_1.5.5.tar.gz
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SightabilityModel_1.5.5.tgz(r-4.6-any)SightabilityModel_1.5.5.tgz(r-4.5-any)
SightabilityModel_1.5.5.tar.gz(r-4.7-any)SightabilityModel_1.5.5.tar.gz(r-4.6-any)
SightabilityModel_1.5.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SightabilityModel/json (API)

# Install 'SightabilityModel' in R:
install.packages('SightabilityModel', repos = c('https://jfieberg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jfieberg/sightabilitymodel/issues

Datasets:
  • exp.m - Experimental (test trials) data set used to estimate detection probabilities for moose in MN
  • g.fit - Mountain Goat Sightability Model Information
  • gdat - Mountain Goat Survey Data from Olympic National park
  • obs.m - MN moose survey data
  • sampinfo.m - Data set containing sampling information for observation survey of moose in MN

On CRAN:

Conda:

4.98 score 1 stars 24 scripts 365 downloads 17 exports 27 dependencies

Last updated from:a6a3eb3101. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK221
source / vignettesOK301
linux-release-x86_64OK226
macos-release-arm64OK189
macos-oldrel-arm64OK301
windows-develOK106
windows-releaseOK123
windows-oldrelOK113
wasm-releaseOK166

Exports:check.sightability.model.argscompute.detect.probcompute.SCFcovthetaMoosePopRMoosePopR_DomStratMoosePopR_DomStrat_bootrepSight.EstSight.Est.RatioSightabilityPopRSightabilityPopR_DomStratSS.estSS.est.Ratiovardiffvarlog.lamWong.estWong.est.Ratio

Dependencies:cliDBIexpmformula.toolsgenericsgluelatticelifecyclemagrittrMatrixminqamitoolsmsmmvtnormnumDerivoperator.toolspillarpkgconfigplyrRcppRcppArmadillorlangsurveysurvivaltibbleutf8vctrs

c-MoosePopR and SightabilityPopR Demonstration
Availability of code | Introduction | Survey protocol | Data input | Moose data | Block area | Stratum information | Sightability model. | Extracting from AerialSurvey | Reading coefficients of the model | Creation of VegCoverClass variable | Key variables. | Dealing with missing and zero values | Group information | Covariate information | Blocks with no observed groups. | Block information | A single block in a stratum | Analysis | Analysis not adjusting for sightability | Within a stratum | Density | Abundance | Bull to Cow and other ratios | Across all strata | The MoosePopR() function. | Sample Analyses | Density of all moose | Abundance of all moose | Number of bulls and number of cows | Final object | Adjusting for sightability | The SightabilityPopR() function | Dealing with missing values in the sightability covariates | Domain estimation | Domain at PSU (block) level; domain population information known | Example | Domain at PSU (block) level; domain population information unknown. | Domain at group level; domain population information known | Domain at group level; domain population information unknown. | References
Rendered fromc-MoosePopR-SightabilityPopR-Demo.Rmdusingknitr::rmarkdown

Last update: 2023-02-17
Started: 2022-05-18

a-Estimating Population Abundance Using Sightability Models: R SightabilityModel Package
Introduction | Modified Horvitz-Thompson estimator | Variance estimators | Package description and example applications | Future work
Rendered froma-SightabilityModel.Rnwusingutils::Sweave

Last update: 2022-05-18
Started: 2022-05-18

b-Implementing the Ratio Estimator
Introduction | Implementation | References
Rendered fromb-RatioEstimator.pdf.asisusingR.rsp::asis

Last update: 2022-05-18
Started: 2022-05-18

d-DomainStratification-method-of-Heard-2008
1 Availability of code | 2 Introduction | 3 Types of stratification | 3.1 Across sampling-unit stratification | 3.2 Within sampling-unit stratification (domain estimation) | 3.3 Combined designs | 3.4 CAUTIONS | 4 Data structures that allow for both types of stratification | 4.1 Stratum Totals | 4.2 Sampling unit information | 4.3 Way point (group) information | 4.4 Sightability Model | 5 Example | 5.1 Survey Design | 5.2 Data Values | 5.3 Uncorrected Estimation | 5.4 Corrected for sightability estimation | 5.5 SCF < 1 - Why does this happen? | 5.6 Adjusting data for SCF using MoosePopR() | 6 Final estimates | 6.1 Abundance of all moose - corrected for sightability and domain stratification | 6.2 Density of all moose - corrected for sightability and domain stratification | 6.3 Bulls:100 Cows - corrected for sightability and domain stratification | 7 Summary and Recommendations | 7.1 Survey Design | 7.2 Data structures | 7.3 Include schematic of design in report | 7.4 Analysis | 8 References
Rendered fromd-DomainStratification-method-of-Heard-2008.html.asisusingR.rsp::asis

Last update: 2022-05-18
Started: 2022-05-18

Readme and manuals

Help Manual

Help pageTopics
Wildlife Sightability ModelingSightabilityModel-package SightabilityModel
Check the sightability model arguments for consistencycheck.sightability.model.args
Compute the detection probability given a sightability modelcompute.detect.prob
Compute the sightability correction factor given a sightability and covariatescompute.SCF
Estimates var/cov matrix of inflation factors (1/prob detection) using a non-parametric bootstrap.covtheta
Experimental (test trials) data set used to estimate detection probabilities for moose in MNexp.m
Mountain Goat Sightability Model Informationg.fit
Mountain Goat Survey Data from Olympic National parkgdat
R function that gives the same functionality as the MoosePop program.MoosePopR
Classical and Domain Stratification using MoosePopR()MoosePopR_DomStrat
Generate a bootstrap replicate of data for call to MoosePopR_DomStrat()MoosePopR_DomStrat_bootrep
MN moose survey dataobs.m
Print method for sightability estimatorsprint.sightest print.sightest_ratio
Data set containing sampling information for observation survey of moose in MNsampinfo.m
Sightability Model EstimatorSight.Est
Sightability Model Estimator - Ratio of variablesSight.Est.Ratio
R function that interfaces with the SightabilityModel package and gives similar functionality as the AerialSurvey programSightabilityPopR
Classical and Domain Stratification using SightabilityPopR()SightabilityPopR_DomStrat
Sightability estimate with variance components estimator from Steinhorst and Samuel (1989) and Samuel et al. (1992).SS.est
Sightability estimate or ratio with variance components estimator from Steinhorst and Samuel (1989) and Samuel et al. (1992). This is merely a stub and has not been implemented.SS.est.Ratio
Summarize sightability estimatorsummary.sightest summary.sightest_ratio
Function to estimate the variance of the difference between two population estimatesvardiff
Calculates the variance of the log rate of change between 2 population estimates that rely on the same sightability model.varlog.lam
Sightability estimate with variance components estimator from Wong (1996)Wong.est
Sightability estimate of ratio with variance components estimator from Wong (1996)Wong.est.Ratio