Package: extBatchMarking 1.0.1
extBatchMarking: Extended Batch Marking Models
A system for batch-marking data analysis to estimate survival probabilities, capture probabilities, and enumerate the population abundance for both marked and unmarked individuals. The estimation of only marked individuals can be achieved through the batchMarkOptim() function. Similarly, the combined marked and unmarked can be achieved through the batchMarkUnmarkOptim() function. The algorithm was also implemented for the hidden Markov model encapsulated in batchMarkUnmarkOptim() to estimate the abundance of both marked and unmarked individuals in the population. The package is based on the paper: "Hidden Markov Models for Extended Batch Data" of Cowen et al. (2017) <doi:10.1111/biom.12701>.
Authors:
extBatchMarking_1.0.1.tar.gz
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extBatchMarking_1.0.1.tgz(r-4.4-x86_64)extBatchMarking_1.0.1.tgz(r-4.4-arm64)extBatchMarking_1.0.1.tgz(r-4.3-x86_64)extBatchMarking_1.0.1.tgz(r-4.3-arm64)
extBatchMarking_1.0.1.tar.gz(r-4.5-noble)extBatchMarking_1.0.1.tar.gz(r-4.4-noble)
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extBatchMarking.pdf |extBatchMarking.html✨
extBatchMarking/json (API)
# Install 'extBatchMarking' in R: |
install.packages('extBatchMarking', repos = c('https://olobatuyi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/olobatuyi/extbatchmarking/issues
- WeatherLoach - Weather Loach data
Last updated 8 months agofrom:a7459c7983. Checks:OK: 9. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 08 2024 |
R-4.5-win-x86_64 | OK | Sep 08 2024 |
R-4.5-linux-x86_64 | OK | Sep 08 2024 |
R-4.4-win-x86_64 | OK | Sep 08 2024 |
R-4.4-mac-x86_64 | OK | Sep 08 2024 |
R-4.4-mac-aarch64 | OK | Sep 08 2024 |
R-4.3-win-x86_64 | OK | Sep 08 2024 |
R-4.3-mac-x86_64 | OK | Sep 08 2024 |
R-4.3-mac-aarch64 | OK | Sep 08 2024 |
Exports:batchMarkHmmLLbatchMarkOptimbatchMarkUnmarkHmmLLbatchMarkUnmarkOptim
Dependencies:codetoolsdoParallelforeachiteratorslatticeMatrixoptimbaseRcppRcppArmadillo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
batchLL function provides the batch marking log-likelihood | batchLL |
batchLogit function | batchLogit |
Log-likelihood function for marked model. | batchMarkHmmLL |
Marked model only. | batchMarkOptim |
Log-likelihood function for combined model. | batchMarkUnmarkHmmLL |
Combined Marked and Unmarked models. | batchMarkUnmarkOptim |
batchUnmark2Viterbi function provides a wrapper for the batchUnmarkViterbi to compute the popuation abundance | batchUnmark2Viterbi |
batchUnmarkHmmLL function provides the unmarked function to be optimized | batchUnmarkHmmLL |
batchUnmarkViterbi function provides the implementation of the Viterbi alogrithm for the unmarked model | batchUnmarkViterbi |
Convolution of Poisson and Binomial for Batch | dbinpois |
initial probability function | delta_g |
Transition State Probability 'gamma_gt' computes the transition probability matrix | gamma_gt |
State-dependent probability function | probs |
Weather Loach data | WeatherLoach |