README.md

In SNARL1/mrmr: Mark recapture miscellany in R

mrmr: mark recapture miscellany in R

This package automates common data processing steps for mark recapture data, with an emphasis on data collected by folks at the Sierra Nevada Aquatic Research Lab (SNARL). Many of the assumptions made in the data processing and modeling are pinned to the type of capture-recapture data collected by the SNARL team, and as a result, this package should not be thought of as a general purpose mark-recapture modeling toolbox (for that, see the RMark, unmarked, multimark or Rcapture packages).

Installation

remotes::install_github("SNARL1/mrmr")

Usage

This package consists of three core functions to use consecutively:

1. clean_data() ingests capture-recapture, introduction, and survey data.
2. fit_model() fits a Jolly-Seber mark recapture model to quickly estimate demographic parameters and population abundance.
3. plot_model() generates plots of abundance and recruitment over time, or of the survival of introduced cohorts.

For an in-depth look at how to use these functions, see the vignette An Introduction to the mrmr package.

Background

Customized mark recapture modeling can be time and resource intensive, especially when there are unique features of a study system that prevent or complicate the immediate use of a general purpose package. For example, the model described in Joseph and Knapp 2018 Ecosphere (https://doi.org/10.1002/ecs2.2499) - which accounts for introductions into a population, and continuous, time-varying, incompletely observed individual-level covariates on detection and survival - takes considerable effort to develop and deploy. There is a need in this particular research group for models that can be used in near-real time as data are available to inform conservation decisions. This package fills this need, with the primary goal of estimating abundance and recruitment through time in montane amphibian populations.

License

This package is licensed under the MIT license.

Copyright 2019 Maxwell B. Joseph

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

SNARL1/mrmr documentation built on Nov. 23, 2023, 7:04 a.m.