extinct

Shiny app for modeling probability of extinction based on survey data

https://github.com/hcliedtke/extinct

Repository

Shiny app for modeling probability of extinction based on survey data

README.html

Extinct

The App
This is a Shiny app for modeling probability of extinction based on
survey data.
Launch the app here: https://hcliedtke.shinyapps.io/extinct/


Background
Thompson
et al. 2013 published a method for estimating detection
probabilities of a target species from survey data. It takes into
account successful sightings (records) as well as search efforts that
did not result in sightings (surveys), as well as the probabilities of
surveys having been adequately conducted. The authors provide R code to
execute their model and this Shiny app implements this code to produce a
platform for estimating your own detection probabilities and for
interactively adjusting survey adequacy probabilities to see how this
affects detection probabilities.


Data input


Records and Surveys
For the correct implementation of this app, I refer you to Thompson
et al. 2013. In brief, this application requires two input tables as
.csv files, that summarize the sightings and absence of sightings for
years where the target species was actively looked for.

Records data - a table with tree columns with the following headers:
year, pci_lower, pci_upper
Surveys data - a table with seven columns with the following
headers: year, eps_lower, eps_upper, pi_lower, pi_upper, pr_lower,
pr_upper

The lower and upper bounds refer to:

eps: the proportion of the taxon’s habitat within its likely entire
range that was surveyed (0 to 1)
pi: the probability that the taxon, or recent evidence of it, could
have been reliably identified in the survey if it had been recorded (0
to 1)
pr: the probability that the taxon, or recent evidence of it, would
have been recorded in the survey (0 to 1)
pci: the probability that the taxon is correctly identified as
extant (0 to 1)


Example of Records data



year
pci_lower
pci_upper




1929
0.95
0.99


1947
0.1
0.4


1960
0.95
0.99


1963
0.75
0.94


1969
0.75
0.94


1970
0.1
0.4


1971
0.1
0.4


1972
0.6
0.8


1982
0.6
0.8


1985
0.6
0.8





Example of Surveys data



year
eps_lower
eps_upper
pi_lower
pi_upper
pr_lower
pr_upper




1986
0.4
0.8
0.7
0.95
0.7
0.95


1988
0.4
0.8
0.7
0.95
0.7
0.95


1989
0.8
0.95
0.7
0.95
0.7
0.95


1999
0.8
0.95
0.7
0.95
0.7
0.95


2000
0.7
0.9
0.7
0.95
0.7
0.95


2004
0.8
0.95
0.7
0.95
0.7
0.95


2009
0.8
0.95
0.7
0.95
0.7
0.95






Passive Years
In addition to “active” survey years, this model assumes that during
“passive” years, i.e. years between active surveys, there might still
have been some chance of someone recording the target species. This
could have been an amateur naturalist, someone living in the area etc.
For these passive survey years, we also need to specify upper and lower
eps, pi and pr bounds. By default, these are set to the suggested values
in the original publication, but they can be interactively adjusted in
the shiny app to see how these affect the resulting model.


Cite this app
The model was developed by:
Thompson, C. J., Koshkina, V., Burgman, M. A., Butchart, S. H., &
Stone, L. (2017). Inferring extinctions II: a practical, iterative model
based on records and surveys. Biological Conservation, 214, 328-335.
Please cite their publication when using their models, including via
this Shiny app. If this shiny app was useful to you, please cite this
GitHub repository as well:
Liedtke, H. C. (2024). Extinct: A shiny app for inferring extinction
v1.0.0

Owner

Citation (CITATION.cff)

cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Liedtke
    given-names: H. Christoph
    orcid: https://orcid.org/0000-0002-6221-8043
title: "Extinct"
version: 1.0.0
identifiers:
  - type: doi
    value: 
date-released: 2024-02-14

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