Commit 2dd3eb65 authored by Chris Holbrook's avatar Chris Holbrook

Changes to be committed:

version up
	modified:   DESCRIPTION

add otn_deployments, residence_index, REI
	modified:   R/package-glatos.r
	modified:   ReadMe.md

rebuild vignette
	modified:   inst/supplemental_docs/gganimate_handout.Rmd
	modified:   man/glatos.Rd
	modified:   vignettes/data_loading_vignette.html
	modified:   vignettes/data_loading_vignette.pdf
	modified:   vignettes/data_requirements_vignette.html
	modified:   vignettes/data_requirements_vignette.pdf
	modified:   vignettes/detection_range_handout.html
	modified:   vignettes/detection_range_handout.pdf
	modified:   vignettes/gganimate_handout.html
	modified:   vignettes/gganimate_handout.pdf
	modified:   vignettes/receiver_efficiency_index_handout.html
	modified:   vignettes/receiver_efficiency_index_handout.pdf
	modified:   vignettes/residence_index_handout.html
	modified:   vignettes/residence_index_handout.pdf
parent 974ec0de
......@@ -2,7 +2,7 @@ Package: glatos
Type: Package
Title: A package for the Great Lakes Acoustic Telemetry Observation System
Description: Functions useful to members of the Great Lakes Acoustic Telemetry Observation System www.glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
Version: 0.3.0.9011
Version: 0.3.0
Date: 2019-02-26
Depends: R (>= 3.2.0)
Imports:
......
......@@ -23,10 +23,10 @@
#' data loading from standard GLATOS and OTN data files to a single structure
#' that is compatible with other glatos functions.}
#'
#' \item{\link{read_glatos_receivers}}{ Reads receiver location histories from
#' standard GLATOS data files to a single structure that is compatible with
#' other glatos functions.}
#'
#' \item{\link{read_glatos_receivers} and \link{read_otn_deployments}}{
#' Reads receiver location histories from standard GLATOS and OTN data files
#' to a single structure that is compatible with other glatos functions.}
#'
#' \item{\link{read_glatos_workbook}}{ Reads project-specific receiver history
#' and fish taggging and release data from a standard glatos workbook file.}
#'
......@@ -54,6 +54,12 @@
#' number of detections, first and last detection timestamps, and/or mean
#' location of receivers or groups, depending on specific type of summary
#' requested.}
#'
#' \item{\link{residence_index}} calculates the relative proportion of time
#' spent at each location.
#'
#' \item{\link{REI}} calculates the relative activity at each receiver based
#' on number of unique species and individual animals.
#' }
#'
#' @section Visualization and data exploration: \describe{
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......@@ -4,11 +4,10 @@ subtitle: "Workshop Handout - GLATOS, February 28, 2019"
author: "Todd Hayden (haydento@msu.edu), Mike Lowe"
date: "Updated: `r Sys.Date()`"
output:
rmarkdown::pdf_document:
toc: false
rmarkdown::html_document:
theme: default
rmarkdown::pdf_document:
toc: false
---
# Introduction
......
......@@ -32,10 +32,10 @@ telemetry applications.
data loading from standard GLATOS and OTN data files to a single structure
that is compatible with other glatos functions.}
\item{\link{read_glatos_receivers}}{ Reads receiver location histories from
standard GLATOS data files to a single structure that is compatible with
other glatos functions.}
\item{\link{read_glatos_receivers} and \link{read_otn_deployments}}{
Reads receiver location histories from standard GLATOS and OTN data files
to a single structure that is compatible with other glatos functions.}
\item{\link{read_glatos_workbook}}{ Reads project-specific receiver history
and fish taggging and release data from a standard glatos workbook file.}
......@@ -65,6 +65,12 @@ telemetry applications.
number of detections, first and last detection timestamps, and/or mean
location of receivers or groups, depending on specific type of summary
requested.}
\item{\link{residence_index}} calculates the relative proportion of time
spent at each location.
\item{\link{REI}} calculates the relative activity at each receiver based
on number of unique species and individual animals.
}
}
......
......@@ -1535,7 +1535,7 @@ div.tocify {
<h1 class="title toc-ignore">Data loading methods for the R package glatos</h1>
<h4 class="date"><em>Updated: 2019-02-25</em></h4>
<h4 class="date"><em>Updated: 2019-02-26</em></h4>
</div>
......
......@@ -1535,7 +1535,7 @@ div.tocify {
<h1 class="title toc-ignore">Data requirements of the R package glatos</h1>
<h4 class="date"><em>Updated: 2019-02-25</em></h4>
<h4 class="date"><em>Updated: 2019-02-26</em></h4>
</div>
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......@@ -9,7 +9,7 @@
<meta name="generator" content="pandoc" />
<meta name="author" content="Alex Nunes" />
<meta name="author" content="Alex Nunes (anunes@dal.ca)" />
<title>Receiver Efficiency Index</title>
......@@ -1542,15 +1542,15 @@ div.tocify {
<h1 class="title toc-ignore">Receiver Efficiency Index</h1>
<h3 class="subtitle"><em>Workshop Handout - GLATOS, March 27, 2018</em></h3>
<h4 class="author"><em>Alex Nunes</em></h4>
<h4 class="date"><em>Updated: 2019-02-24</em></h4>
<h3 class="subtitle"><em>Workshop Handout - GLATOS, February 28, 2019</em></h3>
<h4 class="author"><em>Alex Nunes (<a href="mailto:anunes@dal.ca">anunes@dal.ca</a>)</em></h4>
<h4 class="date"><em>Updated: 2019-02-26</em></h4>
</div>
<p>The receiver efficiency index is number between <code>0</code> and <code>1</code> indicating the amount of relative activity at each receiver compared to the entire set of receivers, regardless of positioning. The function takes a set detections and a deployment history of the receivers to create a context for the detections. Both the amount of unique tags and number of species are taken into consideration in the calculation.</p>
<p>The receiver efficiency index implement is implemented based on the paper Acoustic telemetry array evolution: <a href="https://www.sciencedirect.com/science/article/pii/S0165783618302509?via%3Dihub">From species- and project-specific designs to large-scale, multispecies, cooperative networks</a>. Each receiver’s index is calculated on the formula of:</p>
<p>The receiver efficiency index implement is implemented based on the paper Acoustic telemetry array evolution: From species- and project-specific designs to large-scale, multispecies, cooperative networks - <a href="https://www.sciencedirect.com/science/article/pii/S0165783618302509?via%3Dihub">https://www.sciencedirect.com/science/article/pii/S0165783618302509?via%3Dihub</a>. Each receiver’s index is calculated on the formula of:</p>
<blockquote>
<p><span class="math inline">\(REI = \frac{T_r}{T_a} \times \frac{S_r}{S_a} \times \frac{DD_r}{DD_a} \times \frac{D_a}{D_r}\)</span></p>
<p>REI = Receiver Efficiency Index</p>
......@@ -1593,12 +1593,12 @@ detections &lt;- read_glatos_detections(detection_file)</code></pre>
<p>The resulting dataframe looks like this:</p>
<pre class="r"><code>head(rei)
station latitude longitude rei
1 DRF-004 42.24937 -83.11824 0.001238344
2 DRL-004 42.12746 -83.11873 0.001562131
3 DRL-010 42.07690 -83.12096 0.001413048
4 DRL-011 42.09637 -83.11681 0.001162268
5 DRU-001 42.35693 -82.93016 0.001685864
6 DRU-002 42.35278 -82.92844 0.001576595</code></pre>
1 DRF-004 42.24937 -83.11824 0.001238345
2 DRL-004 42.12746 -83.11873 0.001562132
3 DRL-010 42.07690 -83.12096 0.001413049
4 DRL-011 42.09637 -83.11681 0.001162269
5 DRU-001 42.35693 -82.93016 0.001685865
6 DRU-002 42.35278 -82.92844 0.001576596</code></pre>
</div>
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......@@ -9,7 +9,7 @@
<meta name="generator" content="pandoc" />
<meta name="author" content="Alex Nunes" />
<meta name="author" content="Alex Nunes (anunes@dal.ca)" />
<title>Residence Index</title>
......@@ -1542,9 +1542,9 @@ div.tocify {
<h1 class="title toc-ignore">Residence Index</h1>
<h3 class="subtitle"><em>Workshop Handout - GLATOS, March 27, 2018</em></h3>
<h4 class="author"><em>Alex Nunes</em></h4>
<h4 class="date"><em>Updated: 2019-02-24</em></h4>
<h3 class="subtitle"><em>Workshop Handout - GLATOS, February 28, 2019</em></h3>
<h4 class="author"><em>Alex Nunes (<a href="mailto:anunes@dal.ca">anunes@dal.ca</a>)</em></h4>
<h4 class="date"><em>Updated: 2019-02-26</em></h4>
</div>
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