README.md

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actel

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Overview

If you are using acoustic telemetry to track animals as they move inside a study area or as they migrate somewhere, actel is the package for you. By bringing together the study area configuration and the recorded detections, actel provides a systematic way of analysing fish migration and residency data.

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Main functions:

1. explore()

explore() allows you to quickly get a summary of your data. You can use explore() to get a general feel for the study results, and check if the input files are behaving as expected. It is also a good candidate if you just want to validate your detections for later use in other analyses.

2. migration()

The migration() analysis runs the same initial checks as explore(), but on top of it, it analyses the fish behaviour. By selecting the arrays that lead to success, you can define whether or not your fish survived the migration. Additional plots help you find out if some fish has been acting odd. Multiple options allow you to tweak the analysis to fit your study perfectly.

3. residency()

The residency() analysis runs the same initial checks as explore(), but, similarly to migration, explores particular points of the fish behaviour. If you want to know where your fish were in each day of the study, how many fish were in each section each day, and other residency-focused variables, this is the analysis you are looking for!

Unlock actel's full potential

To truly learn how to operate actel, you must read the package vignettes. These have been arranged so that you can prepare your analysis as you learn; quite soon you will get your first results!

Here are some examples:

Movement tables:

|Array | Detections|First station |Last station |First time |Last time |Time travelling |Time on array | |:------|----------:|:-------------|:------------|:-------------------|:-------------------|:---------------|:-------------| |River1 | 14|St.1 |St.2 |2019-05-15 10:30:00 |2019-05-15 13:00:00 |NA |3:30 | |River2 | 3|St.4 |St.4 |2019-05-15 13:50:00 |2019-05-15 14:40:00 |0:50 |0:50 | |River3 | 8|St.5 |St.6 |2019-05-15 16:00:00 |2019-05-15 16:20:00 |1:20 |0:20 | |Fjord2 | 21|St.10 |St.11 |2019-05-16 15:10:00 |2019-05-16 18:00:00 |22:50 |2:50 | |Sea1 | 1|St.18 |St.18 |2019-05-18 09:45:00 |2019-05-18 09:45:00 |15:45 |0:00 |

Detection graphics

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Times of arrival and summary information

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Array efficiency and fish progression

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Individual residency

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Global residency

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Installing actel

Current version: 0.1.2

To install actel, you will need to have the devtools package installed.

install.packages("devtools")
library("devtools")

Now you can either install actel sourcing remotely or locally.

a) install directly from the repository:

devtools::install_github("hugomflavio/actel", build_opts = c("--no-resave-data", "--no-manual"))

b) install locally:

  1. Download actel's source files here: actel-master.zip
  2. Unzip the file and move your R session into the newly created folder
  3. Run:
    devtools::install("actel-devel", build_vignettes = TRUE)
    

Have a look at the manual:

After installing, you should read the package vignettes (i.e. the manual), which can be found by running:

browseVignettes('actel')

Note:

  1. If the vignettes are not showing up with the command above, you can download them directly here: compiled_vignettes.zip
  2. If you are getting "pandoc document conversion" errors during the package installation, try installing the newest version of pandoc, restarting R and trying again.


hugomflavio/actel documentation built on Jan. 11, 2020, 11:36 a.m.