catsr_readme

catsr

catsr is an R package for reading and visualizing CATS PRH files. For information on the PRH creation tools and workflow, see CATS-Methods-Materials and the CATS Data Processing Workshop.

Installation

catsr is available on GitHub and you can install it using devtools package. If you don’t have devtools installed, uncomment the line below. See section Troubleshooting at the end of this document for common errors.

# install.packages("devtools")
devtools::install_github("FlukeAndFeather/catsr")

Reading data

Read a CATS PRH file in netCDF format with read_nc(). The .nc file for deployment mn200312-58 is included in the package. Note: triaxial variables (aw, mw, gw) are stored as three-column matrices, so only the first column (corresponding to the x-axis) shows up in View().

library(catsr)
nc_path <- system.file("extdata", "mn200312-58_prh10.nc", package = "catsr")
mn200312_58_from_nc <- read_nc(nc_path)
mn200312_58_from_nc
#> # A tibble: 147,671 x 15
#>         dn       p aw[,1]  [,2]  [,3] mw[,1]  [,2]  [,3]  gw[,1]    [,2]    [,3]
#>      <dbl>   <dbl>  <dbl> <dbl> <dbl>  <dbl> <dbl> <dbl>   <dbl>   <dbl>   <dbl>
#>  1 737863. -0.0494 -0.797 -8.06  6.32  -23.1 -21.5  19.0 -0.0524 -0.0436  0.0300
#>  2 737863. -0.0295 -0.343 -8.44  6.40  -23.0 -21.7  18.6  0.0686 -0.0645  0.0282
#>  3 737863. -0.0262 -0.341 -9.04  6.34  -22.8 -21.4  18.9  0.296  -0.127  -0.0438
#>  4 737863. -0.0465 -0.675 -7.93  5.46  -22.7 -20.8  20.1  0.256  -0.145  -0.0796
#>  5 737863. -0.0468 -0.281 -7.29  5.76  -22.1 -20.9  20.6  0.0505 -0.0854 -0.0175
#>  6 737863. -0.0441 -0.130 -7.37  6.52  -22.0 -21.0  20.6  0.0696 -0.0973 -0.0175
#>  7 737863. -0.0456 -0.191 -7.03  5.77  -21.7 -20.5  21.5  0.114  -0.115  -0.0201
#>  8 737863. -0.0478 -0.249 -7.52  5.17  -21.2 -20.2  21.6 -0.0664 -0.0496  0.0386
#>  9 737863. -0.0304 -0.464 -7.58  5.07  -21.7 -20.2  21.4 -0.0306 -0.0151  0.0199
#> 10 737863. -0.0256 -0.405 -7.03  5.05  -21.7 -20.3  21.3 -0.0925  0.0373  0.0460
#> # … with 147,661 more rows, and 10 more variables: speed <dbl>, pitch <dbl>,
#> #   roll <dbl>, head <dbl>, x <dbl>, y <dbl>, z <dbl>, dt <dttm>, secs <dbl>,
#> #   jerk <dbl>

Visualizing data

Examine PRH variables (e.g. depth, pitch, and roll) in an interactive plot with view_cats(). This package also provides deployment mn200312-58 directly for use in R.

view_cats(mn200312_58, c("p", "pitch", "roll"))

Triaxial variables (such as accelerometry - aw) are represented in multiple colors.

view_cats(mn200312_58, c("p", "aw", "mw"))

Explore the animal’s 3d movement trajectory.

view_cats_3d(mn200312_58)

Troubleshooting

All platforms:

If you encounter an error installing catsr (or devtools), close all instances of R (including RStudio). Start a new session and run the install command again.

Windows:

Installing devtools on R>=4.0.0 requires Rtools40.

Mac OSX:

Installing devtools on Mac OSX requires Command Line Tools. In your terminal, run xcode-select --install.