README.md

In LuisLauM/oXim: Oxycline Index from Matrix Echograms

## 
## 'oXim': Tools for read Echopen outputs and get oxycline limits from echogram data.
## https://cran.r-project.org/web/packages/oXim/index.html
## 
## 'Echopen': toolbox for the multifrequency analysis of fisheries acoustics data.
## http://www.france-nord.ird.fr/les-ressources/outils-informatiques

oXim

Oxycline Index from Matrix Echograms

This package is built to take echogram data from Echopen software outputs and calculate oxycline depth limits using image-filtering algoriths.

Installation

Get the development version from github:

# install.packages("devtools")
devtools::install_github("LuisLauM/oXim")

Examples

Read data from Echopen outputs

For reading data, it is necesary to specify Echopen outputs files (.m extension). ´readEchograms´ function returns an object of class 'echoData', so some methods may be applied: print, summary and plot.

# Set directories where the Echopen's outputs are located
fileMode <- list(fish38_file   = system.file("extdata", "fish38.mat", package = "oXim"),
                 fluid120_file = system.file("extdata", "fluid120.mat", package = "oXim"),
                 blue38_file   = system.file("extdata", "blue38.mat", package = "oXim"))


# Read echograms (echoData object)
echoData <- readEchograms(fileMode = fileMode)

# Print method
print(echoData)
#> 
#> Number of echograms:  1 
#> 
#> For echogram 1:
#>  Range lon:  From 74.167° W to 74.113° W 
#>  Range lat:  From 17.218° S to 17.187° S 
#>  Range time: From 2011-09-12 00:54:29 to 2011-09-12 01:18:37

# Summary method
summaryEchodata <- summary(echoData)

# Print summary
print(summaryEchodata)
#> 
#> Number of echograms:  1 
#> 
#> For echogram 1:
#>      sA  lon lat time    
#>  Min.    -40950  -74.17  -17.22  2011-09-12 00:54:29 
#>  1st Qu. -19.28  -74.15  -17.21  2011-09-12 00:59:50 
#>  Median  0   -74.14  -17.2   2011-09-12 01:06:06 
#>  Mean    -5426   -74.14  -17.2   2011-09-12 01:06:09 
#>  3rd Qu. 0   -74.13  -17.19  2011-09-12 01:12:21 
#>  Max.    0   -74.11  -17.19  2011-09-12 01:18:37 

# Plot method
plot(echoData)

Calculate oxycline depth limits

For oxycline depth calculation, getOxyrange function provides an easy-to-use way for applying median-filter and 2D convolution-based filters.

For calculate oxycline depth limits from echoData objects, getOxyrange should be applied as follows:

# Set directories where the Echopen's outputs are located
fileMode <- list(fish38_file   = system.file("extdata", "fish38.mat", package = "oXim"),
                 fluid120_file = system.file("extdata", "fluid120.mat", package = "oXim"),
                 blue38_file   = system.file("extdata", "blue38.mat", package = "oXim"))


# Read echograms (echoData object)
echoData <- readEchograms(fileMode = fileMode)

# Calculate oxycline limits (oxyclineData object)
oxyLimits <- getOxyrange(fluidMatrix = echoData)

# Print method
print(oxyLimits)
#> 
#> For echogram 1:
#>  Range lon:  From 74.167° W to 74.113° W 
#>  Range lat:  From 17.218° S to 17.187° S 
#>  Range time: From 2011-09-12 00:54:29 to 2011-09-12 01:18:37 
#>  Range oxycline depth:   From 63.6 m to 95.3 m

# Summary method
summary(oxyLimits)
#> 
#> Number of database:  1 
#> 
#> For database 1:
#>      lon lat limits  time    
#>  Min.    -74.17  -17.22  -95.31  2011-09-12 00:54:29 
#>  1st Qu. -74.15  -17.21  -81.18  2011-09-12 00:59:50 
#>  Median  -74.14  -17.2   -76.76  2011-09-12 01:06:06 
#>  Mean    -74.14  -17.2   -76.95  2011-09-12 01:06:09 
#>  3rd Qu. -74.13  -17.19  -72.59  2011-09-12 01:12:21 
#>  Max.    -74.11  -17.19  -63.57  2011-09-12 01:18:37 

# Plot method
plot(oxyLimits)
#> [inverse distance weighted interpolation]

LuisLauM/oXim documentation built on May 7, 2019, 2:03 p.m.