README.md

In dankelley/dfo: Handle Dept. Fisheries & Oceans Data Formats

dfo

The goal of dfo is to facilitate the reading of several file formats used by the Department of Fisheries and Oceans (DFO), Canada.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("dankelley/dfo")

Example

The following reads, summarizes, and plots an IOS-formatted CTD file that is provided with the package. (Type ?read.ctd.ios in an R console for more details.)

library(dfo)
#> Loading required package: oce
#> Loading required package: gsw
#> Loading required package: testthat
#> Loading required package: sf
#> Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1
#> Loading required package: ncdf4
file <- system.file("extdata", "2007-019-055.ctd", package="dfo")
ctd <- read.ctd.ios(file)
summary(ctd)
#> CTD Summary
#> -----------
#> 
#> * Chief scientist:     Zimmermann S.
#> * Start time:          2007-07-24 12:58:49
#> * Station:             CAA12
#> * Location:            68.679N 103.92W
#> * Data Overview
#> 
#>                                 Min.    Mean   Max. Dim. NAs              OriginalName
#>     pressure [dbar]                3  51.497   99.9   98   0                  Pressure
#>     depth [m]                    2.9  51.237   99.4   98   0                     Depth
#>     temperature [°C, ITS-90] -1.6028 -1.3202 0.5814   98   0       Temperature:Primary
#>     transmissivity ["%"/m]       0.8  61.467   68.2   98   0            Transmissivity
#>     fluorescence [mg/m³]       0.094 0.61771  4.557   98   1 Fluorescence:URU:Seapoint
#>     par [μE/m²/s]                  0  13.885  129.9   98   0                       PAR
#>     parReference [μE/m²/s]     665.3  670.77  682.6   98   0             PAR:Reference
#>     salinity [PSS-78]         13.283  28.802 29.736   98   0            Salinity:T0:C0
#>     oxygen [ml/l]               8.05  8.7396   9.56   98   0      Oxygen:Dissolved:SBE
#>     oxygen2 [μmol/kg]          351.1  381.35  417.5   98   0      Oxygen:Dissolved:SBE
#>     nitrate_plus_nitrite [V]   0.662 0.77972   1.74   98   0 Nitrate_plus_nitrite:ISUS
#>     ndata                          4  24.663     51   98   0     Number_of_bin_records
#> 
#> * Processing Log
#> 
#>     - 2021-02-09 12:11:32 UTC: `create 'ctd' object`
#>     - 2021-02-09 12:11:32 UTC: `read.ctd.ios.text("/private/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T/Rtmp3dFc8i/temp_libpath82a11df38d28/dfo/extdata/2007-019-055.ctd", missingValue=-99, debug=0)
#> `
plot(ctd)

dankelley/dfo documentation built on Nov. 21, 2022, 2:35 a.m.