The goal of dfo is to facilitate the reading of several file formats used by the Department of Fisheries and Oceans (DFO), Canada.
You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("dankelley/dfo")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)