The goal of sbe is to provide an R interface to ‘Seabird’ files and programs. This package is totally unofficial and very experimental.
Installation
You can install the development version from GitHub with:
# install.packages("remotes")
remotes::install_github("paleolimbot/sbe")Example
This is a basic example which shows you how to solve a common problem:
library(sbe)
# run SBEDataProcessing tools from R
faroe_dir <- system.file("extdata/faroe", package = "sbe")
out_dir <- sbe_run_tool(
"datcnv",
psa = file.path(faroe_dir, "faroe.psa"),
input = file.path(faroe_dir, "faroe.dat"),
con = file.path(faroe_dir, "faroe.con")
)
#> Generated batchfile:
#> Datcnv /pC:\Users\dunningtond\Documents\R\win-library\4.0\sbe\extdata\faroe\faroe.psa /iC:\Users\dunningtond\Documents\R\win-library\4.0\sbe\extdata\faroe\faroe.dat /cC:\Users\dunningtond\Documents\R\win-library\4.0\sbe\extdata\faroe\faroe.con /oC:\Users\DUNNIN~1\AppData\Local\Temp\2\RtmpEZkTTH\file3da85ee6454\file3da81279a4c
#> Running \
#> "C:/Program Files (x86)/Sea-Bird/SBEDataProcessing-Win32/SBEBatch.exe" \
#> "C:\Users\DUNNIN~1\AppData\Local\Temp\2\RtmpEZkTTH\file3da8379367c5.txt"
# read cnv files as data frames
out_sbe_cnv <- list.files(out_dir, full.names = TRUE)
read_sbe_cnv(out_sbe_cnv)
#> # A tibble: 15,225 x 4
#> prDM t190C `c1S/m` flag
#> <dbl> <dbl> <dbl> <dbl>
#> 1 4.55 8.30 3.66 0
#> 2 4.51 8.30 3.66 0
#> 3 4.55 8.30 3.66 0
#> 4 4.51 8.30 3.66 0
#> 5 4.50 8.30 3.66 0
#> 6 4.51 8.30 3.66 0
#> 7 4.51 8.30 3.66 0
#> 8 4.51 8.30 3.66 0
#> 9 4.50 8.30 3.66 0
#> 10 4.49 8.30 3.66 0
#> # ... with 15,215 more rows
read_sbe_cnv_colmeta(out_sbe_cnv)
#> # A tibble: 4 x 4
#> index name long_name unit
#> <dbl> <chr> <chr> <chr>
#> 1 1 prDM Pressure, Digiquartz db
#> 2 2 t190C Temperature, 2 ITS-90, deg C
#> 3 3 c1S/m Conductivity, 2 S/m
#> 4 4 flag Flag <NA>
