README.md

In paleolimbot/dalcwrs: R Functions for the CWRS

dalcwrs

The goal of dalcwrs is to ...

Installation

You can install dalcwrs from github with:

# install.packages("devtools")
devtools::install_github("paleolimbot/dalcwrs")

Load the package:

library(tidyverse)
#> Loading tidyverse: ggplot2
#> Loading tidyverse: tibble
#> Loading tidyverse: tidyr
#> Loading tidyverse: readr
#> Loading tidyverse: purrr
#> Loading tidyverse: dplyr
#> Conflicts with tidy packages ----------------------------------------------
#> filter(): dplyr, stats
#> lag():    dplyr, stats
library(dalcwrs)

Reading ICP-MS data files

Reading ICP files...

df <- read_icpms(system.file("test_icpms/test_icpms.xlsx", package = "dalcwrs"))
str(df)
#> Classes 'tbl_df', 'tbl' and 'data.frame':    132 obs. of  14 variables:
#>  $ source      : chr  "/home/dewey/R/x86_64-pc-linux-gnu-library/3.4/dalcwrs/test_icpms/test_icpms.xlsx" "/home/dewey/R/x86_64-pc-linux-gnu-library/3.4/dalcwrs/test_icpms/test_icpms.xlsx" "/home/dewey/R/x86_64-pc-linux-gnu-library/3.4/dalcwrs/test_icpms/test_icpms.xlsx" "/home/dewey/R/x86_64-pc-linux-gnu-library/3.4/dalcwrs/test_icpms/test_icpms.xlsx" ...
#>  $ sample_id   : chr  "Blank 1" "Blank 1" "Blank 1" "Blank 1" ...
#>  $ datetime    : POSIXct, format: "2015-07-17 14:23:56" "2015-07-17 14:23:56" ...
#>  $ extra       : chr  NA NA NA NA ...
#>  $ run         : chr  "1" "2" "3" "x" ...
#>  $ 4.5Bkg_ppb  : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ 27Al_ppb    : num  0.078 -0.035 -0.043 0 0.068 ...
#>  $ 45Sc_ppb    : num  0.975 1.009 1.016 1 0.022 ...
#>  $ 56Fe_ppb    : num  2.702 -0.864 -1.838 0 2.39 ...
#>  $ 65Cu_ppb    : num  0.028 -0.015 -0.014 0 0.025 ...
#>  $ 115In_ppb   : num  0.9762 1.0068 1.017 1 0.0212 ...
#>  $ 159Tb_ppb   : num  0.9724 1.0088 1.0188 1 0.0244 ...
#>  $ 208Pb_ppb   : num  0.014 -0.007 -0.008 0 0.012 ...
#>  $ 220.5Bkg_ppb: num  0 0 0 0 0 0 0 0 0 0 ...

Get tidy versions of ICP files in parameter-long form:

tidy <- tidy_icpms(df) 
str(tidy)
#> Classes 'tbl_df', 'tbl' and 'data.frame':    198 obs. of  12 variables:
#>  $ source   : chr  "/home/dewey/R/x86_64-pc-linux-gnu-library/3.4/dalcwrs/test_icpms/test_icpms.xlsx" "/home/dewey/R/x86_64-pc-linux-gnu-library/3.4/dalcwrs/test_icpms/test_icpms.xlsx" "/home/dewey/R/x86_64-pc-linux-gnu-library/3.4/dalcwrs/test_icpms/test_icpms.xlsx" "/home/dewey/R/x86_64-pc-linux-gnu-library/3.4/dalcwrs/test_icpms/test_icpms.xlsx" ...
#>  $ sample_id: chr  "Blank 1" "Blank 1" "Blank 1" "Blank 1" ...
#>  $ datetime : POSIXct, format: "2015-07-17 14:23:56" "2015-07-17 14:23:56" ...
#>  $ extra    : chr  NA NA NA NA ...
#>  $ isotope  : num  115 159 208 220 27 ...
#>  $ element  : chr  "In" "Tb" "Pb" "Bkg" ...
#>  $ value    : num  1 1 -0.000333 0 0 ...
#>  $ sd       : num  0.0212 0.0244 0.0124 0 0.0677 ...
#>  $ unit     : chr  "ppb" "ppb" "ppb" "ppb" ...
#>  $ n        : int  3 3 3 3 3 3 3 3 3 3 ...
#>  $ n_na     : int  0 0 0 0 0 0 0 0 0 0 ...
#>  $ rsd      : num  2.12 2.44 -3726.93 NaN Inf ...

paleolimbot/dalcwrs documentation built on May 19, 2019, 1:43 a.m.