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A wrapper for readr's read_csv & readxl's read_excel for reading trial data

Source: R/read_workbooks.R
read_workbooks.Rd

A wrapper for readr's read_csv & readxl's read_excel for reading trial data

Usage

read_workbooks(
  dir = t_dir,
  season = NULL,
  read_subfolder = FALSE,
  s = ".csv|.xlsx",
  sub_folder = "Data/Curated Data",
  subset = FALSE,
  n = NULL,
  multiple = FALSE,
  sheet_name = NULL,
  skip = 0,
  file_to_read = NULL,
  merge = FALSE,
  update_plot = TRUE
)

Arguments

dir

trial data home directory

season

trial season

read_subfolder

logical. TRUE if data lives inside a subfolder in season

s

a regular expression used to keep relevant files

sub_folder

character of subfolder containing data e.g "Data/Curated Data"

subset

ogical. TRUE if you want to read just a subset of files

n

integer. Number of files to subset e.g, 1, -1 1:4.

multiple

logical. TRUE if you want to read nultiple excel sheets from the same workbook

sheet_name

character. used to specify excel sheet name of interest, e.g., "fieldbook"

skip

integer. number of rows to skip when reading data from an excel workbook

file_to_read

character.file name to read e.g., generated by system.file()

merge

logical. whether or not to merge data from multiple sheets

update_plot

logical. whether or not to update plot column to conform to SOP. This applies to trials preceeding season 2025.

Value

a list of trial dataframes

Examples

f <- system.file("uon-trial-1.csv", package = "pbwrangler")
d <- read_workbooks(dir = NULL, file_to_read = f)
#> Rows: 108 Columns: 32
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (8): unique, geno, flowering_date, flower_colour, flesh_colour, skin_co...
#> dbl (24): plot, entry, row, col, rep, ntp, npe, growth_speed, pgh, plant_uni...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
lapply(d, function(x) x[1:5, 1:5])
#> $`UON-TRIAL-1`
#>           unique              plot          geno entry row
#> 1 1CIP317004.001 UON-TRIAL-1-00001 CIP317004.001    12   1
#> 2 2CIP317005.036 UON-TRIAL-1-00002 CIP317005.036    14   2
#> 3 3CIP317007.103 UON-TRIAL-1-00003 CIP317007.103    20   3
#> 4 4CIP317013.120 UON-TRIAL-1-00004 CIP317013.120    23   4
#> 5 5CIP317026.004 UON-TRIAL-1-00005 CIP317026.004    28   5
#>