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Process 1 water data file

Source: R/data_pipeline.R
process_water.Rd

Reads, cleans, filters, and offsets a water file:

  1. Safely read the CSV

  2. Rename columns

  3. Drop unwanted cows & transponders

  4. Keep only specified bins

  5. Subset to desired columns

  6. Add an offset to bin IDs, so that water bin ID differs from feed bin ID

Usage

process_water(
  file,
  col_names = NULL,
  id_col = id_col2(),
  drop_ids = NULL,
  trans_col = trans_col2(),
  drop_trans = NULL,
  bin_col = bin_col2(),
  bins = bins_wat2(),
  select_cols = NULL,
  bin_offset = bin_offset2(),
  sep = ",",
  header = FALSE
)

Arguments

file

What's the path to your data file? This should be a single string giving the path to the file.

col_names

A character vector of column names to assign when header = FALSE. This vector must match the number of columns in the raw data. If header = TRUE, the file’s existing column names are used and col_names is ignored.

id_col

What's the name of the column recording animal ID? This should be a Single string. (default: "cow").

drop_ids

Which animals do you wish to drop? This should be a vector indicating values in id_col that you wish to remove (default: NULL, so remove nothing).

trans_col

What's the name of the column recording transponder ID for each visit? This should be a single string. (default: "transponder").

drop_trans

Which transponders do you wish to delete because they are not part of your study? This should be a vector indicating values in trans_col that you wish to remove (default: NULL, so remove nothing).

bin_col

What's the name of the column recording the ID of the bin for each visit? This should be a single string. (default: "bin").

bins

Which water bins are included in your study for analysis? This should be a numeric vector of bin IDs to keep. You can supply individual values (e.g. c(1, 3, 5)) or a sequence (e.g. 2:4). Default is set to 1:5

select_cols

Which columns in the dataframe do you wish to keep in your original data frame after cleaning? This should be a character vector indicating columns to retain in the final output. Default is NULL, so we select all columns.

bin_offset

A single numeric value to add to each matching bin ID. Default is 100.

sep

Field separator; passed to read.table(). Defaults to "," for comma delimited files like .csv and .DAT.

header

Logical; does your data file have a header row (i.e., column names)? Defaults to FALSE. If yor file contains column names at the top, please set this to TRUE.

Value

A cleaned water data frame with shifted bin IDs.

Examples

# create a toy data file
original <- data.frame(
  cow = c("D", "E", "F", "D"),
  transponder = c("Y1", "Y2", "Y3", "Y2"),
  bin = c(5, 6, 7, 6),
  value = c(50, 60, 70, 80),
  stringsAsFactors = FALSE
)
print(original)
#>   cow transponder bin value
#> 1   D          Y1   5    50
#> 2   E          Y2   6    60
#> 3   F          Y3   7    70
#> 4   D          Y2   6    80
tmp <- tempfile(fileext = ".csv")
write.table(original, tmp, sep = ",", row.names = FALSE, col.names = FALSE)

# Drop nothing, keep bins 5:7, offset +100, select cow, bin, value
process_water(
  file = tmp,
  col_names = c("cow", "transponder", "bin", "value"),
  drop_ids = NULL,
  drop_trans = NULL,
  bins = 5:7,
  select_cols = c("cow", "bin", "value"),
  bin_offset = 100,
  header = FALSE
)
#>   cow bin value
#> 1   D 105    50
#> 2   E 106    60
#> 3   F 107    70
#> 4   D 106    80
unlink(tmp)