prep

Invoked by: vaxstats prep

The prep command is designed to clean and prepare data from various experimental sources for uniform processing in vaxstats. It addresses the common challenge of inconsistent data formats by allowing you to specify the crucial data elements and their formats.

Usage

vaxstats prep <file_path> --date_idx <index> --time_idx <index> --y_idx <index> [options]

Examples

vaxstats prep example.xlsx --date_idx 0 --time_idx 1 --y_idx 6

vaxstats prep ./data/2024-2-8.xlsx --date_idx 3 --time_idx 2 --y_idx 4 --input_date_fmt "%Y-%m-%d"

Required Arguments

Argument	Description	Example
file_path	Path to Excel or CSV file containing the data.	2024-08-04.xlsx, data/exp001.csv
--date_idx	Column index containing date information.	0, 1, etc.
--time_idx	Column index containing time information.	0, 1, etc.
--y_idx	Column index containing the target variable (e.g., temperatures).	0, 1, etc.

Note

All column indices are zero-based, meaning the first column has index 0.

Optional Arguments

Option	Description	Default	Example
--input_date_fmt	Format of the input date strings.	%m-%d-%y	%Y-%m-%d, %d/%m/%Y
--input_time_fmt	Format of the input time strings.	%I:%M:%S %p	%H:%M:%S, %I:%M %p
--output_fmt	Format of the output datetime strings.	%Y-%m-%d %H:%M:%S	%Y-%m-%dT%H:%M:%S
--output	Name of the output CSV file.	output.csv	prepared_data.csv

Input Format Specifications

• For --input_date_fmt and --input_time_fmt, use Python's strftime format codes.
• Common format specifiers:
  • %Y: Year with century (e.g., 2024)
  • %y: Year without century as zero-padded decimal number (01, 02, 99).
  • %m: Month as a zero-padded number (01-12)
  • %d: Day of the month as a zero-padded number (01-31)
  • %H: Hour (24-hour clock) as a zero-padded number (00-23)
  • %I: Hour (12-hour clock) as a zero-padded number (01-12)
  • %M: Minute as a zero-padded number (00-59)
  • %S: Second as a zero-padded number (00-59)
  • %p: Locale's equivalent of AM or PM

Output

The prep command will generate a CSV file (default name: output.csv) with the following columns:

1. unique_id: A unique identifier for each row (always set to 0 in the current version).
2. ds: The combined and formatted date and time.
3. y: The target variable (from the column specified by --y_idx).

This output format is designed to be compatible with various forecasting and analysis tools.

Tip

If your input data has a non-standard date or time format, use the --input_date_fmt and --input_time_fmt options to specify the correct format. This ensures accurate parsing of your datetime information.