SHARK4R (version 1.0.2)

read_ptbx: Read a Plankton Toolbox export file

Description

This function reads a sample file exported as an Excel (.xlsx) file from Plankton Toolbox and extracts data from a specified sheet. The default sheet is "sample_data.txt", which contains count data.

Usage

read_ptbx(
  file_path,
  sheet = c("sample_data.txt", "sample_info.txt", "counting_method.txt",
    "Sample summary", "README")
)

Value

A tibble containing the contents of the selected sheet.

Arguments

file_path

Character. Path to the Excel file.

sheet

Character. The name of the sheet to read. Must be one of: "sample_data.txt", "Sample summary", "sample_info.txt", "counting_method.txt", or "README". Default is "sample_data.txt".

See Also

https://nordicmicroalgae.org/plankton-toolbox/ for downloading Plankton Toolbox.

https://github.com/planktontoolbox/plankton-toolbox/ for Plankton Toolbox source code.

Examples

# Read the default data sheet
sample_data <- read_ptbx(system.file("extdata/Anholt_E_2024-09-15_0-10m.xlsx",
                                     package = "SHARK4R"))

# Print output
sample_data


# Read a specific sheet
sample_info <- read_ptbx(system.file("extdata/Anholt_E_2024-09-15_0-10m.xlsx",
                                     package = "SHARK4R"),
                         sheet = "sample_info.txt")
# Print output
sample_info