filters and converts raw data files

Uses to convert and format (strip from unused columns and rows) the raw '.txt' data file to produce a .csv file that is required for `MMR` and `SMR` functions.

Usage

textFileConvert(
  txt_file,
  type_file,
  nrowSkip = NULL,
  N_Ch = 4,
  local_path = TRUE,
  exclude_rows = NULL,
  exclude_first_measurement_s = 0,
  convert_units = FALSE,
  units_from = NULL,
  units_to = NULL,
  channels = c(1, 2, 3, 4),
  salinity = 0,
  atm_pressure = 1,
  temperature = NULL,
  temperature_Ch = 1,
  device = "A",
  file_extension_id = ""
)

Arguments

txt_file

The name of the original “.txt” file from oxygen meter

type_file

Indicates the type of software that was used to record raw data, options: "Firesting_pre2023", "Firesting_2023", "Witrox_2023", "PreSense_microplate"

nrowSkip

The number of rows to skip if the default does not work; the argument 'type_file' determines the default N rows to skip "Firesting_pre2023" = 19, "Firesting_2023" = 70, "Witrox_2023" = 41; "PreSense_microplate" = 10, these rows in raw txt file often contain calibration information, the IDs of the probes and other user defined settings

N_Ch

The number of oxygen meter channels that described the physical device, not how many channels were plugged in; this is an argument that describes hardware. Options include 2, 4, 8, 24. (microplate). If a 2-channel oxygen meter was used, this argument could be ignored, or enter 4

local_path

Logical. If TRUE (default) all returned files will be saved in the local working directory.

exclude_rows

Rows to be excluded; used when there are unwanted NAs, or no sensor data. etc.

exclude_first_measurement_s

DEPRECATED Nov 2024: use 'exclude_measurement_s' (see documentation), The number measurement point to be excluded from the beginning of the file (in addition to the nrowSkip argument)

convert_units

Logical (FALSE = default). If true, the function is passed to rMR function DO.unit.convert to convert O2 content units.

units_from

default NULL, options:"mg/L", "PP", "pct". passed down to rM::DO.unit.convert arg. DO.units.in

units_to

= default NULL, options:"mg/L", "PP", "pct". passed down to rM::DO.unit.convert arg. DO.units.out

channels

= c(1,2,3,4), indicate which channels the unit conversion will be applied to

salinity

= 0, passed down to rMR::DO.unit.convert arg. salinity (must be in "pp.thou")

atm_pressure

= 1, passed down to rMR::DO.unit.convert arg. bar.press (must be in "atm")

temperature

user set consistent temperature for all channels (ºC)

temperature_Ch

Numerical, select the channel to use for temperature recording. This is used only for 4-channel Firesting, when probe/channel 1 was not plugged in and therefore has all values as "NA". default is 'NULL'0' which then chooses data from the first available channel

device

only for for "Firesting_2023" output files. Results from multiple devices can be recorded on one file. These are differentiated by uppper case letters "A", "B", etc. use this argument to specify which device is used, default is "A".

file_extension_id

custom file extension for the saved csv file, default is 'blank'

Value

The output from print