Class for Logger File Data Format

Source: R/model.R

This class is used for parsing source TXT/CSV files downloaded from microclimatic loggers.

Details

myClim offers several pre-defined logger file data formats, such as TOMST TMS or HOBO. Users can also define custom readings for their own loggers. Pre-defined and custom loggers in myClim each have their own specific object of class mc_{logger}DataFormat, which defines the parameters for handling logger files. The pre-defined logger definitions are stored in the R environment object ./data/mc_data_formats.rda.

Slots

skip

The number of rows to skip before the first row containing microclimatic records. For example, to skip the header (default 0).

separator

The column separator (default is a comma ",").

date_column

The index of the date column - required (default NA).

date_format

The format of the date (default NA).

For a description of the date_format parameter, see strptime(). If the format is in ISO8601 and the function vroom::vroom() automatically detects datetime values, the date_format parameter can be NA.

na_strings

Strings for representing NA values, e.g., "-100", "9999" (default "").

error_value

The value that represents an error of the sensor, e.g., 404, 9999 (default NA).

The error_value is replaced by NA, and intervals of errors are flagged in sensor$states (see myClim-package).

columns

A list with names and indexes of value columns - required (default list()).

Names come from names(mc_data_sensors). Names are defined as constants mc_const_SENSOR_*. For example, if the third column is temperature, you can define it as columns[[mc_const_SENSOR_T_C]] <- 3. There are universal sensors for arbitrary value types: mc_const_SENSOR_real, mc_const_SENSOR_integer and mc_const_SENSOR_logical. Multiple columns with same sensor type can be defined as columns[[mc_const_SENSOR_real]] <- c(2, 3, 4). The names in this example will be real1, real2 and real3.

col_types

Parameter for vroom::vroom() (default NA).

To ensure the correct reading of values, you have the possibility to strictly define the types of columns.

filename_serial_number_pattern

A character pattern for detecting the serial number from the file name (default NA).

The regular expression with brackets around the serial number. For example, the pattern for old TOMST files is "data_(\\d+)_\\d+\\.csv$". If the value is NA, the name of the file is used as the serial number.

data_row_pattern

A character pattern for detecting the correct file format (default NA).

The regular expression. If data_row_pattern is NA, then the file format is not checked.

logger_type

The type of logger: TMS, TMS_L45, Thermo, Dendro, HOBO, ... (default NA).

tz_offset

The timezone offset in minutes from UTC - required (default NA).

If the value of the tz_offset parameter is 0, then datetime values are in UTC. If the time zone offset is defined in the value, e.g., "2020-10-06 09:00:00+0100", and date_format is "%Y-%m-%d %H:%M:%S%z", the value is automatically converted to UTC.