Package index • myClim

myClim structure Description of package with definition of data structure
`myClim` `myClim-package`	myClim: Microclimatic Data Processing
Classes
`mc_DataFormat-class` `mc_DataFormat`	Class for Logger File Data Format
`mc_HOBODataFormat-class` `mc_HOBODataFormat`	Class for reading HOBO logger files
`mc_LocalityMetadata-class` `mc_LocalityMetadata`	Class for locality metadata
`mc_LoggerCleanInfo-class` `mc_LoggerCleanInfo`	Class for logger clean info
`mc_LoggerMetadata-class` `mc_LoggerMetadata`	Class for logger metadata
`mc_MainMetadata-class` `mc_MainMetadata`	Class for myClim object metadata
`mc_MainMetadataAgg-class` `mc_MainMetadataAgg`	Class for myClim object metadata in Agg-format
`mc_Physical-class` `mc_Physical`	Class for physical
`mc_Sensor-class` `mc_Sensor`	Class for sensor definition
`mc_SensorMetadata-class` `mc_SensorMetadata`	Class for sensor metadata
`mc_TOMSTDataFormat-class` `mc_TOMSTDataFormat`	Class for reading TOMST logger files
`mc_TOMSTJoinDataFormat-class` `mc_TOMSTJoinDataFormat`	Class for reading TMS join files
Data
`mc_data_example_agg`	Example data in Agg-format.
`mc_data_example_clean`	Example cleaned data in Raw-format.
`mc_data_example_raw`	Example data in Raw-format
`mc_data_formats`	Formats of source data files
`mc_data_heights`	Default heights of sensors
`mc_data_physical`	Physical quantities definition
`mc_data_sensors`	Sensors definition.
`mc_data_vwc_parameters`	Volumetric water content parameters
Read functions Read functions are used to reading source data files.
`mc_read_data()`	Reading files with locality metadata
`mc_read_files()`	Reading files or directories
`mc_read_long()`	Reading data from long data.frame
`mc_read_tubedb()`	Reading data from TubeDB
`mc_read_wide()`	Reading data from wide data.frame
Info functions Functions return data.frame with information about data.
`mc_info()`	Get sensors info table
`mc_info_clean()`	Call cleaning log
`mc_info_count()`	Count data
`mc_info_logger()`	Get loggers info table
`mc_info_meta()`	Get localities metadata table
`mc_info_range()`	Get table of sensors range
`mc_info_states()`	Get states (tags) info table
Reshape functions Functions convert data to data.frame.
`mc_reshape_long()`	Export values to long table
`mc_reshape_wide()`	Export values to wide table
Preparing functions Functions are used to prepare input data for aggregation.
`mc_prep_TMSoffsoil()`	Detection of out-of-soil measurements from TMS logger
`mc_prep_calib()`	Sensors calibration
`mc_prep_calib_load()`	Load sensor calibration parameters to correct microclimatic records
`mc_prep_clean()`	Cleaning datetime series
`mc_prep_crop()`	Crop datetime
`mc_prep_fillNA()`	Fill NA
`mc_prep_merge()`	Merge myClim objects
`mc_prep_meta_locality()`	Set metadata of localities
`mc_prep_meta_sensor()`	Set metadata of sensors
`mc_prep_solar_tz()`	Set solar time offset against UTC time
States functions Functions are used to manage sensor states.
`mc_states_delete()`	Delete sensor states (tags)
`mc_states_from_sensor()`	Convert a sensor to a state
`mc_states_insert()`	Insert new sensor states (tags)
`mc_states_join()`	Create states for join conflicts
`mc_states_outlier()`	Create states for outlying values
`mc_states_replace()`	Replace values by states with tag
`mc_states_to_sensor()`	Convert states to logical (TRUE/FALSE) sensor
`mc_states_update()`	Update sensor states (tags)
Joining functions Functions are used to join loggers from one locality.
`mc_join()`	Joining time-series from repeated downloads
Aggregation function
`mc_agg()`	Aggregate data by function
Calculation functions Functions are used to calculation new sensors derived from anothers.
`mc_calc_cumsum()`	Cumulative sum
`mc_calc_fdd()`	Freezing Degree Days
`mc_calc_gdd()`	Growing Degree Days
`mc_calc_snow()`	Snow detection from temperature
`mc_calc_snow_agg()`	Summary of TRUE/FALSE snow sensor
`mc_calc_tomst_dendro()`	Converting Tomst dendrometer values to micrometers
`mc_calc_vpd()`	Calculate vapor pressure deficit (in kPa)
`mc_calc_vwc()`	Conversion of raw TMS soil moisture values to volumetric water content (VWC)
Plot functions
`mc_plot_image()`	Plot data - image
`mc_plot_line()`	Plot data - ggplot2 geom_line
`mc_plot_loggers()`	Plot data from loggers
`mc_plot_raster()`	Plot data - ggplot2 geom_raster
Environment functions Functions returns environment variables.
`mc_env_moist()`	Standardised myClim soil moisture variables
`mc_env_temp()`	Standardised myClim temperature variables
`mc_env_vpd()`	Standardised myClim vapor pressure deficit variables
Other functions
`length(<myClimList>)`	Length function for myClim object
`myClimList()`	Custom list for myClim object
`print(<myClimList>)`	Print function for myClim object
`[`(<myClimList>)	Extract localities with []
`mc_filter()`	Filter data from myClim object
`mc_save()`	Save myClim object
`mc_save_localities()`	Save myClim object separated by localities
`mc_load()`	Load myClim object
`mc_calib_moisture()`	Calculates coefficients for TMS moisture conversion to VWC
Constants
`mc_const_CALIB_MOIST_ACOR_T`	Default temperature drift for TMS moisture in the air.
`mc_const_CALIB_MOIST_REF_T`	Default ref. temperate for TMS moisture calibration
`mc_const_CALIB_MOIST_WCOR_T`	Default temperature drift for TMS moisture in the water
`mc_const_SENSOR_Dendro_T`	Default sensor for TOMST Dendrometer temperature
`mc_const_SENSOR_Dendro_raw`	Default sensor for TOMST Dendrometer radius difference
`mc_const_SENSOR_FDD`	Freezing Degree Days sensor id see `mc_calc_fdd()`
`mc_const_SENSOR_GDD`	Growing Degree Days sensor id see `mc_calc_gdd()`
`mc_const_SENSOR_HOBO_EXTT`	Onset HOBO external temperature sensor id
`mc_const_SENSOR_HOBO_RH`	Onset HOBO humidity sensor id
`mc_const_SENSOR_HOBO_T`	Onset HOBO temperature sensor id
`mc_const_SENSOR_RH`	Relative humidity sensor id
`mc_const_SENSOR_TMS_T1`	Default sensor for TOMST TMS soil temperature
`mc_const_SENSOR_TMS_T2`	Default sensor for TOMST TMS temperature of soil surface
`mc_const_SENSOR_TMS_T3`	Default sensor for TOMST TMS air temperature
`mc_const_SENSOR_TMS_moist`	Default sensor for TOMST TMS raw soil moisture
`mc_const_SENSOR_T_C`	Temperature sensor id
`mc_const_SENSOR_Thermo_T`	Default sensor for TOMST Thermologger temperature
`mc_const_SENSOR_VPD`	Vapor Pressure Deficit sensor id see `mc_calc_vpd()`
`mc_const_SENSOR_VWC`	Volumetric soil moisture sensor id see `mc_calc_vwc()`
`mc_const_SENSOR_count`	Count sensor id see `mc_agg()`
`mc_const_SENSOR_coverage`	Coverage sensor id see `mc_agg()`
`mc_const_SENSOR_dendro_l_um`	Radius difference sensor id
`mc_const_SENSOR_integer`	General integer sensor id
`mc_const_SENSOR_logical`	General logical sensor id
`mc_const_SENSOR_precipitation`	Precipitation sensor id
`mc_const_SENSOR_real`	General real sensor id
`mc_const_SENSOR_snow_bool`	Snow existence sensor id see `mc_calc_snow()`
`mc_const_SENSOR_snow_fresh`	Height of newly fallen snow sensor id
`mc_const_SENSOR_snow_total`	Height snow sensor id
`mc_const_SENSOR_sun_shine`	Time of sun shine sensor id
`mc_const_SENSOR_wind_speed`	Speed of wind sensor id

Reference

myClim structure

Classes

Data

Read functions

Info functions

Reshape functions

Preparing functions

States functions

Joining functions

Aggregation function

Calculation functions

Plot functions

Environment functions

Other functions

Constants