Package: myClim 1.3.4

Vojtěch Kalčík

myClim: Microclimatic Data Processing

Handling the microclimatic data in R. The 'myClim' workflow begins at the reading data primary from microclimatic dataloggers, but can be also reading of meteorological station data from files. Cleaning time step, time zone settings and metadata collecting is the next step of the work flow. With 'myClim' tools one can crop, join, downscale, and convert microclimatic data formats, sort them into localities, request descriptive characteristics and compute microclimatic variables. Handy plotting functions are provided with smart defaults.

Authors:Matěj Man [aut], Vojtěch Kalčík [aut, cre], Martin Macek [aut], Josef Brůna [aut], Lucia Hederová [aut], Jan Wild [aut], Martin Kopecký [aut], Institute of Botany of the Czech Academy of Sciences [cph]

myClim_1.3.4.tar.gz
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myClim.pdf |myClim.html✨
myClim/json (API)
NEWS

# Install 'myClim' in R:
install.packages('myClim', repos = c('https://ibot-geoecology.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ibot-geoecology/myclim/issues

Datasets:

On CRAN:

6.84 score 6 stars 24 scripts 511 downloads 85 exports 88 dependencies

Last updated 7 hours agofrom:3f27bb4885. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winNOTENov 21 2024
R-4.4-macNOTENov 21 2024
R-4.3-winNOTENov 21 2024
R-4.3-macNOTENov 21 2024

Exports:mc_aggmc_calc_cumsummc_calc_fddmc_calc_gddmc_calc_snowmc_calc_snow_aggmc_calc_tomst_dendromc_calc_vpdmc_calc_vwcmc_calib_moisturemc_const_CALIB_MOIST_ACOR_Tmc_const_CALIB_MOIST_REF_Tmc_const_CALIB_MOIST_WCOR_Tmc_const_SENSOR_countmc_const_SENSOR_coveragemc_const_SENSOR_dendro_l_ummc_const_SENSOR_Dendro_rawmc_const_SENSOR_Dendro_Tmc_const_SENSOR_FDDmc_const_SENSOR_GDDmc_const_SENSOR_HOBO_EXTTmc_const_SENSOR_HOBO_RHmc_const_SENSOR_HOBO_Tmc_const_SENSOR_integermc_const_SENSOR_logicalmc_const_SENSOR_precipitationmc_const_SENSOR_realmc_const_SENSOR_RHmc_const_SENSOR_snow_boolmc_const_SENSOR_snow_freshmc_const_SENSOR_snow_totalmc_const_SENSOR_sun_shinemc_const_SENSOR_T_Cmc_const_SENSOR_Thermo_Tmc_const_SENSOR_TMS_moistmc_const_SENSOR_TMS_T1mc_const_SENSOR_TMS_T2mc_const_SENSOR_TMS_T3mc_const_SENSOR_VPDmc_const_SENSOR_VWCmc_const_SENSOR_wind_speedmc_env_moistmc_env_tempmc_env_vpdmc_filtermc_infomc_info_cleanmc_info_countmc_info_loggermc_info_metamc_info_rangemc_info_statesmc_joinmc_loadmc_plot_imagemc_plot_linemc_plot_loggersmc_plot_rastermc_prep_calibmc_prep_calib_loadmc_prep_cleanmc_prep_cropmc_prep_fillNAmc_prep_mergemc_prep_meta_localitymc_prep_meta_sensormc_prep_solar_tzmc_prep_TMSoffsoilmc_read_datamc_read_filesmc_read_longmc_read_tubedbmc_read_widemc_reshape_longmc_reshape_widemc_savemc_states_deletemc_states_from_sensormc_states_insertmc_states_joinmc_states_outliermc_states_replacemc_states_to_sensormc_states_updatemyClimList

Dependencies:askpassbase64encbitbit64bslibcachemclicolorspacecpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggforceggplot2gluegridExtragtablehighrhmshtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypolyclipprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownsassscalesstringistringrsyssystemfontstibbletidyrtidyselecttimechangetinytextweenrtzdbutf8vctrsviridisviridisLitevroomwithrxfunyamlzoo

myClim: microclimatic data in R

Rendered frommyclim-demo.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-11-16
Started: 2022-03-10

myClim: reading user-defined loggers

Rendered frommyclim-custom-loggers.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-11-09
Started: 2023-10-02

Readme and manuals

Help Manual

Help pageTopics
Extract localities with [][.myClimList
Length function for myClim objectlength.myClimList
Aggregate data by functionmc_agg
Cumulative summc_calc_cumsum
Freezing Degree Daysmc_calc_fdd
Growing Degree Daysmc_calc_gdd
Snow detection from temperaturemc_calc_snow
Summary of TRUE/FALSE snow sensormc_calc_snow_agg
Converting Tomst dendrometer values to micrometersmc_calc_tomst_dendro
Calculate vapor pressure deficit (in kPa)mc_calc_vpd
Conversion of raw TMS soil moisture values to volumetric water content (VWC)mc_calc_vwc
Calculates coefficients for TMS moisture conversion to VWCmc_calib_moisture
Default temperature drift for TMS moisture in the air.mc_const_CALIB_MOIST_ACOR_T
Default ref. temperate for TMS moisture calibrationmc_const_CALIB_MOIST_REF_T
Default temperature drift for TMS moisture in the watermc_const_CALIB_MOIST_WCOR_T
Count sensor id see 'mc_agg()'mc_const_SENSOR_count
Coverage sensor id see 'mc_agg()'mc_const_SENSOR_coverage
Radius difference sensor idmc_const_SENSOR_dendro_l_um
Default sensor for TOMST Dendrometer radius differencemc_const_SENSOR_Dendro_raw
Default sensor for TOMST Dendrometer temperaturemc_const_SENSOR_Dendro_T
Freezing Degree Days sensor id see 'mc_calc_fdd()'mc_const_SENSOR_FDD
Growing Degree Days sensor id see 'mc_calc_gdd()'mc_const_SENSOR_GDD
Onset HOBO external temperature sensor idmc_const_SENSOR_HOBO_EXTT
Onset HOBO humidity sensor idmc_const_SENSOR_HOBO_RH
Onset HOBO temperature sensor idmc_const_SENSOR_HOBO_T
General integer sensor idmc_const_SENSOR_integer
General logical sensor idmc_const_SENSOR_logical
Precipitation sensor idmc_const_SENSOR_precipitation
General real sensor idmc_const_SENSOR_real
Relative humidity sensor idmc_const_SENSOR_RH
Snow existence sensor id see 'mc_calc_snow()'mc_const_SENSOR_snow_bool
Height of newly fallen snow sensor idmc_const_SENSOR_snow_fresh
Height snow sensor idmc_const_SENSOR_snow_total
Time of sun shine sensor idmc_const_SENSOR_sun_shine
Temperature sensor idmc_const_SENSOR_T_C
Default sensor for TOMST Thermologger temperaturemc_const_SENSOR_Thermo_T
Default sensor for TOMST TMS raw soil moisturemc_const_SENSOR_TMS_moist
Default sensor for TOMST TMS soil temperaturemc_const_SENSOR_TMS_T1
Default sensor for TOMST TMS temperature of soil surfacemc_const_SENSOR_TMS_T2
Default sensor for TOMST TMS air temperaturemc_const_SENSOR_TMS_T3
Vapor Pressure Deficit sensor id see 'mc_calc_vpd()'mc_const_SENSOR_VPD
Volumetric soil moisture sensor id see 'mc_calc_vwc()'mc_const_SENSOR_VWC
Speed of wind sensor idmc_const_SENSOR_wind_speed
Example data in Agg-format.mc_data_example_agg
Example cleaned data in Raw-format.mc_data_example_clean
Example data in Raw-formatmc_data_example_raw
Formats of source data filesmc_data_formats
Default heights of sensorsmc_data_heights
Physical quantities definitionmc_data_physical
Sensors definition.mc_data_sensors
Volumetric water content parametersmc_data_vwc_parameters
Class for Logger File Data Formatmc_DataFormat mc_DataFormat-class
Standardised myClim soil moisture variablesmc_env_moist
Standardised myClim temperature variablesmc_env_temp
Standardised myClim vapor pressure deficit variablesmc_env_vpd
Filter data from myClim objectmc_filter
Class for reading HOBO logger filesmc_HOBODataFormat mc_HOBODataFormat-class
Get sensors info tablemc_info
Call cleaning logmc_info_clean
Count datamc_info_count
Get loggers info tablemc_info_logger
Get localities metadata tablemc_info_meta
Get table of sensors rangemc_info_range
Get states (tags) info tablemc_info_states
Joining time-series from repeated downloadsmc_join
Load myClim objectmc_load
Class for locality metadatamc_LocalityMetadata mc_LocalityMetadata-class
Class for logger clean infomc_LoggerCleanInfo mc_LoggerCleanInfo-class
Class for logger metadatamc_LoggerMetadata mc_LoggerMetadata-class
Class for myClim object metadatamc_MainMetadata mc_MainMetadata-class
Class for myClim object metadata in Agg-formatmc_MainMetadataAgg mc_MainMetadataAgg-class
Class for physicalmc_Physical mc_Physical-class
Plot data - imagemc_plot_image
Plot data - ggplot2 geom_linemc_plot_line
Plot data from loggersmc_plot_loggers
Plot data - ggplot2 geom_rastermc_plot_raster
Sensors calibrationmc_prep_calib
Load sensor calibration parameters to correct microclimatic recordsmc_prep_calib_load
Cleaning datetime seriesmc_prep_clean
Crop datetimemc_prep_crop
Fill NAmc_prep_fillNA
Merge myClim objectsmc_prep_merge
Set metadata of localitiesmc_prep_meta_locality
Set metadata of sensorsmc_prep_meta_sensor
Set solar time offset against UTC timemc_prep_solar_tz
Detection of out-of-soil measurements from TMS loggermc_prep_TMSoffsoil
Reading files with locality metadatamc_read_data
Reading files or directoriesmc_read_files
Reading data from long data.framemc_read_long
Reading data from TubeDBmc_read_tubedb
Reading data from wide data.framemc_read_wide
Export values to long tablemc_reshape_long
Export values to wide tablemc_reshape_wide
Save myClim objectmc_save
Class for sensor definitionmc_Sensor mc_Sensor-class
Class for sensor metadatamc_SensorMetadata mc_SensorMetadata-class
Delete sensor states (tags)mc_states_delete
Convert a sensor to a statemc_states_from_sensor
Insert new sensor states (tags)mc_states_insert
Create states for join conflictsmc_states_join
Create states for outlying valuesmc_states_outlier
Replace values by states with tagmc_states_replace
Convert states to logical (TRUE/FALSE) sensormc_states_to_sensor
Update sensor states (tags)mc_states_update
Class for reading TOMST logger filesmc_TOMSTDataFormat mc_TOMSTDataFormat-class
Class for reading TMS join filesmc_TOMSTJoinDataFormat mc_TOMSTJoinDataFormat-class
Custom list for myClim objectmyClimList
Print function for myClim objectprint.myClimList