Changelog

Source: NEWS.md

myClim 1.5.02025-09-30

• The new function mc_prep_expandtime has been added to expand time series to shorter steps.

myClim 1.4.5

• Empty calibration parameters are now removed from joined data in the mc_join function.

myClim 1.4.4

• The mc_read_data function now skips empty data files.
• The minimum required R version is now 4.0.

myClim 1.4.3

• The new function mc_info_calib has been added to provide an overview of the calibration parameters.
• The output table of the mc_info function has been extended with the height and calibrated columns.
• The mc_prep_calib function skips sensors that are already calibrated.

myClim 1.4.2

• Only one logger can be used for uncleaned data in the mc_reshape_wide function.
• The raw indexes are loaded from TOMST files to logger metadata.
• The new function mc_prep_delete has been added.
• The loggers parameter has been added to the mc_filter function.
• The sensor without states in the mc_plot_line function has been fixed.
• The missing states in mc_states_join have been fixed.
• The new parameter older_newer_suffix has been added to the mc_states_join function.
• The multiple parameters can be combined in the mc_filter function, if reverse is TRUE.
• The unexistent tag issue in the mc_states_replace function has been fixed.

myClim 1.4.1

• The calculated sensor in mc_states_join issue has been fixed.

myClim 1.4.02025-02-21

• The save localities unit test has been fixed.
• CRAN version.

myClim 1.3.11

• The numbers in the TOMS_join format can be in scientific notation.

myClim 1.3.10

• The environment mc_read_problems with vroom parse problems has been added.

myClim 1.3.9

• The clean_conflict states issue in the mc_prep_clean function has been fixed.
• The NA values in the mc_prep_TMSoffsoil function have been fixed.

myClim 1.3.8

• The tag parameter has been added to the mc_plot_line function.

myClim 1.3.7

• The uninitialsed date_format warning in the mc_read_data function has been fixed.
• The cropt_table parameter has been added to the mc_prep_crop function.
• The start and end parameters in the mc_prep_crop function can be only single value.
• The crop_margins_NA parameter has been added to the mc_states_replace function.

myClim 1.3.6

• A new function mc_save_localities has been added.
• The function mc_load can load multiple files.
• The function mc_load can load all .RDS files in a directory.
• The warnings about missing sensors have been removed.

myClim 1.3.5

• The logger_name is used in the mc_states_join function instead of the logger_index as value in the states table.
• The result of mc_prep_TMSoffsoil function has been changed to TRUE/FALSE instead of 1/0.

myClim 1.3.4

• The logger_name is used in myClim object instead of the logger_index.
• The logger_name is visible in mc_plot_line.
• The show_logger_name parameter has been added to the mc_reshape_wide function.
• The serias_name label changed to series in mc_plot_line.
• The progress bar is added to mc_prep_crop.
• The mc_prep_clean step warning is fixed.

myClim 1.3.3

• A performance issue in the mc_prep_crop function has been fixed.
• The parameters tolerance and by_type have been added to the mc_join function.
• The class mc_LocalityMetadata has been extended with the join_serial slot.
• The new function mc_states_join has been added.
• The function mc_info_join has been deleted.

myClim 1.3.2

• The parameter tolerance has been added to the mc_prep_clean function.
• The result table of the mc_info_clean function has been extended with the logger_index column.
• The plot colors of sensors have been updated.
• The colors issue in the mc_plot_line function has been fixed.

myClim 1.3.1

• The conflict state issue in the mc_prep_clean function has been fixed.

myClim 1.3.02024-10-21

• Published on CRAN.

myClim 1.2.6

• New functions mc_info_range and mc_states_outlier have been added.

myClim 1.2.5

• The issue with the HOBO logger_type in the mc_read_data function has been fixed.

myClim 1.2.4

• The multiple custom date formats issue for HOBO logger in the mc_read_data function has been fixed.

myClim 1.2.3

• It is possible to define multiple custom date formats in the mc_read_data function.

myClim 1.2.2

• The issue in the mc_join function with the use always newer logger option has been fixed.

myClim 1.2.1

• The new functions mc_states_from_sensor and mc_states_to_sensor have been added.

myClim 1.2.02024-08-21

• The color palette of mc_plot_line function has been extended.

myClim 1.1.6

• New function mc_states_replace has been added.

myClim 1.1.5

• Updated the color palette of mc_plot_line for greater differentiation between values.

myClim 1.1.4

• Fixed the issue with the joined series of loggers in the mc_plot_line function.
• Added a new parameter color_by_logger to the mc_plot_line function.
• Added a new parameter logger_types to the mc_filter function.

myClim 1.1.3

• Fixed reading of TOMST Thermologger data CSV. The data format has changed in the new version of Lolly.

myClim 1.1.2

• The mc_prep_clean function now selects a conflicted value based on the best match with the new rounded date and time.
• A new parameter, resolve_conflicts, has been added to the mc_prep_clean function to allow checking uncleaned data.
• Fixed the round-off issue of datetimes in states when an unconventional step is used.

myClim 1.1.1

• New functions mc_info_states, mc_states_insert, mc_states_update, and mc_states_delete have been added.
• The mc_agg function now rounds states by period.

myClim 1.1.02024-02-16

• Fixed an issue with the read progress bar when some files were skipped.
• Changed the logger type HOBO to HOBO_U23-001A.
• Added support for the logger type HOBO_U23-004.

myClim 1.0.19

• Fixed an issue that affected the calibration table after calling the mc_join() function.
• Added a file counter to the mc_plot_loggers() function.

myClim 1.0.18

• Fixed temperature drift correction in the mc_calc_vwc() function.
• Resolved the issue where the vroom::problems() function did not function properly when tidyverse was imported. This is now handled in the read functions.
• Disabled progress bar for the vroom::vroom() function.

myClim 1.0.17

• Multiple custom date formats can be defined for TOMST data format.

myClim 1.0.16

• A new function, mc_info_join(), has been added. This function attempts to join myClim objects and returns an overview of the operation.
• The skip option has been added to the mc_join() function.
• The mc_read_data() function can now read HOBO files which use a comma as the decimal separator.
• The logger index has now been added to the column name in the mc_reshape_wide() function.
• Progress bars have been added to the mc_read_data(), mc_prep_clean(), mc_join(), and mc_agg() functions.
• When new sensors are created from a custom function in the mc_agg() function, they now inherit the sensor_id from the parent sensors.
• If a wrong physical unit is input into the calc functions, it will now result in a warning instead of an error.

myClim 1.0.15

• when reading TOMST_join format (internal TOMST data format used by IBOT researchers) the mc_read_data() function now uses the Thermo value of the logger_type parameter when reading TOMST Termo Logger and does not detect the type of the logger from the data.
• A new function, mc_info_logger(), has been added. This function returns an overview table of loggers in myClim Raw-format.
• The issue with NA values in the mc_join() function has been fixed.
• The issue with always choices in the mc_join() function has been fixed.
• The TRUE value in TOMST_join is now correctly detected.
• The mc_join() function does not fail if a wrong logger type is defined.

myClim 1.0.14

• The function mc_read_data() now skips non-existent files.
• The length() function now returns the number of localities for myClim object.
• Detection of TOMST_join format is now fixed for negative values of moisture.

myClim 1.0.13

• The issue of NA values at the beginning of TOMST_join format data files has been resolved.

myClim 1.0.122023-11-16

• A new facet parameter has been added to the mc_plot_line() function to provide more flexibility in data visualization.
• The y-axis labels for Boolean sensors in the mc_plot_line() function have been updated to TRUE and FALSE.
• The function mc_calib_moisture() now produces renamed results to enhance consistency.
• The manual and vignettes have been enhanced to provide more comprehensive and user-friendly documentation.

myClim 1.0.11

• The reading of TOMST data with a comma decimal separator was incorrect in the 1.0.9 and 1.0.10 versions. This error has been fixed.

myClim 1.0.10

• Dependency on the package runner is removed and data.table is added as a new dependency.
• In the functions mc_read_files() and mc_read_data(), a new parameter user_data_formats is added for custom source file data formats.
• A new vignette for user data formats is added.
• A check for different values in same time is added to the function mc_prep_clean().
• A new function mc_prep_TMSoffsoil() is added for detecting when TMS is out of soil.

myClim 1.0.9

• The citation of the package has been changed to the article myClim: Microclimate data handling and standardised analyses in R.
• The reading of CSV data files is now processed by the vroom package, which provides a faster and more efficient way to read CSV data.

myClim 1.0.8

• The calibration constants for the mc_calc_vwc() function are now visible to the user under new names: mc_const_CALIB_MOIST_REF_T, mc_const_CALIB_MOIST_ACOR_T, and mc_const_CALIB_MOIST_WCOR_T.
• The sensor ID constants are now visible to the user under new names: mc_const_SENSOR_*.
• The soiltype parameter in the mc_calc_vwc() function can now be a list with user-defined parameters in the format list(a=number1, b=number2, c=number3).

myClim 1.0.7

• The temperature correction is no longer applied in the mc_calc_vwc() function when the temp_sensor value is NA.

myClim 1.0.6

• The mc_prep_crop() function now includes a new parameter localities, which allows for specific localities to be selected.
• The definitions of physicals, loggers, and sensors have been modified.
  • TMS_TMSmoisture -> TMS_moist
  • TS_T -> Thermo_T
  • DEND_T -> Dendro_T
  • DEND_TOMSTdendro -> Dendro_raw
  • HOBO_T_C -> HOBO_T
  • moisture -> VWC
  • RH_perc -> RH
  • wind -> wind_speed
  • deleted HOBO_T_F
• Data from HOBO loggers in °F are now automatically converted to °C.

myClim 1.0.5

• Metadata of a locality can now be loaded from a table using the mc_read_data() function.
• The parameter use_utc has been added to the following functions: mc_reshape_wide(), mc_reshape_long(), mc_plot_image(), mc_plot_line() and mc_plot_raster(). This parameter allows for the use of local time.

myClim 1.0.4

• Updated the print(myClim_data) function to display the metadata of the myClim object and the head of the table from mc_info().
• Enabled the use of the extraction operator [] to extract specific localities from the myClim object.

myClim 1.0.3

• Function mc_plot_raster() can plot bool type sensors, such as snow.

myClim 1.0.2

• Enhanced help texts.
• Added a check in mc_prep_calib_load() to verify if the type of calib_table$datetime is POSIXct.

myClim 1.0.12023-05-08

• Updated help texts to comply with CRAN rules.
• Restored options and par using the on.exit() function.
• Replaced print() with message() in the code.
• Utilized temporary directories in tests, examples, and vignettes.
• Some dontrun examples have been modified to run.
• Detection of the installed plotly package using the system.file() function.

myClim 1.0.0

• Improved the vignette.
• Added the ability to specify multiple TubeDB regions using the region parameter in the mc_read_tubedb() function, providing more flexibility in data retrieval.
• Automatically prepared the sensor_ids parameter in the mc_read_tubedb() function even if region is NULL.
• Fixed the issue with factors in the localities_table in the mc_read_data() function.
• Fixed the issue with factors in the states table in the sensor data list.
• Concluded beta testing.

myClim 0.3.1

• Deletion of duplicated items in function mc_prep_clean() is more effective.
• The parameter sensor_ids in function mc_read_tubedb() is prepared automatically if names in TubeDB are identical with names in myClim.
• Conversion of datetimes in function mc_read_tubedb() is fixed. The problem is in function rTubeDB::query_timeseries if the parameter datetimeFormat = "POSIXct" is used.
• The issue with loading data from TubeDB when the elevation is missing has been fixed.

myClim 0.3.0

• Behavior of mc_filter(data, localities="locality_abc", sensors="sensor1", reverse=TRUE) has changed. Sensor sensor1 is removed only from locality locality_abc. Other localities remain unchanged.
• Function mc_join() is fixed. Multiple sensors with the same height caused an error.