Man pages for dendRoAnalyst
A Tool for Processing and Analyzing Dendrometer Data
| clim.twd | Calculate relative dendrometer change during adverse climate... |
| clim.twd.stats | Calculate tree-, species-, or site-level statistics from... |
| clim.twd.test | Statistical testing for clim.twd output |
| daily.data | Daily statistics of dendrometer data |
| dendro.resample | Resampling temporal resolution of dendrometer and climate... |
| dendro.truncate | Truncation of dendrometer data |
| dm_add_climate | Add climate information to dendrometer outputs |
| dm_daily_clim | Daily climate summaries for dendrometer analyses |
| dm.detrend.fit | Detrend and standardize dendrometer series from growth-fit... |
| dmea_apply_fun | Apply an aggregation function |
| dmea_extract_from_anchors | Extract climate values around anchor times |
| dmea_filter_time_table | Filter a table by calendar year and day-of-year |
| dmea_parse_time | Parse date-time values for SEA |
| dmea_prepare_climate | Prepare climate data for superposed epoch analysis |
| dmea_sample_anchor_one | Sample one null anchor time |
| dmea_stat_fun | Composite statistic helper |
| dmea_step_seconds | Convert SEA step size to seconds |
| dmea_time_filter_index | Filter timestamps by calendar year and day-of-year |
| dmea_unit_string | Create a lubridate period string |
| dm_epoch_extract | Build an epoch table around event times |
| dm_epoch_test | Test superposed epoch composites against a null distribution |
| dm_event_climate | Extract climate at and before phase events |
| dm_event_climate_summary | Summarize event-based climate results |
| dm_event_climate_test | Test differences in event-based climate between groups |
| dm_event_times | Extract event times from phase.zg() or phase.sc() output |
| dm.fit.gompertz | Fitting gompertz function on annual dendrometer data |
| dmgf_add_anchor_points | Add zero-growth anchor points |
| dmgf_build_season_table | Build vegetation-season table |
| dmgf_cummax_na | Cumulative maximum while preserving missing values |
| dmgfd_add_anchor_points | Add zero-growth anchor point |
| dmgfd_add_overall_rate_timing | Add overall rate-based timing |
| dmgfd_add_overall_timing | Add overall cumulative-growth timing |
| dmgfd_build_season_table | Build vegetation-season table |
| dmgfd_cummax_na | Cumulative maximum while preserving missing values |
| dmgfd_detect_two_pulse_pattern | Detect two-pulse pattern from fitted growth rate |
| dmgfd_doy_to_date | Convert year and day-of-year to Date |
| dmgfd_empty_model_params | Empty parameter template for double growth fitting |
| dmgfd_first_non_na | Return first non-missing value |
| dmgfd_fit_model_double_gompertz | Fit double-Gompertz model |
| dmgfd_fit_model_double_richards | Fit double-Richards model |
| dmgfd_fit_model_single_gompertz | Fit single-Gompertz fallback model |
| dmgfd_fit_model_single_richards | Fit single-Richards fallback model |
| dmgfd_fit_one_curve | Fit one double growth curve |
| dmgfd_fit_single_fallback | Fit single-curve fallback |
| dmgfd_growth_rate | Calculate non-negative fitted growth rate |
| dmgfd_guess_two_pulses | Guess two pulse locations from growth increments |
| dmgfd_infer_double_gompertz_starts | Infer double-Gompertz starting values |
| dmgfd_infer_double_richards_starts | Infer double-Richards starting values |
| dmgfd_infer_gompertz_starts | Infer single Gompertz starting values |
| dmgfd_infer_logistic_starts | Infer logistic/Richards starting values |
| dmgfd_is_scalar_finite | Check whether a value is a finite numeric scalar |
| dmgfd_local_maxima | Identify local maxima |
| dmgf_doy_to_date | Convert year and day-of-year to Date |
| dmgfd_pulse_window_from_rate | Estimate pulse window from fitted growth rate |
| dmgfd_validate_inputs | Validate inputs for double dendrometer growth fitting |
| dmgf_empty_model_params | Empty model-parameter template |
| dmgf_first_non_na | Return the first non-missing value |
| dmgf_fit_model | Dispatch growth-curve model fitting |
| dmgf_fit_model_gam | Fit GAM growth curve |
| dmgf_fit_model_gompertz | Fit Gompertz growth curve |
| dmgf_fit_model_loess | Fit loess growth curve |
| dmgf_fit_model_logistic | Fit logistic growth curve |
| dmgf_fit_model_richards | Fit Richards growth curve |
| dmgf_fit_model_spline | Fit smoothing-spline growth curve |
| dmgf_fit_one_curve | Fit one growth curve |
| dmgf_growth_rate | Calculate non-negative fitted growth rate |
| dmgf_infer_gompertz_starts | Infer Gompertz starting values |
| dmgf_infer_logistic_starts | Infer logistic starting values |
| dmgf_is_scalar_finite | Check whether a value is a finite numeric scalar |
| dmgf_rate_window | Estimate active-growth window from growth rate |
| dmgf_unique_prediction_curve | Reduce prediction curve to unique x values |
| dmgf_validate_fit_growth_inputs | Validate inputs for dendrometer growth fitting |
| dmgp_prepare_boundary_marks | Prepare timing boundary markers for fitted-curve plots |
| dmgp_prepare_curve_groups | Prepare curve grouping and faceting information |
| dmgp_prepare_timing_plot_data | Prepare timing-summary plot data |
| dmgp_resolve_facet_scales | Resolve facet scales for curve plots |
| dmgp_resolve_timing_facet_scales | Resolve facet scales for timing plots |
| dmgp_resolve_x_axis | Resolve x-axis mode for dendrometer growth-fit plots |
| dmgp_tidy_fit_data | Convert growth-fit object to tidy plotting data |
| dm.growth.evaluate | Compare dendrometer growth-fitting methods using fit... |
| dm.growth.fit | Fit dendrometer growth curves by vegetation season |
| dm.growth.fit.double | Fit bimodal dendrometer growth curves by vegetation season |
| dm_join_daily_clim | Join daily climate summaries to daily dendrometer statistics |
| dm_join_phase_clim | Join climate summaries to dendrometer phase windows |
| dm_join_subdaily_clim | Join subdaily climate features to point-level dendrometer... |
| dm.na.interpolation | Detection and interpolation of missing values in dendrometer... |
| dm_plot_climate | Plot climate attached to dendrometer outputs |
| dm_plot_climate_compare | Compare multiple climate variables attached to dendrometer... |
| dm_standardize | Standardize dendrometer series within seasonal years |
| dm_subdaily_clim | Subdaily climate features for dendrometer analyses |
| dm_wavelet | Wavelet analysis of dendrometer series |
| dm_wavelet_coherence | Wavelet coherence between dendrometer and climate series |
| dm_wavelet_reconstruct | Reconstruct or remove selected cycle components from a... |
| gf_nepa17 | Dendrometer data of Kathmandu for 2017 with gap filled |
| i.jump.locator | Removing artefacts due to manual adjustments of dendrometers... |
| jump.locator | Removing artefacts due to manual adjustments of dendrometers... |
| ktm_clim_hourly | Hourly climate data for Kathmandu derived from ERA5-Land |
| ktm_rain17 | Daily rainfall data of Kathmandu for 2017. |
| mean_detrended.dm | Calculate the mean detrended dendrometer series |
| mov.cor.dm | Running correlation between dendrometer data and climate |
| nepa | Dendrometer data from Kathmandu |
| nepa17 | Dendrometer data of Kathmandu for 2017 |
| nepa2 | Dendrometer data from Kathmandu version 2 |
| network.interpolation | Interpolate missing dendrometer values using a site network |
| phase.sc | Application of the stem-cycle approach to classify... |
| phase.zg | Apply the Zero-Growth (ZG) approach to segment dendrometer... |
| plot.clim_twd_stats | Plot method for clim.twd.stats output |
| plot.clim_twd_test | Plot method for clim.twd.test output |
| plot.daily_output | Plot method for daily dendrometer statistics |
| plot.daily_output_clim | Plot climate-augmented daily dendrometer output |
| plot_dm_assessment | Plot interpolation assessment metrics |
| plot.dm_detrended | Plot detrended dendrometer series |
| plot.dm_epoch | Plot a dm_epoch object |
| plot_dm_gaps | Plot detected gaps in dendrometer data |
| plot.dm_growth_evaluation | Plot growth-fitting evaluation statistics |
| plot.dm_growth_fit | Plot dendrometer growth-fit results |
| plot_dm_interpolation | Plot original and interpolated dendrometer series |
| plot.dm_na_interpolation | Plot method for dendrometer NA interpolation results |
| plot.dm_standardized | Plot method for standardized dendrometer output |
| plot.dm_wavelet | Plot method for wavelet analysis output |
| plot.dm_wavelet_coherence | Plot method for dm_wavelet_coherence objects |
| plot.dm_wavelet_reconstruct | Plot method for dm_wavelet_reconstruct objects |
| plot_event_climate_box | Plot event-based climate distributions |
| plot_event_climate_relation | Plot event-based climate-response relationships |
| plot.mean_dm_detrended | Plot mean detrended dendrometer series |
| plot_mov.cor | Backward-compatible wrapper for plotting moving correlation |
| plot.mov_cor_dm | Plot method for moving dendrometer-climate correlation |
| plot.network_interpolation | Plot method for network interpolation output |
| plot.SC_output | Plot method for stem-cycle output |
| plot.SC_output_clim | Plot climate-augmented stem-cycle output |
| plot.summary_mov_cor_dm | Plot method for summaries of moving dendrometer-climate... |
| plot.ZG_output | Plot method for zero-growth output |
| plot.ZG_output_clim | Plot climate-augmented zero-growth output |
| print.dm_growth_fit | Print a dm_growth_fit object |
| print.mov_cor_dm | Print method for running dendrometer-climate correlation... |
| print.summary.clim_twd_stats | Print summary of clim.twd.stats output |
| print.summary.clim_twd_test | Print summary of clim.twd.test output |
| print.summary.dm_epoch | Print summary of a dm_epoch object |
| print.summary.dm_growth_fit | Print a summary.dm_growth_fit object |
| print.summary.dm_wavelet_reconstruct | Print method for summary.dm_wavelet_reconstruct |
| print.summary_mov_cor_dm | Print method for summaries of running dendrometer-climate... |
| read.climate | Read and standardize climate data for dendrometer analyses |
| read.dendrometer | Reading dendrometer data |
| reso_dm | Detect Temporal Resolution and Irregularities in Time Series |
| smooth_dm | Smoothing of Dendrometer Time Series |
| summary.clim_twd_stats | Summarize clim.twd.stats output |
| summary.clim_twd_test | Summarize clim.twd.test output |
| summary.dm_epoch | Summarize a dm_epoch object |
| summary.dm_growth_fit | Summarize a dm_growth_fit object |
| summary.dm_wavelet | Summarize a dm_wavelet object |
| summary.dm_wavelet_reconstruct | Summarize a dm_wavelet_reconstruct object |
| summary.mov_cor_dm | Summary method for running dendrometer-climate correlation... |
| twd.maxima | Locating the maxima of TWD periods |
