{
  "_id": "6a1ed461b401979e7340e183",
  "Package": "dendRoAnalyst",
  "Type": "Package",
  "Date": "2026-05-18",
  "Title": "A Tool for Processing and Analyzing Dendrometer Data",
  "Version": "0.1.6",
  "Authors@R": "c(\nperson(\"Sugam\", \"Aryal\", email = \"sugam.aryal@fau.de\", role = c(\"aut\", \"cre\", \"dtc\")),\nperson(\"Martin\", \"Häusser\", email = \"martin.haeusser@fau.de\", role = \"aut\"),\nperson(\"Jussi\", \"Grießinger\", email = \"jussi.griessinger@fau.de\", role = \"aut\"),\nperson(\"Ze-Xin\", \"Fan\", email = \"fanzexin@xtbg.org.cn\", role = \"aut\"),\nperson(\"Achim\", \"Bräuning\", email = \"achim.braeuning@fau.de\", role = c(\"aut\", \"dgs\")))",
  "Maintainer": "Sugam Aryal <sugam.aryal@fau.de>",
  "Description": "There are various functions for managing and cleaning data\nbefore the application of different approaches. This includes\nidentifying and erasing sudden jumps in dendrometer data not\nrelated to environmental change, identifying the time gaps of\nrecordings, and changing the temporal resolution of data to\ndifferent frequencies. Furthermore, the package calculates\ndaily statistics of dendrometer data, including the daily\namplitude of tree growth. Various approaches can be applied to\nseparate radial growth from daily cyclic shrinkage and\nexpansion due to uptake and loss of stem water. In addition, it\nidentifies periods of consecutive days with user-defined\nclimatic conditions in daily meteorological data, then check\nwhat trees are doing during that period.",
  "License": "GPL-3",
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    "User": "root"
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  "Author": "Sugam Aryal [aut, cre, dtc], Martin Häusser [aut], Jussi\nGrießinger [aut], Ze-Xin Fan [aut], Achim Bräuning [aut, dgs]",
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  "Repository": "https://cran.r-universe.dev",
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  "_published": "2026-06-02T13:02:25.137Z",
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  "_assets": [
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    "extra/citation.json",
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  "_exports": [
    "clim.twd",
    "clim.twd.stats",
    "clim.twd.test",
    "daily.data",
    "dendro.resample",
    "dendro.truncate",
    "dm_add_climate",
    "dm_daily_clim",
    "dm_epoch_extract",
    "dm_epoch_test",
    "dm_event_climate",
    "dm_event_climate_summary",
    "dm_event_climate_test",
    "dm_event_times",
    "dm_join_daily_clim",
    "dm_join_phase_clim",
    "dm_join_subdaily_clim",
    "dm_plot_climate",
    "dm_plot_climate_compare",
    "dm_standardize",
    "dm_subdaily_clim",
    "dm_wavelet",
    "dm_wavelet_coherence",
    "dm_wavelet_reconstruct",
    "dm.detrend.fit",
    "dm.fit.gompertz",
    "dm.growth.evaluate",
    "dm.growth.fit",
    "dm.growth.fit.double",
    "dm.na.interpolation",
    "i.jump.locator",
    "jump.locator",
    "mean_detrended.dm",
    "mov.cor.dm",
    "network.interpolation",
    "phase.sc",
    "phase.zg",
    "plot_dm_assessment",
    "plot_dm_gaps",
    "plot_dm_interpolation",
    "plot_event_climate_box",
    "plot_event_climate_relation",
    "plot_mov.cor",
    "read.climate",
    "read.dendrometer",
    "reso_dm",
    "smooth_dm",
    "twd.maxima"
  ],
  "_datasets": [
    {
      "name": "gf_nepa17",
      "title": "Dendrometer data of Kathmandu for 2017 with gap filled",
      "object": "gf_nepa17",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Time",
        "T2",
        "T3"
      ],
      "rows": 8760,
      "table": true,
      "tojson": true
    },
    {
      "name": "ktm_clim_hourly",
      "title": "Hourly climate data for Kathmandu derived from ERA5-Land",
      "object": "ktm_clim_hourly",
      "class": [
        "dm_clim",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "TIME",
        "temp",
        "prec",
        "VPD",
        "RH"
      ],
      "rows": 17520,
      "table": true,
      "tojson": true
    },
    {
      "name": "ktm_rain17",
      "title": "Daily rainfall data of Kathmandu for 2017.",
      "object": "ktm_rain17",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "TIME",
        "rainfall"
      ],
      "rows": 365,
      "table": true,
      "tojson": true
    },
    {
      "name": "nepa",
      "title": "Dendrometer data from Kathmandu",
      "object": "nepa",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Time",
        "T2",
        "T3"
      ],
      "rows": 14543,
      "table": true,
      "tojson": true
    },
    {
      "name": "nepa17",
      "title": "Dendrometer data of Kathmandu for 2017",
      "object": "nepa17",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Time",
        "T2",
        "T3"
      ],
      "rows": 8753,
      "table": true,
      "tojson": true
    },
    {
      "name": "nepa2",
      "title": "Dendrometer data from Kathmandu version 2",
      "object": "nepa2",
      "class": [
        "data.frame"
      ],
      "fields": [
        "year",
        "month",
        "day",
        "hours",
        "minutes",
        "seconds",
        "T2",
        "T3"
      ],
      "rows": 14543,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "clim.twd",
      "title": "Calculate relative dendrometer change during adverse climate periods and the following normal phase",
      "topics": [
        "clim.twd"
      ]
    },
    {
      "page": "clim.twd.stats",
      "title": "Calculate tree-, species-, or site-level statistics from clim.twd output",
      "topics": [
        "clim.twd.stats"
      ]
    },
    {
      "page": "clim.twd.test",
      "title": "Statistical testing for clim.twd output",
      "topics": [
        "clim.twd.test"
      ]
    },
    {
      "page": "daily.data",
      "title": "Daily statistics of dendrometer data",
      "topics": [
        "daily.data"
      ]
    },
    {
      "page": "dendro.resample",
      "title": "Resampling temporal resolution of dendrometer and climate data",
      "topics": [
        "dendro.resample"
      ]
    },
    {
      "page": "dendro.truncate",
      "title": "Truncation of dendrometer data",
      "topics": [
        "dendro.truncate"
      ]
    },
    {
      "page": "dm_add_climate",
      "title": "Add climate information to dendrometer outputs",
      "topics": [
        "dm_add_climate"
      ]
    },
    {
      "page": "dm_daily_clim",
      "title": "Daily climate summaries for dendrometer analyses",
      "topics": [
        "dm_daily_clim"
      ]
    },
    {
      "page": "dm_epoch_extract",
      "title": "Build an epoch table around event times",
      "topics": [
        "dm_epoch_extract"
      ]
    },
    {
      "page": "dm_epoch_test",
      "title": "Test superposed epoch composites against a null distribution",
      "topics": [
        "dm_epoch_test"
      ]
    },
    {
      "page": "dm_event_climate",
      "title": "Extract climate at and before phase events",
      "topics": [
        "dm_event_climate"
      ]
    },
    {
      "page": "dm_event_climate_summary",
      "title": "Summarize event-based climate results",
      "topics": [
        "dm_event_climate_summary"
      ]
    },
    {
      "page": "dm_event_climate_test",
      "title": "Test differences in event-based climate between groups",
      "topics": [
        "dm_event_climate_test"
      ]
    },
    {
      "page": "dm_event_times",
      "title": "Extract event times from phase.zg() or phase.sc() output",
      "topics": [
        "dm_event_times"
      ]
    },
    {
      "page": "dm_join_daily_clim",
      "title": "Join daily climate summaries to daily dendrometer statistics",
      "topics": [
        "dm_join_daily_clim"
      ]
    },
    {
      "page": "dm_join_phase_clim",
      "title": "Join climate summaries to dendrometer phase windows",
      "topics": [
        "dm_join_phase_clim"
      ]
    },
    {
      "page": "dm_join_subdaily_clim",
      "title": "Join subdaily climate features to point-level dendrometer output",
      "topics": [
        "dm_join_subdaily_clim"
      ]
    },
    {
      "page": "dm_plot_climate",
      "title": "Plot climate attached to dendrometer outputs",
      "topics": [
        "dm_plot_climate"
      ]
    },
    {
      "page": "dm_plot_climate_compare",
      "title": "Compare multiple climate variables attached to dendrometer outputs",
      "topics": [
        "dm_plot_climate_compare"
      ]
    },
    {
      "page": "dm_standardize",
      "title": "Standardize dendrometer series within seasonal years",
      "topics": [
        "dm_standardize"
      ]
    },
    {
      "page": "dm_subdaily_clim",
      "title": "Subdaily climate features for dendrometer analyses",
      "topics": [
        "dm_subdaily_clim"
      ]
    },
    {
      "page": "dm_wavelet",
      "title": "Wavelet analysis of dendrometer series",
      "topics": [
        "dm_wavelet"
      ]
    },
    {
      "page": "dm_wavelet_coherence",
      "title": "Wavelet coherence between dendrometer and climate series",
      "topics": [
        "dm_wavelet_coherence"
      ]
    },
    {
      "page": "dm_wavelet_reconstruct",
      "title": "Reconstruct or remove selected cycle components from a dm_wavelet object",
      "topics": [
        "dm_wavelet_reconstruct"
      ]
    },
    {
      "page": "dm.detrend.fit",
      "title": "Detrend and standardize dendrometer series from growth-fit residuals",
      "topics": [
        "dm.detrend.fit"
      ]
    },
    {
      "page": "dm.fit.gompertz",
      "title": "Fitting gompertz function on annual dendrometer data",
      "topics": [
        "dm.fit.gompertz"
      ]
    },
    {
      "page": "dm.growth.evaluate",
      "title": "Compare dendrometer growth-fitting methods using fit statistics",
      "topics": [
        "dm.growth.evaluate"
      ]
    },
    {
      "page": "dm.growth.fit",
      "title": "Fit dendrometer growth curves by vegetation season",
      "topics": [
        "dm.growth.fit"
      ]
    },
    {
      "page": "dm.growth.fit.double",
      "title": "Fit bimodal dendrometer growth curves by vegetation season",
      "topics": [
        "dm.growth.fit.double"
      ]
    },
    {
      "page": "dm.na.interpolation",
      "title": "Detection and interpolation of missing values in dendrometer data",
      "topics": [
        "dm.na.interpolation"
      ]
    },
    {
      "page": "gf_nepa17",
      "title": "Dendrometer data of Kathmandu for 2017 with gap filled",
      "topics": [
        "gf_nepa17"
      ]
    },
    {
      "page": "i.jump.locator",
      "title": "Removing artefacts due to manual adjustments of dendrometers interactively",
      "topics": [
        "i.jump.locator"
      ]
    },
    {
      "page": "jump.locator",
      "title": "Removing artefacts due to manual adjustments of dendrometers automatically for more than one dendrometer",
      "topics": [
        "jump.locator"
      ]
    },
    {
      "page": "ktm_clim_hourly",
      "title": "Hourly climate data for Kathmandu derived from ERA5-Land",
      "topics": [
        "ktm_clim_hourly"
      ]
    },
    {
      "page": "ktm_rain17",
      "title": "Daily rainfall data of Kathmandu for 2017.",
      "topics": [
        "ktm_rain17"
      ]
    },
    {
      "page": "mean_detrended.dm",
      "title": "Calculate the mean detrended dendrometer series",
      "topics": [
        "mean_detrended.dm"
      ]
    },
    {
      "page": "mov.cor.dm",
      "title": "Running correlation between dendrometer data and climate",
      "topics": [
        "mov.cor.dm"
      ]
    },
    {
      "page": "nepa",
      "title": "Dendrometer data from Kathmandu",
      "topics": [
        "nepa"
      ]
    },
    {
      "page": "nepa17",
      "title": "Dendrometer data of Kathmandu for 2017",
      "topics": [
        "nepa17"
      ]
    },
    {
      "page": "nepa2",
      "title": "Dendrometer data from Kathmandu version 2",
      "topics": [
        "nepa2"
      ]
    },
    {
      "page": "network.interpolation",
      "title": "Interpolate missing dendrometer values using a site network",
      "topics": [
        "network.interpolation"
      ]
    },
    {
      "page": "phase.sc",
      "title": "Application of the stem-cycle approach to classify dendrometer phases",
      "topics": [
        "phase.sc"
      ]
    },
    {
      "page": "phase.zg",
      "title": "Apply the Zero-Growth (ZG) approach to segment dendrometer data into TWD/GRO phases",
      "topics": [
        "phase.zg"
      ]
    },
    {
      "page": "plot_dm_assessment",
      "title": "Plot interpolation assessment metrics",
      "topics": [
        "plot_dm_assessment"
      ]
    },
    {
      "page": "plot_dm_gaps",
      "title": "Plot detected gaps in dendrometer data",
      "topics": [
        "plot_dm_gaps"
      ]
    },
    {
      "page": "plot_dm_interpolation",
      "title": "Plot original and interpolated dendrometer series",
      "topics": [
        "plot_dm_interpolation"
      ]
    },
    {
      "page": "plot_event_climate_box",
      "title": "Plot event-based climate distributions",
      "topics": [
        "plot_event_climate_box"
      ]
    },
    {
      "page": "plot_event_climate_relation",
      "title": "Plot event-based climate-response relationships",
      "topics": [
        "plot_event_climate_relation"
      ]
    },
    {
      "page": "plot_mov.cor",
      "title": "Backward-compatible wrapper for plotting moving correlation",
      "topics": [
        "plot_mov.cor"
      ]
    },
    {
      "page": "plot.clim_twd_stats",
      "title": "Plot method for clim.twd.stats output",
      "topics": [
        "plot.clim_twd_stats"
      ]
    },
    {
      "page": "plot.clim_twd_test",
      "title": "Plot method for clim.twd.test output",
      "topics": [
        "plot.clim_twd_test"
      ]
    },
    {
      "page": "plot.daily_output",
      "title": "Plot method for daily dendrometer statistics",
      "topics": [
        "plot.daily_output"
      ]
    },
    {
      "page": "plot.daily_output_clim",
      "title": "Plot climate-augmented daily dendrometer output",
      "topics": [
        "plot.daily_output_clim"
      ]
    },
    {
      "page": "plot.dm_detrended",
      "title": "Plot detrended dendrometer series",
      "topics": [
        "plot.dm_detrended"
      ]
    },
    {
      "page": "plot.dm_epoch",
      "title": "Plot a dm_epoch object",
      "topics": [
        "plot.dm_epoch"
      ]
    },
    {
      "page": "plot.dm_growth_evaluation",
      "title": "Plot growth-fitting evaluation statistics",
      "topics": [
        "plot.dm_growth_evaluation"
      ]
    },
    {
      "page": "plot.dm_growth_fit",
      "title": "Plot dendrometer growth-fit results",
      "topics": [
        "plot.dm_growth_fit"
      ]
    },
    {
      "page": "plot.dm_na_interpolation",
      "title": "Plot method for dendrometer NA interpolation results",
      "topics": [
        "plot.dm_na_interpolation"
      ]
    },
    {
      "page": "plot.dm_standardized",
      "title": "Plot method for standardized dendrometer output",
      "topics": [
        "plot.dm_standardized"
      ]
    },
    {
      "page": "plot.dm_wavelet",
      "title": "Plot method for wavelet analysis output",
      "topics": [
        "plot.dm_wavelet"
      ]
    },
    {
      "page": "plot.dm_wavelet_coherence",
      "title": "Plot method for dm_wavelet_coherence objects",
      "topics": [
        "plot.dm_wavelet_coherence"
      ]
    },
    {
      "page": "plot.dm_wavelet_reconstruct",
      "title": "Plot method for dm_wavelet_reconstruct objects",
      "topics": [
        "plot.dm_wavelet_reconstruct"
      ]
    },
    {
      "page": "plot.mean_dm_detrended",
      "title": "Plot mean detrended dendrometer series",
      "topics": [
        "plot.mean_dm_detrended"
      ]
    },
    {
      "page": "plot.mov_cor_dm",
      "title": "Plot method for moving dendrometer-climate correlation",
      "topics": [
        "plot.mov_cor_dm"
      ]
    },
    {
      "page": "plot.network_interpolation",
      "title": "Plot method for network interpolation output",
      "topics": [
        "plot.network_interpolation"
      ]
    },
    {
      "page": "plot.SC_output",
      "title": "Plot method for stem-cycle output",
      "topics": [
        "plot.SC_output"
      ]
    },
    {
      "page": "plot.SC_output_clim",
      "title": "Plot climate-augmented stem-cycle output",
      "topics": [
        "plot.SC_output_clim"
      ]
    },
    {
      "page": "plot.summary_mov_cor_dm",
      "title": "Plot method for summaries of moving dendrometer-climate correlation",
      "topics": [
        "plot.summary_mov_cor_dm"
      ]
    },
    {
      "page": "plot.ZG_output",
      "title": "Plot method for zero-growth output",
      "topics": [
        "plot.ZG_output"
      ]
    },
    {
      "page": "plot.ZG_output_clim",
      "title": "Plot climate-augmented zero-growth output",
      "topics": [
        "plot.ZG_output_clim"
      ]
    },
    {
      "page": "print.dm_growth_fit",
      "title": "Print a dm_growth_fit object",
      "topics": [
        "print.dm_growth_fit"
      ]
    },
    {
      "page": "print.mov_cor_dm",
      "title": "Print method for running dendrometer-climate correlation objects",
      "topics": [
        "print.mov_cor_dm"
      ]
    },
    {
      "page": "print.summary_mov_cor_dm",
      "title": "Print method for summaries of running dendrometer-climate correlation objects",
      "topics": [
        "print.summary_mov_cor_dm"
      ]
    },
    {
      "page": "print.summary.clim_twd_stats",
      "title": "Print summary of clim.twd.stats output",
      "topics": [
        "print.summary.clim_twd_stats"
      ]
    },
    {
      "page": "print.summary.clim_twd_test",
      "title": "Print summary of clim.twd.test output",
      "topics": [
        "print.summary.clim_twd_test"
      ]
    },
    {
      "page": "print.summary.dm_epoch",
      "title": "Print summary of a dm_epoch object",
      "topics": [
        "print.summary.dm_epoch"
      ]
    },
    {
      "page": "print.summary.dm_growth_fit",
      "title": "Print a summary.dm_growth_fit object",
      "topics": [
        "print.summary.dm_growth_fit"
      ]
    },
    {
      "page": "print.summary.dm_wavelet_reconstruct",
      "title": "Print method for summary.dm_wavelet_reconstruct",
      "topics": [
        "print.summary.dm_wavelet_reconstruct"
      ]
    },
    {
      "page": "read.climate",
      "title": "Read and standardize climate data for dendrometer analyses",
      "topics": [
        "read.climate"
      ]
    },
    {
      "page": "read.dendrometer",
      "title": "Reading dendrometer data",
      "topics": [
        "read.dendrometer"
      ]
    },
    {
      "page": "reso_dm",
      "title": "Detect Temporal Resolution and Irregularities in Time Series",
      "topics": [
        "reso_dm"
      ]
    },
    {
      "page": "smooth_dm",
      "title": "Smoothing of Dendrometer Time Series",
      "topics": [
        "smooth_dm"
      ]
    },
    {
      "page": "summary.clim_twd_stats",
      "title": "Summarize clim.twd.stats output",
      "topics": [
        "summary.clim_twd_stats"
      ]
    },
    {
      "page": "summary.clim_twd_test",
      "title": "Summarize clim.twd.test output",
      "topics": [
        "summary.clim_twd_test"
      ]
    },
    {
      "page": "summary.dm_epoch",
      "title": "Summarize a dm_epoch object",
      "topics": [
        "summary.dm_epoch"
      ]
    },
    {
      "page": "summary.dm_growth_fit",
      "title": "Summarize a dm_growth_fit object",
      "topics": [
        "summary.dm_growth_fit"
      ]
    },
    {
      "page": "summary.dm_wavelet",
      "title": "Summarize a dm_wavelet object",
      "topics": [
        "summary.dm_wavelet"
      ]
    },
    {
      "page": "summary.dm_wavelet_reconstruct",
      "title": "Summarize a dm_wavelet_reconstruct object",
      "topics": [
        "summary.dm_wavelet_reconstruct"
      ]
    },
    {
      "page": "summary.mov_cor_dm",
      "title": "Summary method for running dendrometer-climate correlation objects",
      "topics": [
        "summary.mov_cor_dm"
      ]
    },
    {
      "page": "twd.maxima",
      "title": "Locating the maxima of TWD periods",
      "topics": [
        "twd.maxima"
      ]
    }
  ],
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  "_vignettes": [
    {
      "source": "dendRoAnalyst_vignettes.Rmd",
      "filename": "dendRoAnalyst_vignettes.html",
      "title": "dendRoAnalyst: end-to-end workflow and function tour",
      "author": "Package vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Example datasets",
        "1. Reading dendrometer and climate data",
        "read.dendrometer()",
        "read.climate()",
        "2. Looking for jumps or gaps in dendrometer data",
        "reso_dm()",
        "jump.locator() and i.jump.locator()",
        "dm.na.interpolation() and its plot methods",
        "3. Resample and truncate the dataset",
        "dendro.resample()",
        "dendro.truncate()",
        "4. Smoothing",
        "smooth_dm()",
        "5. Daily approach and daily climate functions",
        "daily.data() and plot.daily_output()",
        "dm_daily_clim() and dm_join_daily_clim()",
        "dm_add_climate() for daily outputs",
        "6. Stem-cycle approach and associated functions",
        "phase.sc() and plot.SC_output()",
        "dm_subdaily_clim(), dm_join_subdaily_clim(), dm_join_phase_clim(), and dm_add_climate()",
        "7. Zero-growth approach and associated functions",
        "phase.zg(), twd.maxima(), and plot.ZG_output()",
        "Climate joins and climate-phase plots",
        "8. Superposed epoch and associated functions",
        "dm_event_times(), dm_epoch_extract(), dm_epoch_test(), and method dispatch",
        "9. Event-based climate functions",
        "10. Growth fit and evaluation",
        "dm.fit.gompertz()",
        "dm.growth.fit(), plot.dm_growth_fit(), and print/summary methods",
        "dm.growth.fit.double() and dm.growth.evaluate()",
        "11. Detrending and associated functions",
        "dm_standardize() and plot.dm_standardized()",
        "12. Moving correlations and associated functions",
        "13. Harsh climate using clim.twd() and associated functions",
        "14. Network interpolation",
        "network.interpolation() and plot.network_interpolation()",
        "15. Wavelet analysis and associated functions",
        "dm_wavelet(), summary.dm_wavelet(), and plot.dm_wavelet()",
        "dm_wavelet_reconstruct() and its methods",
        "dm_wavelet_coherence() and plot.dm_wavelet_coherence()",
        "Closing note",
        "For suggestions, comments and questions please contact : sugam.aryal@fau.de"
      ],
      "created": "2020-07-03 18:00:07",
      "modified": "2026-05-20 16:02:00",
      "commits": 3
    },
    {
      "source": "NEWS.Rmd",
      "filename": "NEWS.html",
      "title": "News in latest version of 'dendRoAnalyst' package",
      "author": "Sugam Aryal",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What's new in dendRoAnalyst 0.1.6",
        "1. Core phase engines are now more modular",
        "2. Dedicated plotting methods for phase outputs",
        "3. Expanded data import, checking, and quality control",
        "4. New and upgraded gap-handling tools",
        "5. Data conditioning tools are broader and clearer",
        "6. Daily summaries are now easier to compute and inspect",
        "7. Climate joining helpers support both daily and subdaily workflows",
        "8. Event-based phase and climate tools were added",
        "9. Growth modelling is more flexible and easier to evaluate",
        "10. Detrending is now better linked to growth fitting",
        "11. Superposed epoch analysis now has a fuller toolkit",
        "12. Wavelet tools were added for time-frequency analysis",
        "13. Moving climate–growth correlations were upgraded",
        "14. Harsh-climate analysis is more complete",
        "15. Package design now emphasizes compute-first, plot-second workflows",
        "Heads-up on namespaces",
        "In short"
      ],
      "created": "2024-03-20 02:30:43",
      "modified": "2026-05-20 16:02:00",
      "commits": 2
    }
  ],
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  "_indexed": true,
  "_nocasepkg": "dendroanalyst",
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