dm_standardize: Standardize dendrometer series within seasonal years

In dendRoAnalyst: A Tool for Processing and Analyzing Dendrometer Data

Standardize dendrometer series within seasonal years

Description

Standardizes one or more dendrometer series within seasonal years so that multiple trees can be brought to a comparable scale while preserving their within-season temporal pattern.

Seasonal years are defined as:

• "NH": Northern Hemisphere year, from 01 Jan to 31 Dec

• "SH": Southern Hemisphere year, from 01 Jul to 30 Jun of the next year

• "CS": Custom season defined by CS_doys = c(doy1, doy2)

For season_type = "CS":

• if CS_doys[1] <= CS_doys[2], the season stays within one calendar year

• if CS_doys[1] > CS_doys[2], the season wraps across years

Standardization is applied separately for each dendrometer series and each seasonal year.

Usage

dm_standardize(
  df,
  season_type = c("NH", "SH", "CS"),
  CS_doys = NULL,
  method = c("center", "amplitude", "robust_amplitude", "minmax", "zscore",
    "robust_zscore", "percentile"),
  ref_type = c("first_value", "first_n_days", "ref_window"),
  ref_n_days = 7,
  ref_doys = NULL,
  q_low = 0.05,
  q_high = 0.95
)

Arguments

df	A data frame whose first column contains date-time (yyyy-mm-dd HH:MM:SS, POSIXct, or Date) and all remaining columns are dendrometer series.
season_type	One of "NH", "SH", or "CS".
CS_doys	Optional numeric vector of length 2 defining the start and end DOY for season_type = "CS".
method	Standardization method. One of: "center": subtract seasonal reference value "amplitude": subtract reference and divide by seasonal range "robust_amplitude": subtract reference and divide by Q_high - Q_low "minmax": rescale to (x - min)/(max - min) "zscore": seasonal z-score "robust_zscore": robust seasonal z-score using median and MAD "percentile": convert seasonal values to percentiles in [0,1]
ref_type	Reference-value definition for methods that need a reference ("center", "amplitude", "robust_amplitude"). One of: "first_value": first non-missing value in the seasonal year "first_n_days": mean of the first ref_n_days unique days "ref_window": mean of values within ref_doys
ref_n_days	Number of initial days used when ref_type = "first_n_days".
ref_doys	Optional numeric vector of length 2 defining a DOY reference window when ref_type = "ref_window".
q_low	Lower quantile used by method = "robust_amplitude".
q_high	Upper quantile used by method = "robust_amplitude".

Value

A list of class "dm_standardized" containing:

• data: wide data frame with columns TIME, season_year, in_season, and standardized dendrometer series

• parameters: tibble with one row per tree and seasonal year, summarizing the reference value and scaling denominator used

• metadata: method and seasonal-year settings

For season_type = "CS", observations outside the custom season are retained in data, but their standardized values are set to NA and in_season = FALSE.

Examples

data(gf_nepa17)

# Northern Hemisphere seasonal-year standardization
out_nh <- dm_standardize(
  df = gf_nepa17,
  season_type = "NH",
  method = "robust_amplitude"
)

# Southern Hemisphere seasonal-year standardization
out_sh <- dm_standardize(
  df = gf_nepa17,
  season_type = "SH",
  method = "center"
)

# Custom season within one year
out_cs1 <- dm_standardize(
  df = gf_nepa17,
  season_type = "CS",
  CS_doys = c(100, 280),
  method = "robust_amplitude"
)

# Custom season wrapping across years
out_cs2 <- dm_standardize(
  df = gf_nepa17,
  season_type = "CS",
  CS_doys = c(250, 120),
  method = "percentile"
)

head(out_nh$data)
head(out_nh$parameters)

dendRoAnalyst documentation built on May 20, 2026, 5:07 p.m.