Julia implementation of the R pkg vegperiod by Robert Nuske: https://github.com/rnuske/vegperiod.
The vegetation period, or growing season, is the period of the year when the weather conditions are sufficient for plants to grow. This package provides methods to calculate climatological or thermal growing seasons solely based on daily mean temperatures and the day of the year (DOY). Because of their simplicity, they are commonly used in plant growth models and climate change impact assessments. Robert Nuske, R pkg vegperiod
Please refer to https://github.com/rnuske/vegperiod for further information about these methods.
This package could potentially be extended with additional methods for vegetation periods that include other drivers besides daily mean temperatures. Please contact us if you're interested in the development.
The package is registerd with the Julia Package Registry, hence installation is done in Julia with:
julia> import Pkg
julia> Pkg.add("VegetationPeriods")using VegetationPeriods
using Dates
dates = Date("2018-01-01"):Day(1):Date("2022-12-31")
Tavg =
30 * (0.3 .+ 1/2*cos.(dayofyear.(dates)/365 * 2π .- π)) .+
rand([-34.9 : 0.1 : 39.9;]/10, length(dates))
# using Plots; plot(dates, Tavg)
vegperiod(
dates,
Tavg,
Menzel("Picea abies (frueh)", est_prev = 2),
VonWilpert())
# 5×5 DataFrame
# Row │ year startdate startDOY enddate endDOY
# │ Int64 Date Int64 Date? Int64?
# ─────┼─────────────────────────────────────────────────
# 1 │ 2018 2018-04-24 114 2018-10-03 276
# 2 │ 2019 2019-04-24 114 2019-09-29 272
# 3 │ 2020 2020-04-25 116 2020-10-02 276
# 4 │ 2021 2021-04-25 115 2021-10-03 276
# 5 │ 2022 2022-04-25 115 2022-10-02 275
using RCall; R"library(vegperiod); data(goe)";
@rget goe
vegperiod(
goe.date,
goe.t,
Menzel("Picea abies (frueh)", est_prev = 2),
VonWilpert())
# 10×5 DataFrame
# Row │ year startdate startDOY enddate endDOY
# │ Int64 Date Int64 Date? Int64?
# ─────┼─────────────────────────────────────────────────
# 1 │ 2001 2001-04-28 118 2001-10-01 274
# 2 │ 2002 2002-05-07 127 2002-10-06 279
# 3 │ 2003 2003-05-05 125 2003-10-06 279
# 4 │ 2004 2004-04-25 116 2004-10-05 279
# 5 │ 2005 2005-05-04 124 2005-10-02 275
# 6 │ 2006 2006-05-06 126 2006-09-28 271
# 7 │ 2007 2007-05-04 124 2007-10-06 279
# 8 │ 2008 2008-05-04 125 2008-10-05 279
# 9 │ 2009 2009-04-25 115 2009-10-06 279
# 10 │ 2010 2010-04-26 116 2010-10-06 279Above example shows the use of the function vegperiod().
To get help for any of these check out the documentation (? followed by the function name) e.g. as below:
help?> vegperiod
search: vegperiod VegetationPeriods
Calculate start and end date of vegetation periods based on daily average air temperature
and the day of the year (DOY). The sum of day degrees within the vegetation period can be
included for convenience.
Common methods for determining the onset and end of thermal vegetation periods are provided,
for details see the documentation of each method. Popular choices with regard to forest
trees in Germany are Menzel and vonWilpert. Climate change impact studies at NW-FVA are
frequently conducted using Menzel with "Picea abies (frueh)" and NuskeAlbert for all tree
species; with tree species specifics accounted for in subsequent statistical models.
Available methods can be queried with subtypes(VegetationStartMethod) and
subtypes(VegetationEndMethod)
Arguments:
• dates is a vector of calendar dates (object of class Date). Must contain entire
years if est_prev > 0 else the first year may comprise only November and December.
• Tavg is a vector of daily average air temperatures in degree Celsius. Same length
as dates.
• start_method is a VegetationStartMethod.
• end_method is a VegetationEndMethod.
• Tsum_out is a boolean. Return the sum of daily mean temperatures above Tsum_crit
within vegetation period, also known as growing day degrees.
• Tsum_crit threshold for sum of day degrees. Only daily mean temperatures above
Tsum_crit will be tallied. The default of 0 prevents negative daily temperatures
from reducing the sum. Climate change studies often use a threshold of 5.
• check_data is a boolean. Perform plausibility checks on the temperature data.
Plausible range is -35 to +40°C.
Returns: A DataFrame with year, date and DOY of start and end day of the vegetation period
for (each) year of the input data.
Or for the start method Menzel():
help?> Menzel
search: Menzel
Menzel(species; est_prev::Int = 0)
The start method Menzel implements the algorithm described in Menzel (1997). The method is
parameterized for 10 common tree species. It needs previous year's chill days.
The argument species is required and must be one of
• "Larix decidua",
• "Picea abies (frueh)",
• "Picea abies (spaet)",
• "Picea abies (noerdl.)",
• "Picea omorika",
• "Pinus sylvestris",
• "Betula pubescens",
• "Quercus robur",
• "Quercus petraea",
• "Fagus sylvatica".
The optional argument est_prev is the integer number of years that are used to compute the
average number of November and December chill days as a best guess to be used to start the
first year in case they are missing. Menzel requires the number of chill days of previous
November and December. You can provide them e.g. by starting your time series on November
1st (an set est_prev = 0). If the time series starts on January 1st, the previous chill days
are not available for the first year and hennce we can either drop the first year from the
output (happens with est_prev = 0) or estimate the number of chill days in November and
December previous to the first year in the time series (est_prev = n).
This Julia package was written by Fabian Bernhard. The R package was created by Robert Nuske.
Both are licensed under GPLv3.