bioclim2 {climates}R Documentation

Bioclim - Bioclimatic Variables – simplified

Description

bioclim2 recreates the standard 19 bioclimatic variables (BIOCLIM), as does related command bioclim, that were orginally generated using ANUCLIM http://fennerschool.anu.edu.au/publications/software/anuclim.php or used by Worldclim http://www.worldclim.org/.

These measures are described below but include annual and quarterly summaries of temperature and precipitation.

NOTE: the key differences between this and bioclim is that:
1. this is much faster due to C implementation;
2. this can only use monthly data;
3. will only generate all 19 variables; and
4. can use file names rather than objects in R to save on memory (not all things need to be loaded into memory at once).

!!!ASSUMES no missing data!!!

Usage

bioclim2(tmin = NULL, tmax = NULL, prec = NULL, tmean = NULL,
  cov = FALSE, files.as.inputs = TRUE)

Arguments

tmin

a data.frame or matrix or filename of a csv or RData object having 12 columns representing monthly or weekly minimum temperature data; rows represent different locations.

tmax

a data.frame or matrix or filename as with tmin representing maximum temperature data.

prec

a data.frame or matrix or filename as with tmin representing precipitation data.

tmean

a data.frame or matrix or filename as with tmin representing mean temperature data.

cov

a boolean value where TRUE represents Temperature seasonality (4) is calculated as in ANUCLIM and FALSE is calclated as with Worldclim; see details for further information.

files.as.inputs

defines if the inputs are files.

Details

The variables created here are based primarily on BIOCLIM variables created by ANUCLIM http://fennerschool.anu.edu.au/publications/software/anuclim.php. Below is a description of the variables and how they are calculated from the ANUCLIM website, with Temperature Seasonality description modified for the different method Worldclim uses.

The descriptions below assume you are using a weekly time step. If you are using months, the monthly values rather than the weekly values will be used when calculating these parameters.

The quarterly parameters are not aligned to any calendar quarters. BIOCLIM's definition of a quarter is any 13 consecutive weeks, (or any consecutive 3 months if running with a monthly time step). For example, the driest quarter will be the 13 consecutive weeks that are drier than any other set of 13 consecutive weeks.

  1. Annual Mean Temperature
    The mean of all the weekly mean temperatures. Each weekly mean temperature is the mean of that week's maximum and minimum temperature.

  2. Mean Diurnal Range(Mean(period max-min))
    The mean of all the weekly diurnal temperature ranges. Each weekly diurnal range is the difference between that week's maximum and minimum temperature.

  3. Isothermality 2/7
    The mean diurnal range (parameter 2) divided by the Annual Temperature Range (parameter 7).

  4. Temperature Seasonality
    ANUCLIM (cov=TRUE) returns the temperature Coefficient of Variation (C of V) as the standard deviation of the weekly mean temperatures expressed as a percentage of the mean of those temperatures (i.e. the annual mean). For this calculation, the mean in degrees Kelvin is used. This avoids the possibility of having to divide by zero, but does mean that the values are usually quite small.
    Worldclim (cov=FALSE) returns the the standard deviation of the weekly mean temperatures.

  5. Max Temperature of Warmest Period
    The highest temperature of any weekly maximum temperature.

  6. Min Temperature of Coldest Period
    The lowest temperature of any weekly minimum temperature.

  7. Temperature Annual Range (5-6)
    The difference between the Max Temperature of Warmest Period and the Min Temperature of Coldest Period.

  8. Mean Temperature of Wettest Quarter
    The wettest quarter of the year is determined (to the nearest week), and the mean temperature of this period is calculated.

  9. Mean Temperature of Driest Quarter
    The driest quarter of the year is determined (to the nearest week), and the mean temperature of this period is calculated.

  10. Mean Temperature of Warmest Quarter
    The warmest quarter of the year is determined (to the nearest week), and the mean temperature of this period is calculated.

  11. Mean Temperature of Coldest Quarter
    The coldest quarter of the year is determined (to the nearest week), and the mean temperature of this period is calculated.

  12. Annual Precipitation
    The sum of all the monthly precipitation estimates.

  13. Precipitation of Wettest Period
    The precipitation of the wettest week or month, depending on the time step.

  14. Precipitation of Driest Period
    The precipitation of the driest week or month, depending on the time step.

  15. Precipitation Seasonality(C of V)
    The Coefficient of Variation (C of V) is the standard deviation of the weekly precipitation estimates expressed as a percentage of the mean of those estimates (i.e. the annual mean).

  16. Precipitation of Wettest Quarter
    The wettest quarter of the year is determined (to the nearest week), and the total precipitation over this period is calculated.

  17. Precipitation of Driest Quarter
    The driest quarter of the year is determined (to the nearest week), and the total precipitation over this period is calculated.

  18. Precipitation of Warmest Quarter
    The warmest quarter of the year is determined (to the nearest week), and the total precipitation over this period is calculated.

  19. Precipitation of Coldest Quarter
    The coldest quarter of the year is determined (to the nearest week), and the total precipitation over this period is calculated.

Value

a matrix with columns representing variables requested and the number of rows(and order of them) the same as the input tmin, tmax, prec or tmean.

Author(s)

Jeremy VanDerWal jjvanderwal@gmail.com

Examples

## Not run: 
#need to fill in

## End(Not run)

[Package climates version 0.1-1.6 Index]