Weather coefficient creation for PoPS

Overview

weather coefficient converts raw weather data from Daymet to weather coefficients used in the PoPS model.

Parameters

Parameter - Meaning and/or (Options)

• start - First year that you want to have weather coefficients for
• end - Last year that you want to have weather coefficients for
• time_step - ("daily", "weekly", "monthly")
• directory - Local directory with Daymet files
• output_directory - Output directory you want the function to write the weather coefficient files to
• study_area - Use raster for predefined areas and states if you want your data for whole states ("states" or "raster")
• states_of_interest - only used if study_area = "states" (eg: "California")
• lethal_temperature - (YES or NO)
• lethal_month - (between "01" and "12")
• lethal_min - Does your specie experience mortality below a certain temperature ("YES" or "NO")
• lethal_temperature_value - The value that your species experiences mortality
• future_scenarios - Used to create best, average, adn worst case weather scenarios from the historical record. Set to yes if you are projecting into the future for prediction purposes. ('YES', 'NO')
• pest - The name of the pest or pathogen the weather coefficients are to be used for. Naming purposes only. (eg: "SOD")
• prcp_index - Does precipitation affect the survival and reproduction of your pest/pathogen ('YES' or 'NO')
• prcp_method - Method used to convert raw data to precipitation coefficients ('reclass' or 'polynomial')
• temp_index - Does temperature affect the survival and reproduction of your pest/pathogen ('YES' or 'NO')
• temp_method - Method used to convert raw data to temperature coefficients ('reclass' or 'polynomial')
• temp_matrix - Matrix used to reclassify temperatures only used if temp_method = 'reclass'
• prcp_matrix - Matrix used to reclassify temperatures only used if temp_method = 'reclass'

## Example prcp_matrix creation, also works for temp_matrix. matrix must to nx3 col1 = from, col2 = to, col3 = reclass value
prcp_thresh = 2.5
prcp_mat <- c(0, prcp_thresh, 0,  
              prcp_thresh, Inf, 1)
prcp_matrix <- matrix(prcp_mat, ncol=3, byrow=TRUE)
     [,1] [,2] [,3]
[1,]  0.0  2.5    0
[2,]  2.5  Inf    1

## Example of polynomial , works for both temp and prcp polynomials. 
temp_a0 = -0.066
temp_a1 = 0.056
temp_a2 = -0.0036
temp_a3 = -0.0003
temp_x1mod = 0
temp_x2mod = -15
temp_x3mod = -15
temp_thresh = 0
temp = seq(0,30, 1)
temp_coeff = temp_a0 + temp_a1*(temp + temp_x1mod) + temp_a2*((temp + temp_x2mod)^2) + temp_a3*((temp + temp_x3mod)^3)
plot(temp, temp_coeff)

• prcp_a0 - only used if prcp_method = 'polynomial'

• prcp_a1 - only used if prcp_method = 'polynomial'

• prcp_a2 - only used if prcp_method = 'polynomial'

• prcp_a3 - only used if prcp_method = 'polynomial'

• prcp_x1mod - only used if prcp_method = 'polynomial'

• prcp_x2mod - only used if prcp_method = 'polynomial'

• prcp_x3mod - only used if prcp_method = 'polynomial'

• temp_a0 - only used if temp_method = 'polynomial'

• temp_a1 - only used if temp_method = 'polynomial'

• temp_a2 - only used if temp_method = 'polynomial'

• temp_a3 - only used if temp_method = 'polynomial'

• temp_x1mod - only used if temp_method = 'polynomial'

• temp_x2mod - only used if temp_method = 'polynomial'

• temp_x3mod - only used if temp_method = 'polynomial'

Authors

• Chris Jones
• Devon Gaydos (Oregon_test)

License

Permission to use, copy, modify, and distribute this software and its documentation under the terms of the GNU General Public License is hereby granted. No representations are made about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. See the GNU General Public License for more details.