Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 82:0c807f99a816 draft

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author greg
date Tue, 14 Nov 2017 15:00:21 -0500
parents 5729eb737082
children 8f5c05be4efe
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81:5729eb737082 82:0c807f99a816
30 temperature_data_frame <- read.csv(file=input_file, header=T, strip.white=TRUE, sep=",") 30 temperature_data_frame <- read.csv(file=input_file, header=T, strip.white=TRUE, sep=",")
31 if (dim(temperature_data_frame)[2] == 6) { 31 if (dim(temperature_data_frame)[2] == 6) {
32 # The input data has the following 6 columns: 32 # The input data has the following 6 columns:
33 # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX 33 # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
34 # Add a column containing the daylight length for each day. 34 # Add a column containing the daylight length for each day.
35 temperature_data_frame <- add_daylight_length(latitude, temperature_data_frame, num_rows) 35 temperature_data_frame <- add_daylight_length(temperature_data_frame, num_rows)
36 } 36 }
37 # Return the temperature_data_frame. 37 # Return the temperature_data_frame.
38 temperature_data_frame 38 temperature_data_frame
39 } 39 }
40 40
41 add_daylight_length = function(latitude, temperature_data_frame, num_days) { 41 add_daylight_length = function(temperature_data_frame, num_rows) {
42 # Return a vector of daylight length (photoperido profile) for 42 # Return a vector of daylight length (photoperido profile) for
43 # the number of days specified in the input temperature data 43 # the number of days specified in the input temperature data
44 # (from Forsythe 1995). 44 # (from Forsythe 1995).
45 p = 0.8333 45 p = 0.8333
46 latitude <- temperature_data_frame[1, 1]
46 daylight_length_vector <- NULL 47 daylight_length_vector <- NULL
47 for (i in 1:num_days) { 48 for (i in 1:num_rows) {
48 # Get the day of the year from the current row 49 # Get the day of the year from the current row
49 # of the temperature data for computation. 50 # of the temperature data for computation.
50 doy <- temperature_data_frame[i, 4] 51 doy <- temperature_data_frame[i, 4]
51 theta <- 0.2163108 + 2 * atan(0.9671396 * tan(0.00860 * (doy - 186))) 52 theta <- 0.2163108 + 2 * atan(0.9671396 * tan(0.00860 * (doy - 186)))
52 phi <- asin(0.39795 * cos(theta)) 53 phi <- asin(0.39795 * cos(theta))
199 return = mort.prob 200 return = mort.prob
200 return 201 return
201 } 202 }
202 203
203 temperature_data_frame <- parse_input_data(opt$input, opt$num_days) 204 temperature_data_frame <- parse_input_data(opt$input, opt$num_days)
204 print(temperature_data_frame)
205 latitude <- temperature_data_frame[1, 1] 205 latitude <- temperature_data_frame[1, 1]
206 206
207 cat("Number of days: ", opt$num_days, "\n") 207 cat("Number of days: ", opt$num_days, "\n")
208 208
209 # Initialize matrix for results from all replications. 209 # Initialize matrix for results from all replications.