Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 74:9843894544a8 draft

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author greg
date Tue, 14 Nov 2017 13:57:23 -0500
parents 9bc7ab4da9e7
children 392980f72514
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73:9bc7ab4da9e7 74:9843894544a8
26 args <- parse_args(parser, positional_arguments=TRUE) 26 args <- parse_args(parser, positional_arguments=TRUE)
27 opt <- args$options 27 opt <- args$options
28 28
29 parse_input_data = function(input_file, num_rows, num_columns) { 29 parse_input_data = function(input_file, num_rows, num_columns) {
30 # Read in the input temperature datafile into a data frame. 30 # Read in the input temperature datafile into a data frame.
31 temperature_data_frame <- read.csv(file=input_file, header=T, strip.white=TRUE, sep=",")
31 if (num_rows == 6) { 32 if (num_rows == 6) {
32 # The input data has the following 6 columns: 33 # The input data has the following 6 columns:
33 # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX 34 # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
34 temperature_data_frame <- read.csv(file=input_file, header=T, strip.white=TRUE, sep=",")
35 # Add a column containing the daylight length for each day. 35 # Add a column containing the daylight length for each day.
36 temperature_data_frame <- add_daylight_length(latitude, temperature_data_frame, opt$num_days) 36 temperature_data_frame <- add_daylight_length(latitude, temperature_data_frame, num_days)
37 temperature_data_frame 37 }
38 } 38 # Return the temperature_data_frame.
39 temperature_data_frame
39 } 40 }
40 41
41 add_daylight_length = function(latitude, temperature_data_frame, num_days) { 42 add_daylight_length = function(latitude, temperature_data_frame, num_days) {
42 # Return a vector of daylight length (photoperido profile) for 43 # Return a vector of daylight length (photoperido profile) for
43 # the number of days specified in the input temperature data 44 # the number of days specified in the input temperature data
53 # Compute the length of daylight for the day of the year. 54 # Compute the length of daylight for the day of the year.
54 daylight_length_vector[i] <- 24 - (24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi)))) 55 daylight_length_vector[i] <- 24 - (24 / pi * acos((sin(p * pi / 180) + sin(latitude * pi / 180) * sin(phi)) / (cos(latitude * pi / 180) * cos(phi))))
55 } 56 }
56 # Append daylight_length_vector as a new column to temperature_data_frame. 57 # Append daylight_length_vector as a new column to temperature_data_frame.
57 temperature_data_frame[, 7] <- daylight_length_vector 58 temperature_data_frame[, 7] <- daylight_length_vector
58 # Return the altered temperature_data_frame. 59 # Return the temperature_data_frame.
59 temperature_data_frame 60 temperature_data_frame
60 } 61 }
61 62
62 get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) { 63 get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) {
63 # Base development threshold for Brown Marmolated Stink Bug 64 # Base development threshold for Brown Marmolated Stink Bug
198 } 199 }
199 return = mort.prob 200 return = mort.prob
200 return 201 return
201 } 202 }
202 203
203 temperature_data_frame <- parse_input_data(opt$input, opt$num_rows, opt$num_columns) 204 temperature_data_frame <- parse_input_data(opt$input, opt$num_days, opt$num_columns)
204 latitude <- temperature_data_frame[1, 1] 205 latitude <- temperature_data_frame[1, 1]
205 206
206 cat("Number of days: ", opt$num_days, "\n") 207 cat("Number of days: ", opt$num_days, "\n")
207 208
208 # Initialize matrix for results from all replications. 209 # Initialize matrix for results from all replications.