| Previous changeset 141:14afb6e85581 (2018-11-21) Next changeset 143:7628ba67c7ff (2018-12-20) |
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modified:
insect_phenology_model.R insect_phenology_model.xml test-data/output_combined1.csv test-data/output_combined2.csv test-data/output_combined3.csv test-data/output_combined4.csv test-data/output_f1_3.csv test-data/output_f1_4.csv test-data/output_f2_3.csv test-data/output_f2_4.csv test-data/output_p_3.csv test-data/output_p_4.csv utils.R |
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| diff -r 14afb6e85581 -r b06b3881ecf0 insect_phenology_model.R --- a/insect_phenology_model.R Wed Nov 21 11:33:40 2018 -0500 +++ b/insect_phenology_model.R Thu Dec 20 09:08:50 2018 -0500 |
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| b'@@ -250,50 +250,62 @@\n return(mortality.probability)\n }\n \n-mortality.egg = function(temperature, adj=0) {\n- # If no input from adjustment, default\n- # value is 0 (data from Nielsen, 2008).\n- T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);\n- egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);\n- # Calculates slopes and intercepts for lines.\n- slopes = NULL;\n- intercepts = NULL;\n- for (i in 1:length(T.mortality)) {\n- slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);\n- intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];\n+#mortality.egg = function(temperature, adj=0) {\n+# # If no input from adjustment, default\n+# # value is 0 (data from Nielsen, 2008).\n+# T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);\n+# egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);\n+# # Calculates slopes and intercepts for lines.\n+# slopes = NULL;\n+# intercepts = NULL;\n+# for (i in 1:length(T.mortality)) {\n+# slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);\n+# intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];\n+# }\n+# # Calculates mortality based on temperature.\n+# mortality.probability = NULL;\n+# for (j in 1:length(temperature)) {\n+# mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {\n+# temperature[j] * slopes[1] + intercepts[1];\n+# } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {\n+# temperature[j] * slopes[2] + intercepts[2];\n+# } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {\n+# temperature[j] * slopes[3] + intercepts[3];\n+# } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {\n+# temperature[j] * slopes[4] + intercepts[4];\n+# } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {\n+# temperature[j] * slopes[5] + intercepts[5];\n+# } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {\n+# temperature[j] * slopes[6] + intercepts[6];\n+# } else if (temperature[j] > T.mortality[7]) {\n+# temperature[j] * slopes[7] + intercepts[7];\n+# }\n+# # If mortality > 100, make it equal to 100.\n+# mortality.probability[mortality.probability>100] = 100;\n+# # If mortality <0, make equal to 0.\n+# mortality.probability[mortality.probability<0] = 0;\n+# }\n+# # Make mortality adjustments based on adj parameter.\n+# mortality.probability = (100 - mortality.probability) * adj + mortality.probability;\n+# # if mortality > 100, make it equal to 100.\n+# mortality.probability[mortality.probability>100] = 100;\n+# # If mortality <0, make equal to 0.\n+# mortality.probability[mortality.probability<0] = 0;\n+# # Change percent to proportion.\n+# mortality.probability = mortality.probability / 100;\n+# return(mortality.probability)\n+#}\n+\n+mortality.egg = function(temperature) {\n+ if (temperature < 12.7) {\n+ mortality.probability = 0.8;\n+ } else {\n+ mortality.probability = 0.8 - temperature / 40.0;\n+ if (mortality.probability < 0) {\n+ mortality.probability = 0.01;\n+ }\n }\n- # Calculates mortality based on temperature.\n- mortality.probability = NULL;\n- for (j in 1:length(temperature)) {\n- mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {\n- temperature[j] * slopes[1] + intercepts[1];\n- } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {\n- temperature[j] * slopes[2] + intercepts[2'..b'.probability[mortality.probability<0] = 0;\n- # Change percent to proportion.\n- mortality.probability = mortality.probability / 100;\n- return(mortality.probability)\n+ return (mortality.probability);\n }\n \n mortality.nymph = function(temperature) {\n@@ -311,6 +323,8 @@\n prepend_end_doy_norm = 0;\n # The start DOY for norm data appended to ytd data.\n append_start_doy_norm = 0;\n+ cat("start_date: ", start_date, "\\n");\n+ cat("end_date: ", end_date, "\\n");\n if (is.null(start_date) && is.null(end_date)) {\n # We\'re not dealing with a date interval.\n date_interval = FALSE;\n@@ -326,6 +340,7 @@\n start_date_doy = as.integer(strftime(start_date, format="%j"));\n end_date_doy = as.integer(strftime(end_date, format="%j"));\n }\n+ cat("date_interval: ", date_interval, "\\n");\n if (is.null(input_ytd)) {\n # We\'re processing only the 30 year normals data.\n processing_year_to_date_data = FALSE;\n@@ -363,16 +378,13 @@\n }\n end_date_ytd_row = which(temperature_data_frame$DATE==end_date);\n if (length(end_date_ytd_row) > 0) {\n+ cat("I\'m here...\\n");\n end_date_ytd_row = end_date_ytd_row[1];\n # The end date is contained within the input_ytd data.\n end_doy_ytd = as.integer(temperature_data_frame$DOY[end_date_ytd_row]);\n- if (end_doy_ytd > end_date_ytd_row + 1) {\n- # The input year-to-date dataset is missing 1 or more\n- # days of data.\n- days_missing = end_doy_ytd - end_date_ytd_row;\n- msg = cat("The year-to-date dataset is missing ", days_missing, " days of data.\\n");\n- stop_err(msg);\n- }\n+ cat("end_doy_ytd: ", end_doy_ytd, "\\n");\n+ cat("end_date_ytd_row: ", end_date_ytd_row, "\\n");\n+ cat("start_date_ytd_row: ", start_date_ytd_row, "\\n");\n } else {\n end_date_ytd_row = 0;\n }\n@@ -396,13 +408,10 @@\n # Save the first DOY to later check if start_date is Jan 1.\n start_doy_ytd = as.integer(temperature_data_frame$DOY[1]);\n end_doy_ytd = as.integer(temperature_data_frame$DOY[num_ytd_rows]);\n- if (end_doy_ytd > end_date_ytd_row + 1) {\n- # The input year-to-date dataset is missing 1 or more\n- # days of data.\n- days_missing = end_doy_ytd - end_date_ytd_row;\n- msg = cat("The year-to-date dataset is missing ", days_missing, " days of data.\\n");\n- stop_err(msg);\n- }\n+ cat("I\'m here 2...\\n");\n+ cat("end_doy_ytd: ", end_doy_ytd, "\\n");\n+ cat("end_date_ytd_row: ", end_date_ytd_row, "\\n");\n+ cat("start_date_ytd_row: ", start_date_ytd_row, "\\n");\n }\n } else {\n # We\'re processing only the 30 year normals data, so create an empty\n@@ -557,6 +566,8 @@\n }\n }\n }\n+ # Ensure all DOY values are consectuive integers.\n+ validate_doys(temperature_data_frame);\n # Add a column containing the daylight length for each day.\n temperature_data_frame = add_daylight_length(temperature_data_frame);\n return(list(temperature_data_frame, start_date, end_date, prepend_end_doy_norm, append_start_doy_norm, is_leap_year, location));\n@@ -856,7 +867,8 @@\n }\n if (vector.individual[2] == 0) {\n # Egg.\n- death.probability = opt$egg_mortality * mortality.egg(mean.temp, adj=opt$egg_mortality);\n+ # death.probability = opt$egg_mortality * mortality.egg(mean.temp, adj=opt$egg_mortality);\n+ death.probability = opt$egg_mortality * mortality.egg(mean.temp);\n }\n else if (vector.individual[2] == 1 | vector.individual[2] == 2) {\n # Nymph.\n' |
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| diff -r 14afb6e85581 -r b06b3881ecf0 insect_phenology_model.xml --- a/insect_phenology_model.xml Wed Nov 21 11:33:40 2018 -0500 +++ b/insect_phenology_model.xml Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -66,13 +66,13 @@ <validator type="expression" message="30 year normals temperature data must have 10 columns and 366 rows">value is not None and value.metadata.columns==10 and value.metadata.data_lines==366</validator> </param> <conditional name="merge_ytd_temperature_data_cond"> - <param name="merge_ytd_temperature_data" type="select" label="Merge year-to-date temperature data with 30 year normals temperature data?"> + <param name="merge_ytd_temperature_data" type="select" label="Merge daily actuals temperature data with 30 year normals temperature data?"> <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> <when value="yes"> - <param name="input_ytd" type="data" format="csv" label="Year-to-date temperature data"> - <validator type="expression" message="Year-to-date temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator> + <param name="input_ytd" type="data" format="csv" label="Daily actuals temperature data"> + <validator type="expression" message="Daily actuals temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator> </param> <param name="location" type="text" value="" optional="true" label="Location" help="Enter the location or leave blank to use the station name from 30 year normals data."/> </when> @@ -81,7 +81,7 @@ <param name="insect" type="select" label="Select insect"> <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option> </param> - <param name="replications" type="integer" value="10" min="2" label="Number of replications"/> + <param name="replications" type="integer" value="5" min="2" label="Number of replications"/> <param name="insects_per_replication" type="integer" value="1000" min="100" label="Number of insects with which to start each replication"/> <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination"/> <param name="egg_mortality" type="float" value="1" min="0" max="1" label="Adjustment rate for egg mortality" help="Floating point value between 0 and 1"/> @@ -242,7 +242,7 @@ * **30 year normals temperature data** - the dataset from your history containing the 30-year normals temperature data (available at http://pestwatch.psu.edu/ghcn). * **Merge year-to-date temperature data with 30 year normals temperature data** - select Yes to merge a year-to-date temperature dataset from your history into the selected 30 year normals temperature data. - * **Year-to-date temperature data** - the dataset from your history containing the year-to-date temperature data (available at http://pestwatch.psu.edu/minmax). + * **Daily actuals temperature data** - the dataset from your history containing the daily actuals temperature data (available at http://pestwatch.psu.edu/minmax). * **Location** - the location associated with the selected temperature data. * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed. |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_combined1.csv --- a/test-data/output_combined1.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_combined1.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","YOUNGNYMPH","YOUNGNYMPHSE","PRE.VITADULT","PRE.VITADULTSE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","YOUNGNYMPH","YOUNGNYMPHSE","PRE.VITADULT","PRE.VITADULTSE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_combined2.csv --- a/test-data/output_combined2.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_combined2.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_combined3.csv --- a/test-data/output_combined3.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_combined3.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH","OLDNYMPHSE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","OLDNYMPH","OLDNYMPHSE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_combined4.csv --- a/test-data/output_combined4.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_combined4.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_f1_3.csv --- a/test-data/output_f1_3.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_f1_3.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.F1","OLDNYMPH.F1.SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","OLDNYMPH","OLDNYMPHSE","OLDNYMPH.F1","OLDNYMPH.F1.SE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_f1_4.csv --- a/test-data/output_f1_4.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_f1_4.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.F1","EGG.F1.SE","TOTALNYMPH.F1","TOTALNYMPH.F1.SE","TOTALADULT.F1","TOTALADULT.F1.SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE","EGG.F1","EGG.F1.SE","TOTALNYMPH.F1","TOTALNYMPH.F1.SE","TOTALADULT.F1","TOTALADULT.F1.SE","ALL.TOTAL.F1","ALL.TOTAL.F1.SE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_f2_3.csv --- a/test-data/output_f2_3.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_f2_3.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.F2","OLDNYMPH.F2.SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","OLDNYMPH","OLDNYMPHSE","OLDNYMPH.F2","OLDNYMPH.F2.SE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_f2_4.csv --- a/test-data/output_f2_4.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_f2_4.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.F2","EGG.F2.SE","TOTALNYMPH.F2","TOTALNYMPH.F2.SE","TOTALADULT.F2","TOTALADULT.F2.SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE","EGG.F2","EGG.F2.SE","TOTALNYMPH.F2","TOTALNYMPH.F2.SE","TOTALADULT.F2","TOTALADULT.F2.SE","ALL.TOTAL.F2","ALL.TOTAL.F2.SE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_p_3.csv --- a/test-data/output_p_3.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_p_3.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH.P","OLDNYMPH.P.SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","OLDNYMPH","OLDNYMPHSE","OLDNYMPH.P","OLDNYMPH.P.SE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 test-data/output_p_4.csv --- a/test-data/output_p_4.csv Wed Nov 21 11:33:40 2018 -0500 +++ b/test-data/output_p_4.csv Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -1,1 +1,1 @@ -"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG.P","EGG.P.SE","TOTALNYMPH.P","TOTALNYMPH.P.SE","TOTALADULT.P","TOTALADULT.P.SE","ALL.TOTAL.P","ALL.TOTAL.P.SE" +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","DEGREE.DAYS","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE","EGG.P","EGG.P.SE","TOTALNYMPH.P","TOTALNYMPH.P.SE","TOTALADULT.P","TOTALADULT.P.SE","ALL.TOTAL.P","ALL.TOTAL.P.SE" |
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| diff -r 14afb6e85581 -r b06b3881ecf0 utils.R --- a/utils.R Wed Nov 21 11:33:40 2018 -0500 +++ b/utils.R Thu Dec 20 09:08:50 2018 -0500 |
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| @@ -333,3 +333,21 @@ } return(valid_date); } + +validate_doys = function(temperature_data_frame) { + # Ensure all DOY values are consecutive integers. + last_doy = 0; + num_rows = dim(temperature_data_frame)[1]; + for (i in 1:num_rows) { + doy = as.integer(temperature_data_frame$DOY[i]); + if (last_doy == 0) { + last_doy = doy; + } else { + if (doy != last_doy + 1) { + msg = paste("DOY ", doy, " is not consecutive (previous DOY is ", last_doy, ".", sep=""); + stop_err(msg); + } + last_doy = doy; + } + } +} |