Mercurial > repos > greg > insect_phenology_model
changeset 28:afe6d8bac0c0 draft
Uploaded
author | greg |
---|---|
date | Mon, 12 Mar 2018 09:15:16 -0400 (2018-03-12) |
parents | 452e0e189e84 |
children | dd0f1b7528aa |
files | insect_phenology_model.R insect_phenology_model.xml test-data/output1.csv test-data/output2.csv test-data/output3.csv test-data/output4.csv test-data/plot.pdf test-data/pop_by_generation.pdf |
diffstat | 8 files changed, 87 insertions(+), 82 deletions(-) [+] |
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--- a/insect_phenology_model.R Fri Mar 09 13:41:38 2018 -0500 +++ b/insect_phenology_model.R Mon Mar 12 09:15:16 2018 -0400 @@ -1057,14 +1057,7 @@ if (process_nymphs) { # Calculate nymph populations for selected life stage. for (life_stage_nymph in life_stages_nymph) { - if (life_stage_nymph=="Total") { - # Mean value for all nymphs. - total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean); - temperature_data_frame = append_vector(temperature_data_frame, total_nymphs, "TOTALNYMPH"); - # Standard error for all nymphs. - total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd); - temperature_data_frame = append_vector(temperature_data_frame, total_nymphs.std_error, "TOTALNYMPHSE"); - } else if (life_stage_nymph=="Young") { + if (life_stage_nymph=="Young") { # Mean value for young nymphs. young_nymphs = apply(YoungNymphs.replications, 1, mean); temperature_data_frame = append_vector(temperature_data_frame, young_nymphs, "YOUNGNYMPH"); @@ -1078,20 +1071,20 @@ # Standard error for old nymphs. old_nymphs.std_error = apply(OldNymphs.replications / sqrt(opt$replications), 1, sd); temperature_data_frame = append_vector(temperature_data_frame, old_nymphs.std_error, "OLDNYMPHSE"); + } else if (life_stage_nymph=="Total") { + # Mean value for all nymphs. + total_nymphs = apply((YoungNymphs.replications+OldNymphs.replications), 1, mean); + temperature_data_frame = append_vector(temperature_data_frame, total_nymphs, "TOTALNYMPH"); + # Standard error for all nymphs. + total_nymphs.std_error = apply((YoungNymphs.replications+OldNymphs.replications) / sqrt(opt$replications), 1, sd); + temperature_data_frame = append_vector(temperature_data_frame, total_nymphs.std_error, "TOTALNYMPHSE"); } } } if (process_adults) { # Calculate adult populations for selected life stage. for (life_stage_adult in life_stages_adult) { - if (life_stage_adult=="Total") { - # Mean value for all adults. - total_adults = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, mean); - temperature_data_frame = append_vector(temperature_data_frame, total_adults, "TOTALADULT"); - # Standard error for all adults. - total_adults.std_error = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications); - temperature_data_frame = append_vector(temperature_data_frame, total_adults.std_error, "TOTALADULTSE"); - } else if (life_stage_adult == "Pre-vittelogenic") { + if (life_stage_adult == "Pre-vittelogenic") { # Mean value for previttelogenic adults. previttelogenic_adults = apply(Previttelogenic.replications, 1, mean); temperature_data_frame = append_vector(temperature_data_frame, previttelogenic_adults, "PRE-VITADULT"); @@ -1112,6 +1105,13 @@ # Standard error for vittelogenic adults. diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications); temperature_data_frame = append_vector(temperature_data_frame, diapausing_adults.std_error, "DIAPAUSINGADULTSE"); + } else if (life_stage_adult=="Total") { + # Mean value for all adults. + total_adults = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, mean); + temperature_data_frame = append_vector(temperature_data_frame, total_adults, "TOTALADULT"); + # Standard error for all adults. + total_adults.std_error = apply((Previttelogenic.replications+Vittelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications); + temperature_data_frame = append_vector(temperature_data_frame, total_adults.std_error, "TOTALADULTSE"); } } }
--- a/insect_phenology_model.xml Fri Mar 09 13:41:38 2018 -0500 +++ b/insect_phenology_model.xml Mon Mar 12 09:15:16 2018 -0400 @@ -123,23 +123,23 @@ <param name="plot_egg_life_stage" value="no" /> <param name="life_stages_nymph" value="Young" /> <param name="life_stages_adult" value="Pre-vittelogenic" /> - <output name="output" file="output1.csv" ftype="csv"/> + <output name="output" file="output1.csv" ftype="csv" compare="contains"/> <output_collection name="output_collection" type="list"> - <element name="02_young_nymph_pop.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> - <element name="05_pre-vittelogenic_adult_pop.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> + <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> </output_collection> </test> - <!-- <test> <param name="input" value="state_college.csv" ftype="csv" /> <param name="location" value="State College PA" /> <param name="replications" value="2" /> <param name="plot_generations_separately" value="no" /> + <output name="output" file="output2.csv" ftype="csv" compare="contains"/> <output_collection name="output_collection" type="list"> - <element name="01_egg_pop.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> - <element name="04_total_nymph_pop.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> - <element name="08_total_adult_pop.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> - <element name="09_total_pop.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> + <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> </output_collection> </test> <test> @@ -149,22 +149,23 @@ <param name="plot_egg_life_stage" value="no" /> <param name="life_stages_nymph" value="Old" /> <param name="plot_adult_life_stage" value="no" /> + <output name="output" file="output3.csv" ftype="csv" compare="contains"/> <output_collection name="output_collection" type="list"> - <element name="03_old_nymph_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> + <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> </output_collection> </test> <test> <param name="input" value="state_college.csv" ftype="csv" /> <param name="location" value="State College PA" /> <param name="replications" value="2" /> + <output name="output" file="output4.csv" ftype="csv" compare="contains"/> <output_collection name="output_collection" type="list"> - <element name="01_egg_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> - <element name="04_total_nymph_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> - <element name="08_total_adult_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> - <element name="09_total_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/> + <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> </output_collection> </test> - --> </tests> <help> **What it does**
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.csv Mon Mar 12 09:15:16 2018 -0400 @@ -0,0 +1,1 @@ +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","YOUNGNYMPH","YOUNGNYMPHSE","PRE-VITADULT","PRE-VITADULTSE"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output2.csv Mon Mar 12 09:15:16 2018 -0400 @@ -0,0 +1,1 @@ +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output3.csv Mon Mar 12 09:15:16 2018 -0400 @@ -0,0 +1,1 @@ +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","OLDNYMPH","OLDNYMPHSE"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output4.csv Mon Mar 12 09:15:16 2018 -0400 @@ -0,0 +1,1 @@ +"LATITUDE","LONGITUDE","DATE","DOY","TMIN","TMAX","DAYLEN","EGG","EGGSE","TOTALNYMPH","TOTALNYMPHSE","TOTALADULT","TOTALADULTSE"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plot.pdf Mon Mar 12 09:15:16 2018 -0400 @@ -0,0 +1,52 @@ +%PDF +1 0 obj +<< +/CreationDate +/ModDate +/Title (R Graphics Output) +/Producer +/Creator (R) +<< /Type /Catalog /Pages 3 0 R >> +endobj +7 0 obj +<< /Type /Page /Parent 3 0 R /Contents 8 0 R /Resources 4 0 R >> +endobj +3 0 obj +<< /Type /Pages /Kids [ 7 0 R ] /Count 1 /MediaBox [0 0 1440 2160] >> +endobj +4 0 obj +<< +/ProcSet [/PDF /Text] +/Font <</F2 10 0 R /F3 11 0 R >> +/ExtGState << >> +/ColorSpace << /sRGB 5 0 R >> +>> +endobj +5 0 obj +[/ICCBased 6 0 R] +endobj +6 0 obj +<< /Alternate /DeviceRGB /N 3 /Length 2596 /Filter /FlateDecode >> +stream +endobj +9 0 obj +<< +/Type /Encoding /BaseEncoding /WinAnsiEncoding +/Differences [ 45/minus 96/quoteleft +144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent +/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +>> +endobj +10 0 obj +<< /Type /Font /Subtype /Type1 /Name /F2 /BaseFont /Helvetica +/Encoding 9 0 R >> +endobj +11 0 obj +<< /Type /Font /Subtype /Type1 /Name /F3 /BaseFont /Helvetica-Bold +/Encoding 9 0 R >> +endobj +xref +trailer +<< /Size 12 /Info 1 0 R /Root 2 0 R >> +startxref +%%EOF
--- a/test-data/pop_by_generation.pdf Fri Mar 09 13:41:38 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -%PDF -1 0 obj -<< -/CreationDate -/ModDate -/Title (R Graphics Output) -/Producer -/Creator (R) -<< /Type /Catalog /Pages 3 0 R >> -endobj -7 0 obj -<< /Type /Page /Parent 3 0 R /Contents 8 0 R /Resources 4 0 R >> -endobj -3 0 obj -<< /Type /Pages /Kids [ 7 0 R ] /Count 1 /MediaBox [0 0 1440 2160] >> -endobj -4 0 obj -<< -/ProcSet [/PDF /Text] -/Font <</F2 10 0 R /F3 11 0 R >> -/ExtGState << >> -/ColorSpace << /sRGB 5 0 R >> ->> -endobj -5 0 obj -[/ICCBased 6 0 R] -endobj -6 0 obj -<< /Alternate /DeviceRGB /N 3 /Length 2596 /Filter /FlateDecode >> -stream -endobj -9 0 obj -<< -/Type /Encoding /BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] ->> -endobj -10 0 obj -<< /Type /Font /Subtype /Type1 /Name /F2 /BaseFont /Helvetica -/Encoding 9 0 R >> -endobj -11 0 obj -<< /Type /Font /Subtype /Type1 /Name /F3 /BaseFont /Helvetica-Bold -/Encoding 9 0 R >> -endobj -xref -trailer -<< /Size 12 /Info 1 0 R /Root 2 0 R >> -startxref -%%EOF