Merge branch 'develop' into master

Makefile

@@ -4,11 +4,11 @@
 WD := ../shared-svn/projects/episim/matsim-files
 
 # All available Scenarios
-ALL := BerlinWeek MunichWeek
+ALL := BerlinBrandenburg
 
 JAR := matsim-episim-*.jar
 # Shortcut to the scenario creation tool
-sc = java -Xmx20G -cp $(JAR) org.matsim.run.ScenarioCreation
+sc = java -Xmx30G -cp $(JAR) org.matsim.run.ScenarioCreation
 
 .PHONY: all clean $(ALL)
 
@@ -24,7 +24,7 @@ clean:
 
 # Includes all the scenarios with local variables
 # https://stackoverflow.com/questions/32904790/can-i-have-local-variables-in-included-makefiles
-SUBDIRS := scenarios/Cologne.mk
+SUBDIRS := scenarios/BerlinBrandenburg.mk
 define INCLUDE_FILE
 path = $S
 include $S

README.md

@@ -56,3 +56,4 @@ The **MATSim input files, output files, analysis data and visualizations** are l
 For more information about the methodology and preliminary results, see VSP working paper https://dx.doi.org/10.14279/depositonce-9835 .
 
 For more information about MATSim, see here: https://www.matsim.org/.
+

scenarios/BerlinBrandenburg.mk

@@ -0,0 +1,160 @@
+# To run this, you need a newer version of make. 4.4.1 works (in macOS under the command of gmake)
+# To run, execute "gmake BerlinBrandenburg" in terminal
+in = $(WD)/snz/BerlinBrandenburg/original-data
+out = $(WD)/snz/BerlinBrandenburg/episim-input
+tmp = $(WD)/snz/BerlinBrandenburg/processed-data
+
+BerlinBrandenburg: $(JAR) $(out)/bb_2020-week_snz_episim_events_wt_25pt_split.xml.gz $(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_25pt_split.xml.gz \
+$(out)/bb_2020-week_snz_episim_events_wt_100pt_split.xml.gz $(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt_split.xml.gz
+	echo "Building Berlin Brandenburg Week scenario"
+
+BerlinBrandenburgSamples: $(JAR) $(out)/samples/bb_2020-week_snz_episim_events_wt_10pt_split.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_5pt_split.xml.gz \
+$(out)/samples/bb_2020-week_snz_episim_events_wt_1pt_split.xml.gz
+	echo "Building Berlin Brandenburg Week samples"
+
+$(tmp)/personIds.diluted.txt.gz:
+	$(sc) filterPersons $(in)/de2020gsmwt_events_reduced.xml.gz\
+	 --facilities $(in)/facilities_assigned_simplified.xml.gz\
+	 --attributes $(in)/populationAttributes.xml.gz\
+	 --shape-file $(out)/shape-File/BerlinBrandenburg.shp\
+	 --shape-crs EPSG:25833\
+	 --output $@
+
+
+
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_100pt.xml.gz: $(tmp)/personIds.diluted.txt.gz
+	$(sc) convertPersonAttributes $(in)/populationAttributes.xml.gz\
+   --ids $<\
+   --requireAttribute "microm:modeled:age"\
+   --output $@
+
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt.xml.gz: $(out)/bb_2020-week_snz_entirePopulation_emptyPlans_100pt.xml.gz
+	$(sc) districtLookup $<\
+ 	 --output $@\
+	 --shp ../public-svn/matsim/scenarios/countries/de/episim/original-data/landkreise-in-germany/landkreise-in-germany.shp
+
+########
+# 25pct
+########
+
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_25pt.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_25pt.xml.gz &: \
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt.xml.gz
+	$(sc) downSample 0.25\
+   --population $<\
+   --events $(in)/de2020gsmwt_events_reduced.xml.gz\
+   --events $(in)/de2020gsmsa_events_reduced.xml.gz\
+   --events $(in)/de2020gsmso_events_reduced.xml.gz\
+   --output $(tmp)
+
+	mv $(tmp)/population0.25.xml.gz $(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_25pt.xml.gz
+	mv $(tmp)/de2020gsmwt_events_reduced-0.25.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_25pt.xml.gz
+	mv $(tmp)/de2020gsmsa_events_reduced-0.25.xml.gz $(out)/bb_2020-week_snz_episim_events_sa_25pt.xml.gz
+	mv $(tmp)/de2020gsmso_events_reduced-0.25.xml.gz $(out)/bb_2020-week_snz_episim_events_so_25pt.xml.gz
+
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_25pt_split.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_25pt_split.xml.gz &: \
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_25pt.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_25pt.xml.gz
+	$(sc) splitHomeFacilities $<\
+	 --events $(out)/bb_2020-week_snz_episim_events_wt_25pt.xml.gz\
+	 --events $(out)/bb_2020-week_snz_episim_events_sa_25pt.xml.gz\
+	 --events $(out)/bb_2020-week_snz_episim_events_so_25pt.xml.gz\
+	 --shape-file $(out)/../shape-File/BerlinBrandenburg.shp\
+	 --output $(out)
+
+$(out)/wLeisure/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_25pt_split.xml.gz $(out)/wLeisure/bb_2020-week_snz_episim_events_wt_25pt_split.xml.gz &: \
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_25pt.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_25pt.xml.gz
+	$(sc) splitHomeFacilities $<\
+	 --events $(out)/bb_2020-week_snz_episim_events_wt_25pt.xml.gz\
+	 --events $(out)/bb_2020-week_snz_episim_events_sa_25pt.xml.gz\
+	 --events $(out)/bb_2020-week_snz_episim_events_so_25pt.xml.gz\
+	 --shape-file $(out)/../shape-File/dilutionArea.shp\
+	 --remap visit --remap leisure\
+	 --output $(out)/wLeisure
+
+###########
+# 100 pct
+###########
+
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt_filtered.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_100pt.xml.gz &: \
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt.xml.gz
+	$(sc) downSample 1.0\
+   --population $<\
+   --events $(in)/de2020gsmwt_events_reduced.xml.gz\
+   --events $(in)/de2020gsmsa_events_reduced.xml.gz\
+   --events $(in)/de2020gsmso_events_reduced.xml.gz\
+   --output $(tmp)
+
+	mv $(tmp)/population1.0.xml.gz $(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt_filtered.xml.gz
+	mv $(tmp)/de2020gsmwt_events_reduced-1.0.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_100pt.xml.gz
+	mv $(tmp)/de2020gsmsa_events_reduced-1.0.xml.gz $(out)/bb_2020-week_snz_episim_events_sa_100pt.xml.gz
+	mv $(tmp)/de2020gsmso_events_reduced-1.0.xml.gz $(out)/bb_2020-week_snz_episim_events_so_100pt.xml.gz
+
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt_split.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_100pt_split.xml.gz &: \
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt_filtered.xml.gz $(out)/bb_2020-week_snz_episim_events_wt_100pt.xml.gz
+	$(sc) splitHomeFacilities $<\
+	 --events $(out)/bb_2020-week_snz_episim_events_wt_100pt.xml.gz\
+	 --events $(out)/bb_2020-week_snz_episim_events_sa_100pt.xml.gz\
+	 --events $(out)/bb_2020-week_snz_episim_events_so_100pt.xml.gz\
+	 --shape-file $(out)/../shape-File/dilutionArea.shp\
+	 --output $(out)
+
+#################
+# 10pct 5pct 1pct
+#################
+
+
+$(out)/samples/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_10pt.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_10pt.xml.gz &: \
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt.xml.gz
+	$(sc) downSample 0.1\
+	 --population $<\
+	 --events $(in)/de2020gsmwt_events_reduced.xml.gz\
+	 --events $(in)/de2020gsmsa_events_reduced.xml.gz\
+	 --events $(in)/de2020gsmso_events_reduced.xml.gz\
+	 --output $(tmp)
+
+	mkdir $(out)/samples
+
+	mv $(tmp)/population0.1.xml.gz $(out)/samples//bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_10pt.xml.gz
+	mv $(tmp)/de2020gsmwt_events_reduced-0.1.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_10pt.xml.gz
+	mv $(tmp)/de2020gsmsa_events_reduced-0.1.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_sa_10pt.xml.gz
+	mv $(tmp)/de2020gsmso_events_reduced-0.1.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_so_10pt.xml.gz
+
+
+$(out)/samples/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_5pt_split.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_5pt_split.xml.gz &: \
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt.xml.gz
+	$(sc) downSample 0.05\
+	 --population $<\
+	 --events $(in)/de2020gsmwt_events_reduced.xml.gz\
+	 --events $(in)/de2020gsmsa_events_reduced.xml.gz\
+	 --events $(in)/de2020gsmso_events_reduced.xml.gz\
+	 --output $(tmp)
+
+	mkdir $(out)/samples
+	mv $(tmp)/population0.05.xml.gz $(out)/samples//bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_5pt_split.xml.gz
+	mv $(tmp)/de2020gsmwt_events_reduced-0.05.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_5pt_split.xml.gz
+	mv $(tmp)/de2020gsmsa_events_reduced-0.05.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_sa_5pt_split.xml.gz
+	mv $(tmp)/de2020gsmso_events_reduced-0.05.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_so_5pt_split.xml.gz
+
+$(out)/samples/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_1pt_split.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_1pt_split.xml.gz &: \
+$(out)/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_100pt.xml.gz
+	$(sc) downSample 0.01\
+	 --population $<\
+	 --events $(in)/de2020gsmwt_events_reduced.xml.gz\
+	 --events $(in)/de2020gsmsa_events_reduced.xml.gz\
+	 --events $(in)/de2020gsmso_events_reduced.xml.gz\
+	 --output $(tmp)
+
+	mkdir $(out)/samples
+	mv $(tmp)/population0.01.xml.gz $(out)/samples//bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_1pt_split.xml.gz
+	mv $(tmp)/de2020gsmwt_events_reduced-0.01.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_1pt_split.xml.gz
+	mv $(tmp)/de2020gsmsa_events_reduced-0.01.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_sa_1pt_split.xml.gz
+	mv $(tmp)/de2020gsmso_events_reduced-0.01.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_so_1pt_split.xml.gz
+
+
+$(out)/samples/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_10pt_split.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_10pt_split.xml.gz &: \
+$(out)/samples/bb_2020-week_snz_entirePopulation_emptyPlans_withDistricts_10pt.xml.gz $(out)/samples/bb_2020-week_snz_episim_events_wt_10pt.xml.gz
+	$(sc) splitHomeFacilities $<\
+	 --events $(out)/samples/bb_2020-week_snz_episim_events_wt_10pt.xml.gz\
+	 --events $(out)/samples/bb_2020-week_snz_episim_events_sa_10pt.xml.gz\
+	 --events $(out)/samples/bb_2020-week_snz_episim_events_so_10pt.xml.gz\
+	 --shape-file $(out)/../shape-File/dilutionArea.shp\
+	 --output $(out)/samples

src/main/R/analyseCases.R

@@ -39,13 +39,13 @@ imm_inf <- imm_inf_raw %>%
 
   # mutate(vax = generic + mRNA + vector + ba1Update + ba5Update + natural)
 ggplot() + #nShowingSymptoms # SARS_CoV_2
+  geom_line(snap_inf, mapping = aes(date, nShowingSymptoms , group = seed, col = "base")) +
   geom_line(imm_inf, mapping = aes(date, nShowingSymptoms , group = seed, col = "imm-hist")) +
-  geom_line(snap_inf, mapping = aes(date, nShowingSymptoms , group = seed, col = "snapshot")) +
   scale_color_manual(name='Regression Model',
-                       breaks=c('snapshot', 'imm-hist'),
-                       values=c('snapshot'='red', 'imm-hist'='blue'))+
-  labs(alt = "hello world") +
-  ggtitle("Infections")
+                       breaks=c('base', 'imm-hist'),
+                       values=c('base'='red', 'imm-hist'='blue'))+
+  ggtitle("Cologne Cases") +
+  labs(x="Date", y="New Cases")