Adding ABC stuff

tjhladish · Sep 28, 2020 · 18e9b81 · 18e9b81
1 parent 1afd51c
commit 18e9b81
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diff --git a/exp/abc/Makefile b/exp/abc/Makefile
@@ -0,0 +1,33 @@
+-include local.mk
+
+CPP = g++
+
+#CFLAGS = -g -std=c++11 -Wall -Wextra -Wno-deprecated-declarations --pedantic
+CFLAGS = -O2 -std=c++11 -Wall -Wextra -Wno-deprecated-declarations --pedantic
+ABCDIR = $(HOME)/work/AbcSmc
+COVDIR = $(HOME)/work/covid-abm
+GSL_PATH = $(HOME)/work/AbcSmc/gsl_local
+COVOBJ = $(COVDIR)/Person.o $(COVDIR)/Location.o $(COVDIR)/Community.o $(COVDIR)/Parameters.o $(COVDIR)/Utility.o
+SQLDIR = $(ABCDIR)/sqdb
+
+INCLUDE = -I$(ABCDIR) -I$(COVDIR) -I$(GSL_PATH)/include/ -I$(ABCDIR)/jsoncpp/include
+#ifdef HPC_GSL_INC
+#INCLUDE += -I$$HPC_GSL_INC
+#endif
+
+ABC_LIB = -L$(ABCDIR) -L$(COVDIR) -labc -ljsoncpp -lsqdb $(ABCDIR)/sqlite3.o
+GSL_LIB = -lm -L$(GSL_PATH)/lib/ -lgsl -lgslcblas -lpthread -ldl
+
+libabc:
+	$(MAKE) -C $(ABCDIR) -f Makefile
+
+covid:
+	$(MAKE) -C $(COVDIR) -f Makefile
+
+abc_sql: libabc covid main_abc.cpp
+	$(CPP) $(CFLAGS) $(INCLUDE) -I$(SQLDIR) main_abc.cpp -o abc_sql $(COVOBJ) $(ABC_LIB) $(GSL_LIB)
+
+clean:
+	$(MAKE) -C $(ABCDIR) -f Makefile clean
+	$(MAKE) -C $(COVDIR) -f Makefile clean
+	rm -f abc abc_sql
diff --git a/exp/abc/abc_covid.json b/exp/abc/abc_covid.json
@@ -0,0 +1,137 @@
+{
+    "smc_iterations"            : 10,
+    "num_samples"               : 10000,
+    "predictive_prior_fraction" : 0.05,
+    "pls_training_fraction"     : 0.8,
+    "noise"                     : "MULTIVARIATE",
+
+    "database_filename"         : "abc_covid-escambia.sqlite",
+
+    "parameters" : [
+        {"name"       : "transmissibility",
+         "short_name" : "T",
+         "dist_type"  : "NORMAL",
+         "untransform": {"type"  : "LOGISTIC", "min"   : 0.0, "max"   : 1.0 },
+         "num_type"   : "FLOAT",
+         "par1"       : -1.265666,
+         "par2"       : 0.3},
+
+        {"name"       : "start_date",
+         "short_name" : "start",
+         "dist_type"  : "UNIFORM",
+         "num_type"   : "INT",
+         "par1"       : 30,
+         "par2"       : 60},
+
+        {"name"       : "external_exposures",
+         "short_name" : "ext_exp",
+         "dist_type"  : "NORMAL",
+         "untransform": {"type"  : "LOGISTIC", "min"   : 0.0, "max"   : 1.0 },
+         "num_type"   : "FLOAT",
+         "par1"       : -9.21024,
+         "par2"       : 2.4},
+
+        {"name"       : "first_detection_mild",
+         "short_name" : "fdm",
+         "dist_type"  : "NORMAL",
+         "untransform": {"type"  : "LOGISTIC", "min"   : 0.0, "max"   : 1.0 },
+         "num_type"   : "FLOAT",
+         "par1"       : -1.734601,
+         "par2"       : 1.2},
+
+        {"name"       : "first_detection_severe",
+         "short_name" : "fds",
+         "dist_type"  : "NORMAL",
+         "untransform": {"type"  : "LOGISTIC", "min"   : 0.0, "max"   : 1.0 },
+         "num_type"   : "FLOAT",
+         "par1"       : 0.4054651,
+         "par2"       : 0.9},
+
+        {"name"       : "icu_prob_given_death",
+         "short_name" : "imf",
+         "dist_type"  : "NORMAL",
+         "untransform": {"type"  : "LOGISTIC", "min"   : 0.0, "max"   : 1.0 },
+         "num_type"   : "FLOAT",
+         "par1"       : 0.0,
+         "par2"       : 1.0},
+
+        {"name"       : "mobility_logit_shift",
+         "short_name" : "mob_lsh",
+         "dist_type"  : "NORMAL",
+         "num_type"   : "FLOAT",
+         "par1"       : -2.7,
+         "par2"       : 1.0},
+
+        {"name"       : "mobility_logit_stretch",
+         "short_name" : "mob_lst",
+         "dist_type"  : "NORMAL",
+         "untransform": "POW_10",
+         "num_type"   : "FLOAT",
+         "par1"       : 0.30103,
+         "par2"       : 0.2},
+
+        {"name"       : "icu_mortality_improvement",
+         "short_name" : "icu_mi",
+         "dist_type"  : "NORMAL",
+         "untransform": {"type"  : "LOGISTIC", "min"   : 0.0, "max"   : 1.0 },
+         "num_type"   : "FLOAT",
+         "par1"       : -0.6931472,
+         "par2"       : 0.6264558}
+    ],
+
+    "metrics" : [
+        {"name" : "rc10k_w00", "num_type" : "INT", "value" :    0},
+        {"name" : "rc10k_w01", "num_type" : "INT", "value" :    0},
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+        {"name" : "rd10k_w00", "num_type" : "INT", "value" :    0},
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+     ]
+}