diff --git a/src/BaseModel.py b/src/BaseModel.py
index 316b84c7ee0ca5f06868ef11b386392f6a09ce79..02a9c11e579c75c7c459140d7b20666d4e8844fb 100644
--- a/src/BaseModel.py
+++ b/src/BaseModel.py
@@ -343,7 +343,7 @@ class BaseModel(object):
def sample_predictions(
self,
target_days,
- target_counties,
+ target_counties,
parameters,
init="auto"):
# extract features
diff --git a/src/gridjob_sample_posterior.sge b/src/gridjob_sample_posterior.sge
index f49842a9edfaae115cec1245d2e75cbd5c0d900e..30a861f88ecefa1ef94bfe425a59293ee1484365 100644
--- a/src/gridjob_sample_posterior.sge
+++ b/src/gridjob_sample_posterior.sge
@@ -3,12 +3,12 @@
#$ -t 1-9
#$ -l mem=14G
#$ -m n
-#$ -q ni.q
-#$ -l h='!(ramsauer.ikw.uni-osnabrueck.de|vector.cv.uni-osnabrueck.de|righty.ni.uni-osnabrueck.de)'
-#$ -wd /net/store/ni/projects/BSTIM/src/
-#$ -e /net/store/ni/projects/BSTIM/logs_backup/e_$TASK_ID.txt
-#$ -o /net/store/ni/projects/BSTIM/logs_backup/o_$TASK_ID.txt
-#$ -pe default 4
+echo "#$ -q ni.q"
+echo "#$ -l h='!(ramsauer.ikw.uni-osnabrueck.de|vector.cv.uni-osnabrueck.de|righty.ni.uni-osnabrueck.de)'"
+#$ -wd /net/projects/scratch/summer/valid_until_31_January_2021/leffenberger/BSTIM-Covid19/src
+#$ -e /net/projects/scratch/summer/valid_until_31_January_2021/leffenberger/BSTIM-Covid19/logs_backup/e_$TASK_ID.txt
+#$ -o //net/projects/scratch/summer/valid_until_31_January_2021/leffenberger/BSTIM-Covid19/logs_backup/o_$TASK_ID.txt
+echo "#$ -pe default 4"
echo "Running job ${JOB_ID}, task ${SGE_TASK_ID} on `hostname`."
diff --git a/src/plot_curves_appendix.py b/src/plot_curves_appendix.py
index 76a32592e69e20def084a588c3641840d0e5125b..ff881044fafae0852d7b80263261e437ef9974cf 100644
--- a/src/plot_curves_appendix.py
+++ b/src/plot_curves_appendix.py
@@ -1,3 +1,5 @@
+import matplotlib
+matplotlib.use('TkAgg')
from matplotlib import pyplot as plt
from config import *
from shared_utils import *
@@ -7,7 +9,7 @@ import numpy as np
from collections import OrderedDict
from pymc3.stats import quantiles
-def curves_appendix(use_interactions=True, use_repot_delay=True, save_plot=False):
+def curves_appendix(use_interactions=True, use_report_delay=True, save_plot=False):
with open('../data/counties/counties.pkl', "rb") as f:
counties = pkl.load(f)
@@ -81,19 +83,20 @@ def curves_appendix(use_interactions=True, use_repot_delay=True, save_plot=False
prediction_region = "germany"
data = load_daily_data(disease, prediction_region, counties)
- data = data[data.index < pd.Timestamp(2020, 3, 30)]
+ data = data[data.index < pd.Timestamp(2020, 4, 25)]
_, target, _, _ = split_data(
data, train_start=pd.Timestamp(
2020, 1, 28), test_start=pd.Timestamp(
- 2020, 3, 30), post_test=pd.Timestamp(
- 2020, 3, 31)) # plots for the training period!
+ 2020, 4, 22), post_test=pd.Timestamp(
+ 2020, 4, 24)) # plots for the training period!
county_ids = target.columns
# Load our prediction samples
res = load_pred(disease, use_interactions, use_report_delay)
- n_days = 62 # for now; get from timestamps up top! / configs!
+ n_days = 85 # for now; get from timestamps up top! / configs!
+
prediction_samples = np.reshape(res['y'], (res['y'].shape[0], n_days, -1))
prediction_quantiles = quantiles(prediction_samples, (5, 25, 75, 95))
@@ -198,7 +201,7 @@ def curves_appendix(use_interactions=True, use_repot_delay=True, save_plot=False
va='center', rotation='vertical', fontsize=22)
if save_plot:
- plt.savefig("../figures/curves_{}_appendix.pdf".format(disease))
+ plt.savefig("../figures/luke_curves_{}_appendix.pdf".format(disease))
return plt
diff --git a/src/sample_posterior.py b/src/sample_posterior.py
index 309c87ce59a547024fcee7ceed8753a4b02998ed..05045b140e0e4477c0359b3bea541d8d5ddf425b 100644
--- a/src/sample_posterior.py
+++ b/src/sample_posterior.py
@@ -8,6 +8,7 @@ import os
i = int(os.environ["SGE_TASK_ID"])-1
+
#NOTE: for jureca, extend to the number of available cores (chains and cores!)
num_samples = 250
# num_sample = 1
@@ -34,7 +35,7 @@ data = load_daily_data(disease, prediction_region, county_info)
data_train, target_train, data_test, target_test = split_data(
data,
train_start=pd.Timestamp(2020, 1, 28),
- test_start=pd.Timestamp(2020, 4, 22),
+ test_start=pd.Timestamp(2020, 4, 12),
post_test=pd.Timestamp(2020, 4, 23)
)