Changing folder structure

BDI-pathogens · Aug 17, 2020 · f8433b2 · f8433b2
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diff --git a/combined_pillars_case_data.csv → data/combined_pillars_case_data.csv b/combined_pillars_case_data.csv → data/combined_pillars_case_data.csv
diff --git a/pillar1_case_data.csv → data/pillar1_case_data.csv b/pillar1_case_data.csv → data/pillar1_case_data.csv
diff --git a/pillar2_case_data.csv → data/pillar2_case_data.csv b/pillar2_case_data.csv → data/pillar2_case_data.csv
diff --git a/data/pillar2_case_data_IoW.csv b/data/pillar2_case_data_IoW.csv
@@ -0,0 +1,79 @@
+LTLA_name,specimen_date,Pillar1,Pillar2,total
+Isle of Wight,04-Mar-20,1,,1
+Isle of Wight,10-Mar-20,1,,1
+Isle of Wight,20-Mar-20,1,,1
+Isle of Wight,21-Mar-20,1,,1
+Isle of Wight,22-Mar-20,4,,4
+Isle of Wight,23-Mar-20,2,,2
+Isle of Wight,25-Mar-20,1,,1
+Isle of Wight,26-Mar-20,1,,1
+Isle of Wight,27-Mar-20,1,,1
+Isle of Wight,28-Mar-20,2,,2
+Isle of Wight,30-Mar-20,3,,3
+Isle of Wight,31-Mar-20,1,,1
+Isle of Wight,01-Apr-20,7,,7
+Isle of Wight,02-Apr-20,1,,1
+Isle of Wight,03-Apr-20,1,,1
+Isle of Wight,04-Apr-20,3,,3
+Isle of Wight,05-Apr-20,2,,2
+Isle of Wight,06-Apr-20,4,,4
+Isle of Wight,07-Apr-20,2,,2
+Isle of Wight,08-Apr-20,5,,5
+Isle of Wight,09-Apr-20,2,,2
+Isle of Wight,10-Apr-20,5,,5
+Isle of Wight,11-Apr-20,2,,2
+Isle of Wight,12-Apr-20,2,,2
+Isle of Wight,13-Apr-20,1,,1
+Isle of Wight,15-Apr-20,4,,4
+Isle of Wight,16-Apr-20,8,,8
+Isle of Wight,17-Apr-20,1,,1
+Isle of Wight,18-Apr-20,3,1,4
+Isle of Wight,19-Apr-20,1,,1
+Isle of Wight,21-Apr-20,6,,6
+Isle of Wight,22-Apr-20,4,,4
+Isle of Wight,23-Apr-20,10,,10
+Isle of Wight,24-Apr-20,9,16,25
+Isle of Wight,25-Apr-20,1,9,10
+Isle of Wight,26-Apr-20,,17,17
+Isle of Wight,27-Apr-20,4,2,6
+Isle of Wight,28-Apr-20,9,,9
+Isle of Wight,29-Apr-20,8,26,34
+Isle of Wight,30-Apr-20,1,5,6
+Isle of Wight,01-May-20,12,4,16
+Isle of Wight,02-May-20,6,11,17
+Isle of Wight,03-May-20,1,2,3
+Isle of Wight,04-May-20,3,8,11
+Isle of Wight,05-May-20,1,4,5
+Isle of Wight,06-May-20,2,6,8
+Isle of Wight,07-May-20,4,10,14
+Isle of Wight,08-May-20,1,6,7
+Isle of Wight,09-May-20,1,2,3
+Isle of Wight,10-May-20,1,1,2
+Isle of Wight,11-May-20,1,7,8
+Isle of Wight,12-May-20,3,3,6
+Isle of Wight,13-May-20,7,7,14
+Isle of Wight,14-May-20,4,3,7
+Isle of Wight,15-May-20,5,7,12
+Isle of Wight,16-May-20,1,,1
+Isle of Wight,18-May-20,7,3,10
+Isle of Wight,19-May-20,2,6,8
+Isle of Wight,20-May-20,2,2,4
+Isle of Wight,21-May-20,4,3,7
+Isle of Wight,22-May-20,1,3,4
+Isle of Wight,23-May-20,1,3,4
+Isle of Wight,24-May-20,1,,1
+Isle of Wight,25-May-20,,1,1
+Isle of Wight,26-May-20,3,2,5
+Isle of Wight,28-May-20,,14,14
+Isle of Wight,29-May-20,,5,5
+Isle of Wight,31-May-20,1,,1
+Isle of Wight,02-Jun-20,,1,1
+Isle of Wight,03-Jun-20,,1,1
+Isle of Wight,04-Jun-20,,3,3
+Isle of Wight,05-Jun-20,,1,1
+Isle of Wight,06-Jun-20,,1,1
+Isle of Wight,07-Jun-20,1,,1
+Isle of Wight,09-Jun-20,,1,1
+Isle of Wight,12-Jun-20,1,2,3
+Isle of Wight,15-Jun-20,,3,3
+Isle of Wight,18-Jun-20,,1,1
diff --git a/population_by_region.csv → data/population_by_region.csv b/population_by_region.csv → data/population_by_region.csv
diff --git a/time_series_R.csv → data/time_series_R.csv b/time_series_R.csv → data/time_series_R.csv
diff --git a/Nowcast_IoW.png → figure/Nowcast_IoW.png b/Nowcast_IoW.png → figure/Nowcast_IoW.png
diff --git a/figure/analysis.1-1.png b/figure/analysis.1-1.png
diff --git a/figure/analysis.both.1-1.png b/figure/analysis.both.1-1.png
diff --git a/figure/incidence.p1.and.p2-1.png b/figure/incidence.p1.and.p2-1.png