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Chris Jewell
covid19uk
Commits
b8347746
Commit
b8347746
authored
Mar 04, 2021
by
Chris Jewell
Browse files
Added daily absolute incidence and incidence per 100k to summary_longformat.py
parent
1144f1ec
Changes
1
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Inline
Side-by-side
covid/tasks/summary_longformat.py
View file @
b8347746
...
...
@@ -108,12 +108,23 @@ def summary_longformat(input_files, output_file):
insample_df
[
"value_name"
]
=
"insample14_Cases"
df
=
pd
.
concat
([
df
,
insample_df
],
axis
=
"index"
)
# Medium term incidence
# Medium term
absolute
incidence
medium_term
=
xarray
.
open_dataset
(
input_files
[
3
])
medium_df
=
xarray2summarydf
(
medium_term
[
"events"
][...,
2
].
reset_coords
(
drop
=
True
)
)
medium_df
[
"value_name"
]
=
"Cases"
medium_df
[
"value_name"
]
=
"absolute_incidence"
df
=
pd
.
concat
([
df
,
medium_df
],
axis
=
"index"
)
# Medium term incidence per 100k
medium_df
=
xarray2summarydf
(
(
medium_term
[
"events"
][...,
2
].
reset_coords
(
drop
=
True
)
/
data
[
"N"
][
np
.
newaxis
,
:,
np
.
newaxis
]
)
*
100000
)
medium_df
[
"value_name"
]
=
"incidence_per_100k"
df
=
pd
.
concat
([
df
,
medium_df
],
axis
=
"index"
)
# Weekly incidence per 100k
...
...
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