Commit eaa9500e authored by Chris Jewell's avatar Chris Jewell
Browse files

Merge branch 'add-summaries' into 'master'

Added cumulative incidence to `summary_longformat.xlsx`

See merge request !29
parents f87af58a bc43cd97
......@@ -116,6 +116,13 @@ def summary_longformat(input_files, output_file):
medium_df["value_name"] = "absolute_incidence"
df = pd.concat([df, medium_df], axis="index")
# Cumulative cases
medium_df = xarray2summarydf(
medium_term["events"][..., 2].cumsum(dim="time").reset_coords(drop=True)
)
medium_df["value_name"] = "cumulative_absolute_incidence"
df = pd.concat([df, medium_df], axis="index")
# Medium term incidence per 100k
medium_df = xarray2summarydf(
(
......
......@@ -18,7 +18,6 @@ descartes = "^1.1.0"
matplotlib = "^3.3.2"
xlrd = "^1.2.0"
tqdm = "^4.50.2"
openpyxl = "^3.0.5"
h5py = "^2.10.0"
gemlib = {git = "http://fhm-chicas-code.lancs.ac.uk/GEM/gemlib.git"}
xarray = "^0.16.1"
......@@ -26,6 +25,7 @@ seaborn = "^0.11.0"
ruffus = "^2.8.4"
tensorflow = "^2.4.0"
jedi = "^0.17.2"
XlsxWriter = "^1.3.7"
[tool.poetry.dev-dependencies]
ipython = "^7.18.1"
......
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