diff --git a/covid/tasks/summary_longformat.py b/covid/tasks/summary_longformat.py index 94f8612374d7dc6bd2611ef5e63d655fb40d8353..416e5dee15da1b0afbdb8cb6042c5cc7f0962699 100644 --- a/covid/tasks/summary_longformat.py +++ b/covid/tasks/summary_longformat.py @@ -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( ( diff --git a/pyproject.toml b/pyproject.toml index 998fbc93fcbfe1d3e78ffb70f4d0ee0863acda34..67b91f58b187844f9f64177597bae98aeab8d8c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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"