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Country profiles for SAs and more appendix updates
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@romain-ragonnet
romain-ragonnet committed Nov 30, 2023
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Binary file added docs/school_closures_country_profiles/SA2_no_google_mobility_data.pdf
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1 change: 0 additions & 1 deletion docs/tex/tex_descriptions/projects/sm_covid/results.tex
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Expand Up @@ -137,7 +137,6 @@ \subsection{Likelihood comparisons between analyses}




\clearpage
\newpage
\section{Detailed country-specific results}
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Binary file modified docs/tex/user/rragonnet/sm_covid.pdf
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1 change: 1 addition & 0 deletions docs/tex/user/rragonnet/sm_covid.tex
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Expand Up @@ -2,6 +2,7 @@
% Preamble / options / packages %
% ---------------------------------------- %
\documentclass[10pt,a4paper]{report}
\counterwithout{figure}{chapter}
\author{
--------------- Add Authors List here ---------------
}
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103 changes: 6 additions & 97 deletions user/rragonnet/remote_run_outputs/country_highlights.ipynb
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Expand Up @@ -2,19 +2,9 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING (pytensor.tensor.blas): Using NumPy C-API based implementation for BLAS functions.\n",
"c:\\Users\\rrag0004\\.conda\\envs\\summer2\\lib\\site-packages\\summer\\runner\\vectorized_runner.py:363: NumbaDeprecationWarning: \u001b[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.\u001b[0m\n",
" def get_strain_infection_values(\n"
]
}
],
"outputs": [],
"source": [
"import pandas as pd\n",
"from pathlib import Path\n",
Expand All @@ -27,7 +17,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -40,92 +30,11 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"increased_hh_contacts: ARG\n",
"increased_hh_contacts: AUS\n",
"increased_hh_contacts: AUT\n",
"increased_hh_contacts: BEL\n",
"increased_hh_contacts: BGD\n",
"increased_hh_contacts: BGR\n",
"increased_hh_contacts: BIH\n",
"increased_hh_contacts: BOL\n",
"increased_hh_contacts: BRA\n",
"increased_hh_contacts: CAN\n",
"increased_hh_contacts: CHL\n",
"increased_hh_contacts: COL\n",
"increased_hh_contacts: CRI\n",
"increased_hh_contacts: CZE\n",
"increased_hh_contacts: DEU\n",
"increased_hh_contacts: DNK\n",
"increased_hh_contacts: ECU\n",
"increased_hh_contacts: EGY\n",
"increased_hh_contacts: ESP\n",
"increased_hh_contacts: FIN\n",
"increased_hh_contacts: FRA\n",
"increased_hh_contacts: GBR\n",
"increased_hh_contacts: GEO\n",
"increased_hh_contacts: GRC\n",
"increased_hh_contacts: GTM\n",
"increased_hh_contacts: HND\n",
"increased_hh_contacts: HRV\n",
"increased_hh_contacts: HUN\n",
"increased_hh_contacts: IDN\n",
"increased_hh_contacts: IND\n",
"increased_hh_contacts: IRL\n",
"increased_hh_contacts: IRQ\n",
"increased_hh_contacts: ISR\n",
"increased_hh_contacts: ITA\n",
"increased_hh_contacts: JOR\n",
"increased_hh_contacts: JPN\n",
"increased_hh_contacts: KAZ\n",
"increased_hh_contacts: KEN\n",
"increased_hh_contacts: KOR\n",
"increased_hh_contacts: LBN\n",
"increased_hh_contacts: LKA\n",
"increased_hh_contacts: LTU\n",
"increased_hh_contacts: LVA\n",
"increased_hh_contacts: MAR\n",
"increased_hh_contacts: MDA\n",
"increased_hh_contacts: MEX\n",
"increased_hh_contacts: MKD\n",
"increased_hh_contacts: MMR\n",
"increased_hh_contacts: MYS\n",
"increased_hh_contacts: NLD\n",
"increased_hh_contacts: NPL\n",
"increased_hh_contacts: PAK\n",
"increased_hh_contacts: PAN\n",
"increased_hh_contacts: PER\n",
"increased_hh_contacts: PHL\n",
"increased_hh_contacts: POL\n",
"increased_hh_contacts: PRT\n",
"increased_hh_contacts: PRY\n",
"increased_hh_contacts: ROU\n",
"increased_hh_contacts: RUS\n",
"increased_hh_contacts: SAU\n",
"increased_hh_contacts: SRB\n",
"increased_hh_contacts: SVK\n",
"increased_hh_contacts: SVN\n",
"increased_hh_contacts: SWE\n",
"increased_hh_contacts: THA\n",
"increased_hh_contacts: TUR\n",
"increased_hh_contacts: UKR\n",
"increased_hh_contacts: URY\n",
"increased_hh_contacts: USA\n",
"increased_hh_contacts: VEN\n",
"increased_hh_contacts: VNM\n",
"increased_hh_contacts: ZAF\n",
"increased_hh_contacts: ZWE\n"
]
}
],
"outputs": [],
"source": [
"for analysis in [\"increased_hh_contacts\"]: #analysis_folders:\n",
"for analysis in analysis_folders:\n",
" for iso3 in full_iso3_list:\n",
" print(f\"{analysis}: {iso3}\")\n",
" folder_path = analysis_folders[analysis] / iso3\n",
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22 changes: 6 additions & 16 deletions user/rragonnet/remote_run_outputs/file_gatherer.ipynb
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Expand Up @@ -2,19 +2,9 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING (pytensor.tensor.blas): Using NumPy C-API based implementation for BLAS functions.\n",
"c:\\Users\\rrag0004\\.conda\\envs\\summer2\\lib\\site-packages\\summer\\runner\\vectorized_runner.py:363: NumbaDeprecationWarning: \u001b[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.\u001b[0m\n",
" def get_strain_infection_values(\n"
]
}
],
"outputs": [],
"source": [
"import shutil\n",
"from autumn.projects.sm_covid2.common_school.runner_tools import INCLUDED_COUNTRIES\n",
Expand All @@ -31,12 +21,12 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# analysis_folder = Path.cwd() / \"31747883_full_analysis_26Sep2023_main\"\n",
"analysis_folder = Path.cwd() /\"31902886_full_analysis_05Oct2023_increased_hh_contacts\"\n",
"analysis_folder = Path.cwd() / \"31747883_full_analysis_26Sep2023_main\"\n",
"# analysis_folder = Path.cwd() /\"31902886_full_analysis_05Oct2023_increased_hh_contacts\"\n",
"# analysis_folder = Path.cwd() /\"31915437_full_analysis_05Oct2023_no_google_mobility\"\n",
"\n",
"common_dir = analysis_folder / \"COMMON_DIRECTORY\"\n",
Expand Down Expand Up @@ -82,7 +72,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
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92 changes: 7 additions & 85 deletions user/rragonnet/remote_run_outputs/get_derived_outputs.ipynb
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Expand Up @@ -2,19 +2,9 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"c:\\Users\\rrag0004\\.conda\\envs\\summer2\\lib\\site-packages\\summer\\runner\\vectorized_runner.py:363: NumbaDeprecationWarning: \u001b[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.\u001b[0m\n",
" def get_strain_infection_values(\n",
"WARNING (pytensor.tensor.blas): Using NumPy C-API based implementation for BLAS functions.\n"
]
}
],
"outputs": [],
"source": [
"import pandas as pd\n",
"from pathlib import Path\n",
Expand All @@ -38,7 +28,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -51,7 +41,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -76,79 +66,11 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"no_google_mobility: ARG\n",
"no_google_mobility: AUS\n",
"no_google_mobility: AUT\n",
"no_google_mobility: BEL\n",
"no_google_mobility: BGD\n",
"no_google_mobility: BGR\n",
"no_google_mobility: BIH\n",
"no_google_mobility: BOL\n",
"no_google_mobility: BRA\n",
"no_google_mobility: CAN\n",
"no_google_mobility: CHL\n",
"no_google_mobility: COL\n",
"no_google_mobility: CRI\n",
"no_google_mobility: CZE\n",
"no_google_mobility: DEU\n",
"no_google_mobility: DNK\n",
"no_google_mobility: ECU\n",
"no_google_mobility: EGY\n",
"no_google_mobility: ESP\n",
"no_google_mobility: FIN\n",
"no_google_mobility: FRA\n",
"no_google_mobility: GBR\n",
"no_google_mobility: GEO\n",
"no_google_mobility: GRC\n",
"no_google_mobility: GTM\n",
"no_google_mobility: HND\n",
"no_google_mobility: HRV\n",
"no_google_mobility: HUN\n",
"no_google_mobility: IDN\n",
"no_google_mobility: IND\n",
"no_google_mobility: IRL\n",
"no_google_mobility: IRQ\n",
"no_google_mobility: ISR\n",
"no_google_mobility: ITA\n",
"no_google_mobility: JOR\n",
"no_google_mobility: JPN\n",
"no_google_mobility: KAZ\n",
"no_google_mobility: KEN\n",
"no_google_mobility: KOR\n",
"no_google_mobility: LBN\n",
"no_google_mobility: LKA\n",
"no_google_mobility: LTU\n",
"no_google_mobility: LVA\n",
"no_google_mobility: MAR\n",
"no_google_mobility: MDA\n",
"no_google_mobility: MEX\n",
"no_google_mobility: MKD\n",
"no_google_mobility: MMR\n",
"no_google_mobility: MYS\n",
"no_google_mobility: NLD\n",
"no_google_mobility: NPL\n",
"no_google_mobility: PAK\n",
"no_google_mobility: PAN\n",
"no_google_mobility: PER\n",
"no_google_mobility: PHL\n",
"no_google_mobility: POL\n",
"no_google_mobility: PRT\n",
"no_google_mobility: PRY\n",
"no_google_mobility: ROU\n",
"no_google_mobility: RUS\n",
"no_google_mobility: SAU\n"
]
}
],
"outputs": [],
"source": [
"for analysis in [\"no_google_mobility\"] : #analysis_folders:\n",
"for analysis in analysis_folders:\n",
" for iso3 in full_iso3_list:\n",
" print(f\"{analysis}: {iso3}\")\n",
" derived_outputs = get_mle_derived_outputs(iso3, analysis)"
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