Add link to country profiles stored in GitHub

monash-emu · Nov 30, 2023 · 7f07a6e · 7f07a6e
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diff --git a/docs/tex/tex_descriptions/projects/sm_covid/results.tex b/docs/tex/tex_descriptions/projects/sm_covid/results.tex
@@ -143,7 +143,7 @@ \subsection{Likelihood comparisons between analyses}
 \section{Detailed country-specific results}
 The next pages include detailed country-specific results for the 74 countries included in 
 our analysis, under the base-case configuration. Detailed country-specific results associated
-with the two sensitivity analyses (SA1 and SA2) are available online at \textcolor{red}{ADD LINK TO COUNTRY-SPECIFIC PROFILES SA1-2}.
+with the two sensitivity analyses (SA1 and SA2) are \textcolor{blue}{\textbf{\href{https://github.com/monash-emu/AuTuMN/tree/master/docs/school_closures_country_profiles}{available online}}}.
 
 You can access any country's outputs under the base-case configuration by clicking on the relevant country's name below:\\
 

diff --git a/docs/tex/user/rragonnet/sm_covid.pdf b/docs/tex/user/rragonnet/sm_covid.pdf
diff --git a/user/rragonnet/remote_run_outputs/file_gatherer.ipynb b/user/rragonnet/remote_run_outputs/file_gatherer.ipynb
@@ -31,12 +31,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 4,
    "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",
@@ -82,7 +82,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [

diff --git a/user/rragonnet/remote_run_outputs/get_derived_outputs.ipynb b/user/rragonnet/remote_run_outputs/get_derived_outputs.ipynb
@@ -29,27 +29,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'NLD'"
-      ]
-     },
-     "execution_count": 8,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "full_iso3_list[49]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -87,57 +76,83 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "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"
+      "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"
      ]
     }
    ],
    "source": [
-    "for analysis in [\"increased_hh_contacts\"] : #analysis_folders:\n",
-    "    for iso3 in full_iso3_list[48:]:\n",
+    "for analysis in [\"no_google_mobility\"] : #analysis_folders:\n",
+    "    for iso3 in full_iso3_list:\n",
     "        print(f\"{analysis}: {iso3}\")\n",
     "        derived_outputs = get_mle_derived_outputs(iso3, analysis)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dos = pd.read_pickle(analysis_folders['main'] / 'FRA' / \"derived_outputs.pickle\")"
-   ]
   }
  ],
  "metadata": {