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Create basic layout
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‎.gitignore

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.DS_Store
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.Rhistory
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.Rproj.user/
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analysis/reports/.ipynb_checkpoints/report-checkpoint.ipynb

‎analysis/reports/report.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/markdown": [
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"# <center>Pharmacy First "
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],
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"text/plain": [
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"<IPython.core.display.Markdown object>"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/markdown": [
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"### <center>01-01-2020 through 31-06-2024 by month"
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],
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"text/plain": [
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"<IPython.core.display.Markdown object>"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"import numpy as np\n",
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"from IPython.display import Markdown\n",
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"from PIL import Image\n",
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"\n",
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"start_date = '01-01-2020'\n",
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"end_date = '31-06-2024'\n",
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"\n",
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"display(Markdown(f'# <center>Pharmacy First '))\n",
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"display(Markdown(f'### <center>{start_date} through {end_date} by month'))"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"background\"></a>\n",
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"\n",
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"## Background\n",
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"\n",
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"Add background here\n",
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"\n",
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"## Methods\n",
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"\n",
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"This study used data from OpenSAFELY-TPP, which covers 40% of the population of England. For a description of the representativeness of this sample, please see our manuscript [here](https://doi.org/10.12688/wellcomeopenres.18010.1). Individuals were included if they were alive and registered at a TPP practice each month, across the study period. Patients were excluded if their listed age was not between 0 and 120 years.\n",
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"\n",
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"Counts represent patients with at least one clinical code of relevence in that month. Patients with more than one of the same clinical code in a month were only counted once. Rates divide the count by the included study population and multiply by 1,000 to achieve a rate per 1,000 registered patients.\n",
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"\n",
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"Counts <=7 have been redacted and all numbers rounded to the nearest 5 to avoid potential re-identification of individuals. The rates displayed were computed with these rounded counts.\n",
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"\n",
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"Our data relies on a relevent Pharmacy First code being added to a patient's GP record. The Pharmacy First service relies on [GP Connect: Update Record](https://digital.nhs.uk/services/gp-connect/gp-connect-in-your-organisation/gp-connect-update-record) to update a patient's GP record with consultation information from the community pharmacy. Following the launch of the Pharmacy First service, there has been a [gradual roll-out of GP Connect: Update Record](https://cpe.org.uk/our-news/gp-connect-update-record-rollout-and-flow-of-information/) across the approved community pharmacy IT system suppliers.\n",
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"\n",
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"*Need to complete this*\n",
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"\n",
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"Links to the codelist for each analysis can be found beneath the relevant section.\n",
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"\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<ul id=\"docNav\">\n",
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" <p>This report contains the following sections:</p>\n",
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" <li> <a href=\"#clinical_pathways\">Clinical Pathways</a>\n",
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" <ul>\n",
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" <li> <a href=\"#clinical_condition\">Clinical Condition</a></li>\n",
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" <li> <a href=\"#clinical_condition_days\">Days of the week</a></li>\n",
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" <li> <a href=\"#clinical_condition_region\">NHS Region</a></li>\n",
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" <li> <a href=\"#clinical_condition_ethnicity\">Ethnicity</a></li>\n",
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" <li> <a href=\"#clinical_condition_imd\">IMD</a></li>\n",
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" <li> <a href=\"#shingles\">Shingles</a>\n",
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" <ul>\n",
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" <li><a href=\"shingles_sex\">Sex</a></li>\n",
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" <li><a href=\"shingles_age\">Age</a></li>\n",
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" <li><a href=\"shingles_ethnicity\">Ethnicity</a></li>\n",
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" <li><a href=\"shingles_imd\">IMD</a></li>\n",
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" <li><a href=\"shingles_region\">Region</a></li>\n",
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" <li><a href=\"shingles_medication\">Medication supply</a></li>\n",
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" </ul>\n",
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" </li>\n",
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" <li> <a href=\"#uti\">Urinary tract infection etc.</a>\n",
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" </li> \n",
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" </ul>\n",
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" </li>\n",
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" <li> <a href=\"#hypertension\">Hypertension</a>\n",
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" <ul>\n",
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" <li> <a href=\"#\">Age</a></li>\n",
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" <li> <a href=\"#\">Sex</a></li>\n",
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" <li> <a href=\"#\">Region</a></li>\n",
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" </ul>\n",
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" </li>\n",
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" <li> <a href=\"#contraception\">Contraception</a>\n",
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" <ul>\n",
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" <li> <a href=\"#\">Age</a></li>\n",
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" <li> <a href=\"#\">Region</a></li>\n",
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" </ul>\n",
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" </li>\n",
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"</ul>"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"clinical_pathways\"></a>\n",
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"## Clinical Pathways\n",
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"\n",
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"This section focuses on the Clinical Pathways element of that Pharmacy First service\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"### Clinical Condition\n",
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"\n",
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"This section focuses on the clinical conditions within the Clinical Pathways element of that Pharmacy First service"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"clinical_condition\"></a>\n",
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"#### Counts by clinical condition\n",
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"\n",
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"Here we show the number of consultations for each of the Pharmacy First Clinical Pathways Clinical Conditions\n",
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">LINE CHART WITH COUNT OF EACH CLINICAL CONDITION"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"clinical_condition_days\"></a>\n",
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"#### Counts by day of the week\n",
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"\n",
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"Here we show the number of consultations for the Pharmacy First Clinical Pathways by day of the week the consultation was conducted.\n",
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"(Mainly of interest to show what happens at weekends etc e.g. when GP practices are closed).\n",
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"> BAR CHART WITH COUNT BY DAY OF THE WEEK"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"clinical_condition_region\"></a>\n",
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"#### Rates by region\n",
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"\n",
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"Here we show the rates of consultations for the Pharmacy First Clinical Pathways by the NHS Region in which the patient is registered.\n",
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"(Might not be the region where PF consultation conducted).\n",
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"> RATES OF ANY PF CLINICAL PATHWAY BY REGION"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"clinical_condition_ethnicity\"></a>\n",
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"#### Rates by ethnicity\n",
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"\n",
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"Here we show the rates of consultations for the Pharmacy First Clinical Pathways by patient ethnicity\n",
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"> RATES OF ANY PF CLINICAL PATHWAY BY ETHNICITY"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"clinical_condition_imd\"></a>\n",
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"#### Rates by IMD\n",
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"\n",
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"Here we show the rates of consultations for the Pharmacy First Clinical Pathways by IMD (based on patient address)\n",
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"> RATES OF ANY PF CLINICAL PATHWAY BY IMD"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"shingles\"></a>\n",
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"#### Shingles\n",
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"\n",
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"Here we show the rates specifically for consultations conducted under the Shingles clinical pathway"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"shingles_sex\"></a>\n",
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"##### Rates by sex (I can't make a smaller heading here but this sits under shingles section)\n",
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"Here we show the rates of consultations for the Pharmacy First Shingles Clinical Pathways by sex\n",
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"> RATES OF SHINGLES CLINICAL PATHWAY BY SEX"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"shingles_age\"></a>\n",
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"##### Rates by age\n",
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"Here we show the rates of consultations for the Pharmacy First Shingles Clinical Pathways by age.\n",
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"(Would need to consider age bands as different for each pathway)\n",
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"> RATES OF SHINGLES CLINICAL PATHWAY BY AGE"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"shingles_ethnicity\"></a>\n",
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"##### Rates by ethnicity\n",
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"Here we show the rates of consultations for the Pharmacy First Shingles Clinical Pathways by ethnicity\n",
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"> RATES OF SHINGLES CLINICAL PATHWAY BY ETHNICITY"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"shingles_imd\"></a>\n",
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"##### Rates by IMD\n",
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"Here we show the rates of consultations for the Pharmacy First Shingles Clinical Pathways by IMD\n",
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"> RATES OF SHINGLES CLINICAL PATHWAY BY IMD"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"shingles_region\"></a>\n",
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"##### Rates by region\n",
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"Here we show the rates of consultations for the Pharmacy First Shingles Clinical Pathways by NHS region\n",
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"> RATES OF SHINGLES CLINICAL PATHWAY BY REGION"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<a id=\"shingles_medication\"></a>\n",
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"##### Rates by medication supply\n",
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"Here we show the percentage of consultations for the Pharmacy First Shingles Clinical Pathways with vs without medication supply.\n",
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"(Could also potentially show details of which medication issued)\n",
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"> BAR PLOT OF PERCENTAGE OF SHINGLES CLINICAL PATHWAY WITH/WITHOUT MEDICATION SUPPLIED"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.13"
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},
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"vscode": {
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"interpreter": {
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"hash": "bcc1f730df8fb5742a3ac26bd3a31839bd02ad4e73a558e52498dfe16975ce60"
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}
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"nbformat": 4,
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"nbformat_minor": 2
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}

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