Merge pull request #87 from nhs-r-community/add-getting-started

Add getting started

R/LOS_model.R

@@ -16,7 +16,7 @@
 #' \item{Death}{Binary for death status: 0 = survived, 1= died in hospital}
 #' }
 #'
-#' @source Generated by Chris Mainey \email{[email protected]}, Feb-2019
+#' @source Generated by Chris Mainey, Feb-2019
 #'
 #' @usage data(LOS_model)
 #'

R/ae_attendances.R

@@ -4,8 +4,10 @@
 #' in England for the years 2016/17 through 2018/19 (Apr-Mar). The data has been
 #' tidied to be easily usable within the tidyverse of packages.
 #'
-#' Data sourced from \href{https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/}{NHS England Statistical Work Areas}
-#' which is available under the \href{https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/}{Open Government Licence v3.0}
+#' Data sourced from
+#' \href{https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/}{NHS England Statistical Work Areas}
+#' which is available under the
+#' \href{https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/}{Open Government Licence v3.0}
 #'
 #' @docType data
 #'
@@ -14,12 +16,18 @@
 #' @format Tibble with six columns
 #' \describe{
 #' \item{period}{The month that this data relates to}
-#' \item{org_code}{The \href{https://digital.nhs.uk/services/organisation-data-service}{ODS} code for this provider}
-#' \item{type}{The \href{https://web.archive.org/web/20200128111444/https://www.datadictionary.nhs.uk/data_dictionary/attributes/a/acc/accident_and_emergency_department_type_de.asp}{department type}.
+#' \item{org_code}{The
+#' \href{https://digital.nhs.uk/services/organisation-data-service}{ODS}
+#' code for this provider}
+#' \item{type}{The
+#' \href{https://web.archive.org/web/20200128111444/https://www.datadictionary.nhs.uk/data_dictionary/attributes/a/acc/accident_and_emergency_department_type_de.asp}{department type}.
 #'             either 1, 2 or other}
-#' \item{attendances}{the number of patients who attended this department in this month}
-#' \item{breaches}{the number of patients who breaches the 4 hour target in this month}
-#' \item{admissions}{the number of patients admitted from A&E to the hospital in this month}
+#' \item{attendances}{the number of patients who attended this department in
+#' this month}
+#' \item{breaches}{the number of patients who breaches the 4 hour target in
+#' this month}
+#' \item{admissions}{the number of patients admitted from A&E to the hospital
+#' in this month}
 #' }
 #'
 #' @source \href{https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/}{NHS England Statistical Work Areas}
@@ -28,6 +36,7 @@
 #'
 #' @examples
 #' data(ae_attendances)
+#'
 #' library(dplyr)
 #' library(ggplot2)
 #' library(scales)

R/covid19.R

@@ -42,15 +42,21 @@
 #' library(scales)
 #'
 #' # Create a plot of the performance for England over time
-#' covid19 %>%
+#' covid19 |>
 #'   filter(countries_and_territories ==
-#'     c("United_Kingdom", "Italy", "France", "Germany", "Spain")) %>%
-#'   ggplot(aes(x = date_reported, y = cases, col = countries_and_territories)) +
+#'     c("United_Kingdom", "Italy", "France", "Germany", "Spain")) |>
+#'   ggplot(aes(
+#'     x = date_reported,
+#'     y = cases,
+#'     col = countries_and_territories
+#'   )) +
 #'   geom_line() +
 #'   scale_color_discrete("Country") +
 #'   scale_y_continuous(labels = comma) +
 #'   labs(
-#'     y = "Cases", x = "Date", title = "Covid-19 cases for selected countries",
+#'     y = "Cases",
+#'     x = "Date",
+#'     title = "Covid-19 cases for selected countries",
 #'     alt = "A plot of covid-19 cases in France, Germany, Italy, Spain & the UK"
 #'   ) +
 #'   theme_minimal()

R/ons_mortality.R

@@ -1,10 +1,14 @@
 #' Deaths registered weekly in England and Wales, provisional
 #'
-#' Provisional counts of the number of deaths registered in England and Wales, by age, sex and region, in the latest weeks for which data are available.
+#' Provisional counts of the number of deaths registered in England and Wales,
+#' by age, sex and region, from week commencing 8th January 2010 to
+#' 3rd April 202.
 #'
 #' Source and licence acknowledgement
-#' This data has been made available through Office of National Statistics under the Open Government
-#' Licence \url{http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/}
+#'
+#' This data has been made available through Office of National Statistics under
+#' the Open Government Licence
+#' \url{http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/}
 #'
 #'
 #' @docType data
@@ -13,14 +17,19 @@
 #'
 #' @format Data frame with five columns
 #' \describe{
-#' \item{category_1}{character, containing the names of the groups for counts, for example "Total deaths", "all ages".}
-#' \item{category_2}{character, subcategory of names of groups where necessary, for example details of region: "East", details of age bands "15-44".}
-#' \item{counts}{numeric, numbers of deaths in whole numbers and average numbers with decimal points. To retain the integrity of the format this column data is left as character.}
+#' \item{category_1}{character, containing the names of the groups for counts,
+#' for example "Total deaths", "all ages".}
+#' \item{category_2}{character, subcategory of names of groups where necessary,
+#' for example details of region: "East", details of age bands "15-44".}
+#' \item{counts}{numeric, numbers of deaths in whole numbers and average numbers
+#' with decimal points. To retain the integrity of the format this column data
+#' is left as character.}
 #' \item{date}{date, format is yyyy-mm-dd; all dates are a Friday.}
 #' \item{week_no}{integer, each week in a year is numbered sequentially.}
 #' }
 #'
-#' @source Collected by Zoë Turner \email{[email protected]}, Apr-2020 from \url{https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/datasets/weeklyprovisionalfiguresondeathsregisteredinenglandandwales}
+#' @source Collected by Zoë Turner, Apr-2020 from
+#' \url{https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/datasets/weeklyprovisionalfiguresondeathsregisteredinenglandandwales}
 #'
 #' @usage data(ons_mortality)
 #'

R/stranded_patient_model.R

@@ -1,6 +1,7 @@
 #' Stranded Patient (Patients flagged as having a greater than 7 day LOS) Model
 #'
-#' This model is to be used as a machine learning classification model, for supervised learning. The binary outcome is stranded vs not stranded patients.
+#' This model is to be used as a machine learning classification model, for
+#' supervised learning. The binary outcome is stranded vs not stranded patients.
 #'
 #'
 #' @docType data
@@ -12,23 +13,28 @@
 #' \item{stranded.label}{Outcome variable - whether the patient is stranded or not}
 #' \item{age}{Patient age on admission}
 #' \item{care.home.referral}{Whether than have been referred from a care home}
-#' \item{medicallysafe}{Medically safe for discharge - means the patient is assessed as safe, but has not been discharged yet}
-#' \item{hcop}{Indicates whether they have been triaged from a Health Care for Older People specialty}
-#' \item{mental_health_care}{Flag to indicate whether they need mental health support and care}
+#' \item{medicallysafe}{Medically safe for discharge - means the patient is
+#' assessed as safe, but has not been discharged yet}
+#' \item{hcop}{Indicates whether they have been triaged from a Health Care for
+#' Older People specialty}
+#' \item{mental_health_care}{Flag to indicate whether they need mental health
+#' support and care}
 #' \item{periods_of_previous_care}{Count of the number of previous spells of care}
 #' \item{admit_date}{Date they were admitted to hospital}
-#' \item{frailty_index}{An initial index assessment to say if the patient is frail or not. This is needed for alignment of service provision.}
+#' \item{frailty_index}{An initial index assessment to say if the patient is
+#' frail or not. This is needed for alignment of service provision.}
 #' }
 #'
 #' @source Synthetically generated by Gary Hutson, Mar-2021.
 #'
 #' @usage data(stranded_data)
 #'
 #' @examples
-#' library(magrittr)
 #' library(dplyr)
-#' data("stranded_data")
-#' stranded_data %>%
+#'
+#' data(stranded_data)
+#'
+#' stranded_data |>
 #'   glimpse()
 #'
 "stranded_data"

R/synthetic_news_data.R

@@ -1,7 +1,8 @@
 #' Synthetic National Early Warning Scores Data
 #'
 #' Synthetic NEWS data to show as the results of the NHSR_synpop package.
-#' These datasets have been synthetically generated by this package to be utilised in the NHSRDatasets package.
+#' These datasets have been synthetically generated by this package to be
+#' utilised in the NHSRDatasets package.
 #'
 #' @docType data
 #'
@@ -28,9 +29,11 @@
 #' @usage data(synthetic_news_data)
 #'
 #' @examples
-#' library(magrittr)
+#'
 #' library(dplyr)
+#'
 #' data("synthetic_news_data")
-#' synthetic_news_data %>%
+#'
+#' synthetic_news_data |>
 #'   glimpse()
 "synthetic_news_data"

README.Rmd

@@ -11,10 +11,10 @@ knitr::opts_chunk$set(
 )
 ```
 
-# NHS-R Community Datasets <a href='https://nhsrcommunity.com/'><img src='https://nhs-r-community.github.io/assets/logo/nhsr-logo.png' align="right" height="60" /></a>
+# NHS-R Community Datasets <a href='https://nhsrcommunity.com/'><img src='https://nhs-r-community.github.io/assets/logo/nhsr-logo.png' align="right" height="60" style="float:right; height:200px;"/></a>
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-34-orange.svg?style=flat-square)](#contributors-)
+[![All Contributors](https://img.shields.io/github/all-contributors/projectOwner/projectName?color=ee8449&style=flat-square)](#contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 <!-- badges: start -->
@@ -50,8 +50,8 @@ To install the development version from [GitHub](https://github.com/) with:
 remotes::install_github("nhs-r-community/NHSRdatasets")
 ```
 
-Once installed go to the Getting Started article from the [website](https://nhs-r-community.github.io/NHSRdatasets) and the same link can 
-be found on the top right of the GitHub Repository.
+Once installed go to the Get Started article from the [website](https://nhs-r-community.github.io/NHSRdatasets) (the same link can 
+be found on the top right of the GitHub Repository).
 
 ## Datasets available
 

README.md

@@ -1,5 +1,11 @@
 
-# NHS-R Community Datasets <a href='https://nhsrcommunity.com/'><img src='https://nhs-r-community.github.io/assets/logo/nhsr-logo.png' align="right" height="80" /></a>
+# NHS-R Community Datasets <a href='https://nhsrcommunity.com/'><img src='https://nhs-r-community.github.io/assets/logo/nhsr-logo.png' align="right" height="60" style="float:right; height:200px;"/></a>
+
+<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
+
+[![All
+Contributors](https://img.shields.io/github/all-contributors/projectOwner/projectName?color=ee8449&style=flat-square)](#contributors)
+<!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 <!-- badges: start -->