resolved URLS from win-builder notes and removed outdated comment in …

…readme

R/funnel_plot.R

@@ -68,10 +68,10 @@
 #'    The plot colours deliberately avoid red-amber-green colouring, but you could extract this from the ggplot object and change manually if you like.
 #'    Future versions of `funnelplotr` may allow users to change this.
 #'
-#' @references DerSimonian & Laird (1986)  Meta-analysis in clinical trials. \url{https://doi.org/10.1016/0197-2456(86)90046-2/}
+#' @references DerSimonian & Laird (1986)  Meta-analysis in clinical trials. \url{https://doi.org/10.1016/0197-2456(86)90046-2}
 #' @references Spiegelhalter (2005) Funnel plots for comparing institutional performance  \url{https://doi.org/10.1002/sim.1970}
 #' @references Spiegelhalter et al. (2012) Statistical methods for healthcare regulation: rating, screening and surveillance: \url{https://doi.org/10.1111/j.1467-985X.2011.01010.x}
-#' @references NHS Digital (2020) SHMI Methodology v .134 \url{https://digital.nhs.uk/data-and-information/publications/clinical-indicators/shmi/current/}
+#' @references NHS Digital (2020) SHMI Methodology v .134 \url{https://digital.nhs.uk/data-and-information/publications/ci-hub/summary-hospital-level-mortality-indicator-shmi}
 #'
 #' @examples
 #' # We will use the 'medpar' dataset from the 'COUNT' package.

README.Rmd

@@ -27,12 +27,11 @@ knitr::opts_chunk$set(
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active/)
 [![CRAN version](http://www.r-pkg.org/badges/version/FunnelPlotR)](https://cran.r-project.org/package=FunnelPlotR)
 ![](http://cranlogs.r-pkg.org/badges/grand-total/FunnelPlotR/)
-[![Codecov test coverage](https://codecov.io/gh/nhs-r-community/FunnelPlotR/branch/main/graph/badge.svg)](https://codecov.io/gh/nhs-r-community/FunnelPlotR?branch=main/)
+[![Codecov test coverage](https://codecov.io/gh/nhs-r-community/FunnelPlotR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/nhs-r-community/FunnelPlotR?branch=main/)
 [![R-CMD-check](https://github.com/nhs-r-community/FunnelPlotR/workflows/R-CMD-check/badge.svg)](https://github.com/nhs-r-community/FunnelPlotR/actions/)
 <!-- badges: end -->
 
 ## Funnel Plots
-__This package is the newer version of the older `CMFunnels` package. Development work will focus on this package from now on.__
 
 This is an implementation of the funnel plot processes, and overdispersion methods described in:<br>
 [Statistical methods for healthcare regulation: rating, screening and surveillance. Spiegelhalter et al (2012)](https://doi.org/10.1111/j.1467-985X.2011.01010.x)<br>

README.md

@@ -10,15 +10,12 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re
 version](http://www.r-pkg.org/badges/version/FunnelPlotR)](https://cran.r-project.org/package=FunnelPlotR)
 ![](http://cranlogs.r-pkg.org/badges/grand-total/FunnelPlotR/)
 [![Codecov test
-coverage](https://codecov.io/gh/nhs-r-community/FunnelPlotR/branch/main/graph/badge.svg)](https://codecov.io/gh/nhs-r-community/FunnelPlotR?branch=main/)
+coverage](https://codecov.io/gh/nhs-r-community/FunnelPlotR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/nhs-r-community/FunnelPlotR?branch=main/)
 [![R-CMD-check](https://github.com/nhs-r-community/FunnelPlotR/workflows/R-CMD-check/badge.svg)](https://github.com/nhs-r-community/FunnelPlotR/actions/)
 <!-- badges: end -->
 
 ## Funnel Plots
 
-**This package is the newer version of the older `CMFunnels` package.
-Development work will focus on this package from now on.**
-
 This is an implementation of the funnel plot processes, and
 overdispersion methods described in:<br> [Statistical methods for
 healthcare regulation: rating, screening and surveillance. Spiegelhalter
@@ -103,10 +100,6 @@ summary(mod)
 #> glm(formula = los ~ hmo + died + age80 + factor(type), family = "poisson", 
 #>     data = medpar)
 #> 
-#> Deviance Residuals: 
-#>     Min       1Q   Median       3Q      Max  
-#> -5.7309  -1.9554  -0.5529   0.9717  14.5487  
-#> 
 #> Coefficients:
 #>               Estimate Std. Error z value Pr(>|z|)    
 #> (Intercept)    2.26875    0.01246 182.011  < 2e-16 ***

vignettes/references.bib

@@ -100,7 +100,7 @@ @Article{mohammedBristolShipmanClinical2001
   abstract = {During the past century, manufacturing industry has achieved great success in improving the quality of its products. An essential factor in this success has been the use of Walter A Shewhart's pioneering work in the economic control of variation, which culminated in the development of a simple yet powerful graphical method known as the control chart. This chart classifies variation as having a common cause or special cause and thus guides the user to the most appropriate action to effect improvement. Using six case studies, including the excess deaths after paediatric cardiac surgery seen in Bristol, UK, and the activities of general practitioner turned murderer Harold Shipman, we show a central role for Shewhart's approach in turning the rhetoric of clinical governance into a reality.},
   number = {9254},
   journal = {The Lancet},
-  doi = {10/cqjskf},
+  doi = {10.1016/S0140-6736(00)04019-8},
   author = {Mohammed A Mohammed and KK Cheng and Andrew Rouse and Tom Marshall},
   month = {feb},
   year = {2001},