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chrismaineychrismainey
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bring up to date from main
Merge branch 'main' into renamelegend # Conflicts: # R/funnel_plot.R
2 parents 9a78b71 + 3ebcb92 commit bcc9426

25 files changed

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‎.Rbuildignore‎

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^dev$
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^codecov\.yml$
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^\.github$
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test_func.R

.github/workflows/check-standard.yaml renamed to .github/workflows/R-CMD-check.yaml

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‎.github/workflows/rhub.yaml‎

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# R-hub's generic GitHub Actions workflow file. It's canonical location is at
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# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
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# You can update this file to a newer version using the rhub2 package:
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#
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# rhub::rhub_setup()
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#
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# It is unlikely that you need to modify this file manually.
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name: R-hub
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run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
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on:
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workflow_dispatch:
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inputs:
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config:
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description: 'A comma separated list of R-hub platforms to use.'
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type: string
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default: 'linux,windows,macos'
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name:
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description: 'Run name. You can leave this empty now.'
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type: string
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id:
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description: 'Unique ID. You can leave this empty now.'
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type: string
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jobs:
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setup:
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runs-on: ubuntu-latest
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outputs:
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containers: ${{ steps.rhub-setup.outputs.containers }}
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platforms: ${{ steps.rhub-setup.outputs.platforms }}
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steps:
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# NO NEED TO CHECKOUT HERE
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- uses: r-hub/actions/setup@v1
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with:
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config: ${{ github.event.inputs.config }}
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id: rhub-setup
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linux-containers:
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needs: setup
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if: ${{ needs.setup.outputs.containers != '[]' }}
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runs-on: ubuntu-latest
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name: ${{ matrix.config.label }}
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strategy:
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fail-fast: false
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matrix:
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config: ${{ fromJson(needs.setup.outputs.containers) }}
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container:
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image: ${{ matrix.config.container }}
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steps:
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- uses: r-hub/actions/checkout@v1
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/setup-deps@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/run-check@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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other-platforms:
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needs: setup
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if: ${{ needs.setup.outputs.platforms != '[]' }}
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.label }}
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strategy:
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fail-fast: false
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matrix:
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config: ${{ fromJson(needs.setup.outputs.platforms) }}
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steps:
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- uses: r-hub/actions/checkout@v1
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- uses: r-hub/actions/setup-r@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/setup-deps@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}
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- uses: r-hub/actions/run-check@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}

‎DESCRIPTION‎

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Package: FunnelPlotR
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Type: Package
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Title: Funnel Plots for Comparing Institutional Performance
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Version: 0.4.9999
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Version: 0.5.0
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Authors@R: c(
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person("Chris", "Mainey", ,"c.mainey1@nhs.net", role= c("aut", "cre"),
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comment = c(ORCID ="0000-0002-3018-6171")
@@ -18,18 +18,19 @@ License: MIT + file LICENSE
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URL: https://nhs-r-community.github.io/FunnelPlotR/, https://github.com/nhs-r-community/FunnelPlotR
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BugReports: https://github.com/nhs-r-community/FunnelPlotR/issues
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Encoding: UTF-8
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Imports: dplyr,
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ggrepel,
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ggplot2,
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scales
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RoxygenNote: 7.2.3
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Imports:
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dplyr,
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ggrepel,
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ggplot2,
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scales,
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rlang
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RoxygenNote: 7.3.1
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Suggests:
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testthat (>= 3.0.0),
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knitr,
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rmarkdown,
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COUNT,
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tidyr,
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covr,
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Cairo
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covr
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VignetteBuilder: knitr
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Config/testthat/edition: 3

‎NAMESPACE‎

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importFrom(ggplot2,theme_minimal)
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importFrom(ggrepel,geom_label_repel)
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importFrom(ggrepel,geom_text_repel)
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importFrom(rlang,.data)
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importFrom(scales,comma)
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importFrom(stats,aggregate)
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importFrom(stats,na.omit)

‎NEWS.md‎

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# FunnelPlotR 0.5.0
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- Breaking change
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* Tidyeval approach added, with function now taking the data argument first, allowing piping, and allows unquoted column names to fit with tidyverse / dplyr style approach.
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- Changes
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* Added a `max.overlaps` argument to allow the user to vary this in cases where labels overlap is unhelpful.
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* Changed control limit options to allow both adjusted and unadjusted to be turned off, without turning the other on.
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* Updated README, help files and vignette to use tidyeval approach.
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# FunnelPlotR 0.4.2
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- Changes:
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* Handling of expected values in SHMI calculation was adjusted to allow rounding to two decimal places to match NHSD publication, and as requested by HED Team. Now controlled with additional argument: `SHMI_rounding` = TRUE/FALSE

‎R/build_limits_lookup.R‎

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#' Function to build funnel limits
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#' @description Internal function for funnel plot to build the control limits prior to plotting.
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#' @param min_preds Minimum predicted value for range of x-axis
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#' @param max_preds Maximum predicted value for range of x-axis
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#' @param min_ratio Minimum ratio value for range of y-axis
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#' @param max_ratio Maximum ratio value for range of y-axis
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#' @param draw_unadjusted TRUE/FALSE Draw Poisson distribution limits?
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#' @param min_x Minimum predicted value for range of x-axis
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#' @param max_x Maximum predicted value for range of x-axis
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#' @param min_y Minimum ratio value for range of y-axis
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#' @param max_y Maximum ratio value for range of y-axis
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#' @param draw_adjusted TRUE/FALSE Use overdispersion adjustment
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#' @param tau2 If using draw_adjusted, what is the tau2 ("between" standard error) to use?
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#' @param data_type SR, PR or RC. Used to set target reference
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build_limits_lookup<-function(min_x, max_x, min_y, max_y
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, draw_adjusted, tau2, data_type, sr_method
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, target, multiplier, denominators){
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# general limits + tau2 limits table
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set.seed(1)
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if(data_type=="SR"){
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number.seq <- seq(1.1, as.numeric(max_x), length.out = 1000)
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} else {

‎R/draw_plot.R‎

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draw_plot<-function(mod_plot_agg, limits, x_label, y_label, title, label, multiplier,
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draw_unadjusted, draw_adjusted, target, min_y, max_y, min_x, max_x
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, data_type, sr_method, theme, plot_cols){
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, data_type, sr_method, theme, plot_cols, max.overlaps){
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# Bind variable for NSE
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numerator <- denominator <- number.seq <- ll95 <- ul95 <- ll998 <- ul998 <- odll95 <- odul95 <-
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angle = 0
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), override.aes = list(linetype = c(2,1)) ))
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}
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if (draw_unadjusted == FALSE & draw_adjusted == FALSE){
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funnel_p
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}
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}
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# Apply plot scaling
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# Label points
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if(!is.na(label)){
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if(label=="highlight"){
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funnel_p <- funnel_p +
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geom_label_repel(aes(label = ifelse(highlight == 1,
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as.character(group), NA))
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, size=2.5, point.padding=0, direction = "both", force = 2
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, min.segment.length=0, na.rm=TRUE, max.overlaps = max.overlaps)
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}
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if(draw_adjusted == FALSE & draw_unadjusted == FALSE){
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funnel_p
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}
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if(label=="outlier"){
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funnel_p <- funnel_p +
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geom_label_repel(aes(label = ifelse(outlier == 1,
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as.character(group), NA))
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, size=2.5, point.padding=0, direction = "both", force = 2
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, min.segment.length=0, na.rm=TRUE)
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, min.segment.length=0, na.rm=TRUE, max.overlaps = max.overlaps)
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}
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if(label=="outlier_lower"){
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geom_label_repel(aes(label = ifelse(outlier == 1 & rr < 1,
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as.character(group), NA))
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, size=2.5,point.padding=0, direction = "both", force = 2
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, min.segment.length=0, na.rm=TRUE)
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, min.segment.length=, na.rm=TRUE, max.overlaps = max.overlaps)
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}
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if(label=="outlier_upper"){
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geom_label_repel(aes(label = ifelse(outlier == 1 & rr > 1,
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as.character(group), NA))
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, size=2.5, point.padding=0, direction = "both", force = 2
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, min.segment.length=0, na.rm=TRUE)
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}
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if(label=="highlight"){
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funnel_p <- funnel_p +
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geom_label_repel(aes(label = ifelse(highlight == 1,
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as.character(group), NA))
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, size=2.5, point.padding=0, direction = "both", force = 2
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, min.segment.length=0, na.rm=TRUE)
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, min.segment.length=1, na.rm=TRUE, max.overlaps = max.overlaps)
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}
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if(label=="both"){
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funnel_p <- funnel_p +
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geom_label_repel(aes(label = ifelse((highlight == 1 | outlier == 1) ,
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, size=2.5, point.padding=0, direction = "both", force = 2
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, min.segment.length=0, na.rm=TRUE)
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, min.segment.length=1, na.rm=TRUE, max.overlaps = max.overlaps)
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}
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geom_label_repel(aes(label = ifelse((highlight == 1 | (outlier == 1& rr < 1)) ,
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as.character(group), NA))
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, size=2.5, point.padding=0, direction = "both", force = 2
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, min.segment.length=0, na.rm=TRUE)
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, min.segment.length=1, na.rm=TRUE, max.overlaps = max.overlaps)
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}
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geom_label_repel(aes(label = ifelse((highlight == 1 | (outlier == 1 & rr > 1)) ,
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as.character(group), NA))
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, size=2.5, point.padding=0, direction = "both", force = 2
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, min.segment.length=0, na.rm=TRUE)
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, min.segment.length=1, na.rm=TRUE, max.overlaps = max.overlaps)
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}
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}

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