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Revert "adding hex logo to README and pkgdown"
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@Lextuga007
Lextuga007 authored Dec 5, 2024
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5 changes: 1 addition & 4 deletions README.Rmd
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Expand Up @@ -24,10 +24,7 @@ knitr::opts_chunk$set(
)
```

# NHSRepisodes <img src="https://raw.githubusercontent.com/nhs-r-community/NHSRepisodes/main/inst/images/nhsrepisodeslogo.png" width="120" align = "right" alt = "NHSRepisodeslogo"/>

<a href='https://nhsrcommunity.com/'><img src='https://nhs-r-community.github.io/assets/logo/nhsr-logo.png' width="100"/></a> *This package is part of the NHS-R Community suite of [R packages](https://nhsrcommunity.com/packages.html).*

# NHSRepisodes

<!-- badges: start -->
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
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71 changes: 36 additions & 35 deletions README.md
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@@ -1,11 +1,7 @@

<!-- README.md is generated from README.Rmd. Please edit that file -->

# NHSRepisodes <img src="https://raw.githubusercontent.com/nhs-r-community/NHSRepisodes/main/inst/images/nhsrepisodeslogo.png" width="120" align = "right" alt = "NHSRepisodeslogo"/>

<a href='https://nhsrcommunity.com/'><img src='https://nhs-r-community.github.io/assets/logo/nhsr-logo.png' width="100"/></a>
*This package is part of the NHS-R Community suite of [R
packages](https://nhsrcommunity.com/packages.html).*
# NHSRepisodes

<!-- badges: start -->

Expand Down Expand Up @@ -48,7 +44,6 @@ To expand on issues consider the following small set of episode data:
library(NHSRepisodes)
library(dplyr)
library(ivs)
#> Warning: package 'ivs' was built under R version 4.4.2
library(data.table)

# note - we need functionality introduced in dplyr 1.1.0.
Expand All @@ -65,7 +60,7 @@ mutate(tibble(packages), version = sapply(packages, getNamespaceVersion))
#> <chr> <chr>
#> 1 NHSRepisodes 0.1.0.9000
#> 2 dplyr 1.1.4
#> 3 data.table 1.15.4
#> 3 data.table 1.16.0
#> 4 ivs 0.2.0

# Create a dummy data set give the first and last dates of an episode
Expand Down Expand Up @@ -135,16 +130,16 @@ end2 <- start2 + sample(1:100, size = n * 5, replace = TRUE)
#> # A tibble: 625,000 × 3
#> id start end
#> <int> <date> <date>
#> 1 44036 2020-06-28 2020-09-08
#> 2 118108 2020-08-21 2020-11-25
#> 3 105138 2020-02-18 2020-04-05
#> 4 15354 2020-04-05 2020-05-28
#> 5 100751 2020-01-12 2020-03-05
#> 6 99591 2020-02-05 2020-04-12
#> 7 58097 2020-11-12 2020-12-02
#> 8 37685 2020-06-17 2020-08-19
#> 9 109675 2020-03-05 2020-04-27
#> 10 117425 2020-09-22 2020-11-24
#> 1 47215 2020-12-29 2021-02-16
#> 2 91739 2020-09-16 2020-11-12
#> 3 114791 2020-01-31 2020-02-27
#> 4 83644 2020-08-17 2020-11-04
#> 5 68824 2020-02-14 2020-05-06
#> 6 100194 2020-12-11 2021-03-18
#> 7 3871 2020-06-21 2020-07-06
#> 8 118901 2020-01-09 2020-03-23
#> 9 80676 2020-07-23 2020-08-19
#> 10 84580 2020-07-17 2020-10-07
#> # ℹ 624,990 more rows

# checking the time to run
Expand All @@ -155,7 +150,7 @@ system.time(
reframe(interval = iv_groups(interval, abutting = FALSE), .by = id)
)
#> user system elapsed
#> 34.58 0.47 37.60
#> 17.00 0.28 17.30
```

If you were not already using it, this is likely the time you would
Expand All @@ -182,32 +177,32 @@ fun <- function(s, e) {

system.time(out_dt <- DT[, fun(start, end + 1), by = id])
#> user system elapsed
#> 32.74 0.61 33.84
#> 19.26 0.49 19.77
```

***NHSRepisodes*** solves this with the `merge_episodes()` function:

``` r
merge_episodes(big_dat)
#> # A tibble: 336,162 × 4
#> # A tibble: 335,828 × 4
#> id .interval_number .episode_start .episode_end
#> <int> <int> <date> <date>
#> 1 1 1 2020-01-16 2020-03-26
#> 2 1 2 2020-07-13 2020-09-30
#> 3 1 3 2020-11-18 2020-11-26
#> 4 1 4 2020-12-14 2021-02-20
#> 5 2 1 2020-03-08 2020-04-23
#> 6 2 2 2020-06-06 2020-07-09
#> 7 2 3 2020-09-16 2020-11-03
#> 8 2 4 2020-11-07 2020-11-18
#> 9 2 5 2020-11-19 2021-01-22
#> 10 3 1 2020-01-10 2020-04-19
#> # ℹ 336,152 more rows
#> 1 1 1 2020-01-15 2020-01-27
#> 2 1 2 2020-02-13 2020-11-14
#> 3 1 3 2020-11-15 2021-02-13
#> 4 2 1 2020-01-03 2020-03-25
#> 5 2 2 2020-03-31 2020-06-09
#> 6 2 3 2020-10-31 2020-11-08
#> 7 2 4 2020-12-17 2021-01-23
#> 8 3 1 2020-03-08 2020-03-19
#> 9 3 2 2020-04-13 2020-05-26
#> 10 3 3 2020-11-30 2020-12-01
#> # ℹ 335,818 more rows

# And for comparison with earlier timings
system.time(out <- merge_episodes(big_dat))
#> user system elapsed
#> 0.75 0.00 0.70
#> 0.59 0.11 0.44

# equal output (subject to ordering)
out <- out |>
Expand Down Expand Up @@ -251,13 +246,19 @@ add_parent_interval(dat)
## Contributors

<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->

<!-- prettier-ignore-start -->

<!-- markdownlint-disable -->
<table>
<tbody>
<tr>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/TimTaylor"><img src="https://avatars.githubusercontent.com/u/43499035?v=4?s=100" width="100px;" alt="Tim Taylor"/><br /><sub><b>Tim Taylor</b></sub></a><br /><a href="#doc-TimTaylor" title="Documentation">📖</a> <a href="#test-TimTaylor" title="Tests">⚠️</a> <a href="#code-TimTaylor" title="Code">💻</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://philosopher-analyst.netlify.app/"><img src="https://avatars.githubusercontent.com/u/39963221?v=4?s=100" width="100px;" alt="Zoë Turner"/><br /><sub><b>Zoë Turner</b></sub></a><br /><a href="#doc-Lextuga007" title="Documentation">📖</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://publichealthscotland.scot/"><img src="https://avatars.githubusercontent.com/u/5982260?v=4?s=100" width="100px;" alt="James McMahon"/><br /><sub><b>James McMahon</b></sub></a><br /><a href="#ideas-Moohan" title="Ideas, Planning, & Feedback">🤔</a></td>
</tr>
</tbody>
</table>

<!-- markdownlint-restore -->

<!-- prettier-ignore-end -->

<!-- ALL-CONTRIBUTORS-LIST:END -->

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