Merge pull request #34 from nhs-r-community/all-contributors/add-TimT…

…aylor docs: add TimTaylor as a contributor for doc
nhs-r-community · Oct 7, 2024 · 11ec7e3 · 11ec7e3
2 parents 5ebecda + 9b950e4
commit 11ec7e3
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -1,4 +1,22 @@
 {
   "projectName": "NHSRepisodes",
-  "projectOwner": "nhs-r-community"
+  "projectOwner": "nhs-r-community",
+  "files": [
+    "README.md"
+  ],
+  "commitType": "docs",
+  "commitConvention": "angular",
+  "contributorsPerLine": 7,
+  "contributors": [
+    {
+      "login": "TimTaylor",
+      "name": "Tim Taylor",
+      "avatar_url": "https://avatars.githubusercontent.com/u/43499035?v=4",
+      "profile": "https://github.com/TimTaylor",
+      "contributions": [
+        "doc",
+        "test"
+      ]
+    }
+  ]
 }
diff --git a/README.Rmd b/README.Rmd
@@ -19,7 +19,8 @@ knitr::opts_chunk$set(
     collapse = TRUE,
     comment = "#>",
     fig.path = "man/figures/README-",
-    out.width = "100%"
+    out.width = "100%",
+    cache = TRUE
 )
 ```
 
@@ -28,6 +29,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/nhs-r-community/NHSRepisodes/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nhs-r-community/NHSRepisodes/actions/workflows/R-CMD-check.yaml)
+[![All Contributors](https://img.shields.io/github/all-contributors/nhs-r-community/NHSRepisodes?color=ee8449&style=flat-square)](#contributors)
 <!-- badges: end -->
 
 ## Installation instructions

diff --git a/README.md b/README.md
@@ -8,6 +8,8 @@
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/nhs-r-community/NHSRepisodes/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nhs-r-community/NHSRepisodes/actions/workflows/R-CMD-check.yaml)
+[![All
+Contributors](https://img.shields.io/github/all-contributors/nhs-r-community/NHSRepisodes?color=ee8449&style=flat-square)](#contributors)
 <!-- badges: end -->
 
 ## Installation instructions
@@ -57,7 +59,7 @@ mutate(tibble(packages), version = sapply(packages, getNamespaceVersion))
 #>   packages     version   
 #>   <chr>        <chr>     
 #> 1 NHSRepisodes 0.1.0.9000
-#> 2 dplyr        1.1.4.9000
+#> 2 dplyr        1.1.4     
 #> 3 data.table   1.16.0    
 #> 4 ivs          0.2.0
 
@@ -126,18 +128,18 @@ end2 <- start2 + sample(1:100, size = n * 5, replace = TRUE)
 # creates the object big_dat and shows the first 10 rows as a tibble in the console
 (big_dat <- tibble(id = id2, start = start2, end = end2))
 #> # A tibble: 625,000 × 3
-#>       id start      end       
-#>    <int> <date>     <date>    
-#>  1 90983 2020-02-07 2020-03-18
-#>  2 59640 2020-07-05 2020-08-13
-#>  3 29543 2020-04-05 2020-05-28
-#>  4 17962 2020-06-07 2020-07-21
-#>  5 13032 2020-08-25 2020-09-08
-#>  6 94348 2020-05-11 2020-06-07
-#>  7  7770 2020-03-18 2020-04-03
-#>  8  9570 2020-09-25 2020-12-04
-#>  9 86687 2020-11-04 2021-01-09
-#> 10 66213 2020-04-09 2020-04-16
+#>        id start      end       
+#>     <int> <date>     <date>    
+#>  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
@@ -148,7 +150,7 @@ system.time(
         reframe(interval = iv_groups(interval, abutting = FALSE), .by = id)
 )
 #>    user  system elapsed 
-#>  13.870   0.065  13.996
+#>   17.00    0.28   17.30
 ```
 
 If you were not already using it, this is likely the time you would
@@ -175,32 +177,32 @@ fun <- function(s, e) {
 
 system.time(out_dt <- DT[, fun(start, end + 1), by = id])
 #>    user  system elapsed 
-#>  14.972   0.022  14.984
+#>   19.26    0.49   19.77
 ```
 
 ***NHSRepisodes*** solves this with the `merge_episodes()` function:
 
 ``` r
 merge_episodes(big_dat)
-#> # A tibble: 334,767 × 4
+#> # A tibble: 335,828 × 4
 #>       id .interval_number .episode_start .episode_end
 #>    <int>            <int> <date>         <date>      
-#>  1     1                1 2020-04-16     2020-06-23  
-#>  2     2                1 2020-01-12     2020-02-22  
-#>  3     2                2 2020-07-22     2020-08-16  
-#>  4     2                3 2020-09-27     2021-01-11  
-#>  5     3                1 2020-01-06     2020-03-02  
-#>  6     3                2 2020-03-08     2020-03-16  
-#>  7     3                3 2020-06-05     2020-08-26  
-#>  8     4                1 2020-02-05     2020-05-03  
-#>  9     4                2 2020-05-19     2020-09-08  
-#> 10     5                1 2020-01-14     2020-03-13  
-#> # ℹ 334,757 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 
-#>   0.917   0.000   0.335
+#>    0.59    0.11    0.44
 
 # equal output (subject to ordering)
 out <- out |> 
@@ -240,13 +242,12 @@ add_parent_interval(dat)
 #> 7     1 2020-01-01 2020-01-10 2020-01-01    2020-01-10                 1
 #> 8     1 2020-01-11 2020-01-12 2020-01-11    2020-01-12                 2
 ```
+
 ## Contributors
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
-
 <!-- markdownlint-restore -->
 <!-- prettier-ignore-end -->
-
 <!-- ALL-CONTRIBUTORS-LIST:END -->