Skip to content

Commit

Permalink
Pre-computed vignette https://ropensci.org/blog/2019/12/08/precompute…
Browse files Browse the repository at this point in the history 
…-vignettes/
  • Loading branch information
@Lextuga007
Lextuga007 committed Mar 20, 2024
1 parent b646b7c commit 1075222
Show file tree
Hide file tree
Showing 7 changed files with 318 additions and 29 deletions.
170 changes: 150 additions & 20 deletions vignettes/NHSRpopulation.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,23 +8,15 @@ vignette: >
%\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
echo = TRUE,
eval = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```


### Indices of Multiple Deprivation (IMD)

To get the IMD scores (raw scores and ranked deciles) for a dataset run the
following code to generate some random example postcodes:

```{r, eval=TRUE}

```r
library(tibble)
library(NHSRpopulation)

Expand All @@ -35,11 +27,18 @@ tibble_postcodes <- postcodes |>
dplyr::rename(postcode = value)

tibble_postcodes
#> # A tibble: 3 × 1
#> postcode
#> <chr>
#> 1 HD1 2UT
#> 2 HD1 2UU
#> 3 HD1 2UV
```

Then, using the `get_data()` function for a vector:

```{r,}

```r
# Execution halted
NHSRpopulation::get_data(postcodes) |>
dplyr::select(
Expand All @@ -48,18 +47,48 @@ NHSRpopulation::get_data(postcodes) |>
result_type,
lsoa_code
)
#> ℹ The following postcodes are terminated:
#> HD1 2UT
#> and have been replaced with these current postcodes:
#> HD1 2RD
#> ℹ The following postcodes are invalid:
#> HD1 2UV
#> and have been replaced with these nearby postcodes:
#> HD1 2UD
#> # A tibble: 3 × 4
#> postcode new_postcode result_type lsoa_code
#> <chr> <chr> <chr> <chr>
#> 1 HD1 2UT HD1 2RD terminated E01011107
#> 2 HD1 2UU HD1 2UU valid E01011229
#> 3 HD1 2UV HD1 2UD autocompleted E01011229
```

Or with a data frame:

```{r}

```r
NHSRpopulation::get_data(tibble_postcodes) |>
dplyr::select(
postcode,
new_postcode,
result_type,
lsoa_code
)
#> ℹ The following postcodes are terminated:
#> HD1 2UT
#> and have been replaced with these current postcodes:
#> HD1 2RD
#> ℹ The following postcodes are invalid:
#> HD1 2UV
#> and have been replaced with these nearby postcodes:
#> HD1 2UD
#> Joining with `by = join_by(postcode)`
#> # A tibble: 3 × 4
#> postcode new_postcode result_type lsoa_code
#> <chr> <chr> <chr> <chr>
#> 1 HD1 2UT HD1 2RD terminated E01011107
#> 2 HD1 2UU HD1 2UU valid E01011229
#> 3 HD1 2UV HD1 2UD autocompleted E01011229
```

Note that this function uses the {NHSRpostcodetools} package to offer the
Expand All @@ -69,20 +98,35 @@ the original `postcode` column.
Switching off this automatic fix can be done with the code and will accept both
vectors and data frames:

```{r}

```r
NHSRpopulation::get_data(tibble_postcodes, fix_invalid = FALSE) |>
dplyr::select(
postcode,
new_postcode,
result_type,
lsoa_code
)
#> ℹ The following postcodes are invalid:
#> HD1 2UT
#> but have not been successfully replaced with valid codes.
#> The following postcodes are invalid:
#> HD1 2UV
#> but have not been successfully replaced with valid codes.
#> Joining with `by = join_by(postcode)`
#> # A tibble: 3 × 4
#> postcode new_postcode result_type lsoa_code
#> <chr> <chr> <chr> <chr>
#> 1 HD1 2UT <NA> <NA> <NA>
#> 2 HD1 2UU HD1 2UU valid E01011229
#> 3 HD1 2UV <NA> <NA> <NA>
```

# Index of Multiple Deprivation


```{r, eval=TRUE}

```r
# Note that the third LSOA in this list is incorrect on purpose
imd <- c("E01011107", "E01011229", "E01002")

Expand All @@ -91,18 +135,31 @@ tibble_imd <- imd |>
dplyr::rename(lsoa11 = value)

tibble_imd
#> # A tibble: 3 × 1
#> lsoa11
#> <chr>
#> 1 E01011107
#> 2 E01011229
#> 3 E01002
```

Using the same function but with a parameter/argument to return IMD data:

```{r}

```r
NHSRpopulation::get_data(tibble_imd, url_type = "imd") |>
dplyr::select(
lsoa11,
imd_rank,
imd_decile,
imd_score
)
#> # A tibble: 3 × 4
#> lsoa11 imd_rank imd_decile imd_score
#> <chr> <int> <int> <dbl>
#> 1 E01011107 2928 1 45.6
#> 2 E01011229 9558 3 27.0
#> 3 E01002 NA NA NA
```

Data can be either vectors or data frames.
Expand All @@ -116,39 +173,112 @@ Where data frames are used the expectation of the functions is that postcodes
will be in a column called `postcode` and IMD will be from `lsoa11`, however,
this can be overwritten:

```{r}

```r
# Create datasets
pcs_tb <- dplyr::tibble(
pcs = postcodes
)

pcs_tb
#> # A tibble: 3 × 1
#> pcs
#> <chr>
#> 1 HD1 2UT
#> 2 HD1 2UU
#> 3 HD1 2UV

lsoa_tb <- dplyr::tibble(
lower_soa = imd
)

lsoa_tb
#> # A tibble: 3 × 1
#> lower_soa
#> <chr>
#> 1 E01011107
#> 2 E01011229
#> 3 E01002
```

The argument/parameter `column = ` can be used to set the column name:

```{r}

```r
NHSRpopulation::get_data(pcs_tb,
column = "pcs"
)
#> ℹ The following postcodes are terminated:
#> HD1 2UT
#> and have been replaced with these current postcodes:
#> HD1 2RD
#> ℹ The following postcodes are invalid:
#> HD1 2UV
#> and have been replaced with these nearby postcodes:
#> HD1 2UD
#> Joining with `by = join_by(pcs)`
#> # A tibble: 3 × 40
#> pcs new_postcode result_type quality eastings northings country nhs_ha longitude latitude european_electoral_r…¹
#> <chr> <chr> <chr> <int> <int> <int> <chr> <chr> <dbl> <dbl> <chr>
#> 1 HD1 2UT HD1 2RD terminated 1 414639 416430 England Yorkshire and the … -1.78 53.6 Yorkshire and The Hum…
#> 2 HD1 2UU HD1 2UU valid 1 414433 416422 England Yorkshire and the … -1.78 53.6 Yorkshire and The Hum…
#> 3 HD1 2UV HD1 2UD autocompleted 1 414371 416317 England Yorkshire and the … -1.78 53.6 Yorkshire and The Hum…
#> # ℹ abbreviated name: ¹​european_electoral_region
#> # ℹ 29 more variables: primary_care_trust <chr>, region <chr>, lsoa <chr>, msoa <chr>, incode <chr>, outcode <chr>,
#> # parliamentary_constituency <chr>, parliamentary_constituency_2024 <chr>, admin_district <chr>, parish <chr>,
#> # date_of_introduction <chr>, admin_ward <chr>, ccg <chr>, nuts <chr>, pfa <chr>, admin_district_code <chr>,
#> # admin_county_code <chr>, admin_ward_code <chr>, parish_code <chr>, parliamentary_constituency_code <chr>,
#> # parliamentary_constituency_2024_code <chr>, ccg_code <chr>, ccg_id_code <chr>, ced_code <chr>, nuts_code <chr>, lsoa_code <chr>,
#> # msoa_code <chr>, lau2_code <chr>, pfa_code <chr>
```

```{r}

```r
NHSRpopulation::get_data(lsoa_tb,
column = "lower_soa"
)
#> # A tibble: 3 × 66
#> lower_soa fid lsoa11nm lsoa11nmw st_areasha st_lengths imd_rank imd_decile lsoa01nm la_dcd la_dnm imd_score imd_rank0 imd_dec0
#> <chr> <int> <chr> <chr> <dbl> <dbl> <int> <int> <chr> <chr> <chr> <dbl> <int> <int>
#> 1 E01011107 11200 Kirklees 0… Kirklees… 1921709. 7525. 2928 1 Kirklee… E0800… Kirkl… 45.6 2928 1
#> 2 E01011229 11707 Kirklees 0… Kirklees… 833130. 7023. 9558 3 Kirklee… E0800… Kirkl… 27.0 9558 3
#> 3 E01002 NA <NA> <NA> NA NA NA NA <NA> <NA> <NA> NA NA NA
#> # ℹ 52 more variables: inc_score <dbl>, inc_rank <int>, inc_dec <int>, emp_score <dbl>, emp_rank <int>, emp_dec <int>,
#> # edu_score <dbl>, edu_rank <int>, edu_dec <int>, hdd_score <dbl>, hdd_rank <int>, hdd_dec <int>, cri_score <dbl>, cri_rank <int>,
#> # cri_dec <int>, bhs_score <dbl>, bhs_rank <int>, bhs_dec <int>, env_score <dbl>, env_rank <int>, env_dec <int>, idc_score <dbl>,
#> # idc_rank <int>, idc_dec <int>, ido_score <dbl>, ido_rank <int>, ido_dec <int>, cyp_score <dbl>, cyp_rank <int>, cyp_dec <int>,
#> # as_score <dbl>, as_rank <int>, as_dec <int>, gb_score <dbl>, gb_rank <int>, gb_dec <int>, wb_score <dbl>, wb_rank <int>,
#> # wb_dec <int>, ind_score <dbl>, ind_rank <int>, ind_dec <int>, out_score <dbl>, out_rank <int>, out_dec <int>, tot_pop <int>,
#> # dep_chi <int>, pop16_59 <int>, pop60 <int>, work_pop <dbl>, shape_area <dbl>, shape_length <dbl>
```

```{r}

```r
NHSRpopulation::get_data(pcs_tb,
# url_type is set to postcodes as default
column = "pcs"
)
#> ℹ The following postcodes are terminated:
#> HD1 2UT
#> and have been replaced with these current postcodes:
#> HD1 2RD
#> ℹ The following postcodes are invalid:
#> HD1 2UV
#> and have been replaced with these nearby postcodes:
#> HD1 2UD
#> Joining with `by = join_by(pcs)`
#> # A tibble: 3 × 40
#> pcs new_postcode result_type quality eastings northings country nhs_ha longitude latitude european_electoral_r…¹
#> <chr> <chr> <chr> <int> <int> <int> <chr> <chr> <dbl> <dbl> <chr>
#> 1 HD1 2UT HD1 2RD terminated 1 414639 416430 England Yorkshire and the … -1.78 53.6 Yorkshire and The Hum…
#> 2 HD1 2UU HD1 2UU valid 1 414433 416422 England Yorkshire and the … -1.78 53.6 Yorkshire and The Hum…
#> 3 HD1 2UV HD1 2UD autocompleted 1 414371 416317 England Yorkshire and the … -1.78 53.6 Yorkshire and The Hum…
#> # ℹ abbreviated name: ¹​european_electoral_region
#> # ℹ 29 more variables: primary_care_trust <chr>, region <chr>, lsoa <chr>, msoa <chr>, incode <chr>, outcode <chr>,
#> # parliamentary_constituency <chr>, parliamentary_constituency_2024 <chr>, admin_district <chr>, parish <chr>,
#> # date_of_introduction <chr>, admin_ward <chr>, ccg <chr>, nuts <chr>, pfa <chr>, admin_district_code <chr>,
#> # admin_county_code <chr>, admin_ward_code <chr>, parish_code <chr>, parliamentary_constituency_code <chr>,
#> # parliamentary_constituency_2024_code <chr>, ccg_code <chr>, ccg_id_code <chr>, ced_code <chr>, nuts_code <chr>, lsoa_code <chr>,
#> # msoa_code <chr>, lau2_code <chr>, pfa_code <chr>
```

Loading

0 comments on commit 1075222

Please sign in to comment.