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Merge pull request #43 from nhs-r-community/41-link-apis
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Changed columns to search for the name and updated vignette
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@Lextuga007
Lextuga007 committed Mar 20, 2024
2 parents b263dfa + 173c3b3 commit 2148338
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5 changes: 4 additions & 1 deletion R/get_data.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,10 @@ get_data <- function(data,
req = req
)

data_out
pc_data |>
dplyr::left_join(data_out,
dplyr::join_by(lsoa_code == lsoa11cd))

} else if (exists("pc_data") && url_type == "postcode") {
pc_data
} else {
Expand Down
138 changes: 96 additions & 42 deletions vignettes/NHSRpopulation.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,12 +55,9 @@ NHSRpopulation::get_data(postcodes) |>
#> 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
#> Error in `dplyr::select()`:
#> ! Can't select columns that don't exist.
#> ✖ Column `postcode` doesn't exist.
```

Or with a data frame:
Expand Down Expand Up @@ -164,15 +161,16 @@ NHSRpopulation::get_data(tibble_imd, url_type = "imd") |>

Data can be either vectors or data frames.

No corrections are made to incorrect LSOA codes and the current join to the API
is on `lsoa11` data.
No corrections are made to incorrect LSOA codes.

# Column names

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:

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


```r
# Create datasets
Expand All @@ -188,6 +186,34 @@ pcs_tb
#> 2 HD1 2UU
#> 3 HD1 2UV

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 primary_care_trust region lsoa msoa incode
#> <chr> <chr> <chr> <int> <int> <int> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 HD1 2UT HD1 2RD terminated 1 414639 416430 England Yorkshir… -1.78 53.6 Yorkshire and The Hum… Kirklees Yorks… Kirk… Kirk… 2RD
#> 2 HD1 2UU HD1 2UU valid 1 414433 416422 England Yorkshir… -1.78 53.6 Yorkshire and The Hum… Kirklees Yorks… Kirk… Kirk… 2UU
#> 3 HD1 2UV HD1 2UD autocompleted 1 414371 416317 England Yorkshir… -1.78 53.6 Yorkshire and The Hum… Kirklees Yorks… Kirk… Kirk… 2UD
#> # ℹ abbreviated name: ¹​european_electoral_region
#> # ℹ 24 more variables: 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

lsoa_tb <- dplyr::tibble(
lower_soa = imd
)
Expand All @@ -199,15 +225,34 @@ lsoa_tb
#> 1 E01011107
#> 2 E01011229
#> 3 E01002

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 inc_score inc_rank inc_dec emp_score
#> <chr> <int> <chr> <chr> <dbl> <dbl> <int> <int> <chr> <chr> <chr> <dbl> <int> <int> <dbl> <int> <int> <dbl>
#> 1 E01011107 11200 Kirklees… Kirklees… 1921709. 7525. 2928 1 Kirklee… E0800… Kirkl… 45.6 2928 1 0.256 3753 2 0.176
#> 2 E01011229 11707 Kirklees… Kirklees… 833130. 7023. 9558 3 Kirklee… E0800… Kirkl… 27.0 9558 3 0.092 17587 6 0.068
#> 3 E01002 NA <NA> <NA> NA NA NA NA <NA> <NA> <NA> NA NA NA NA NA NA NA
#> # ℹ 48 more variables: 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>
```

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

## Getting IMD data from postcodes

If the data has postcodes (which automatically connects to the postcode API) and
IMD information is wanted, the argument/parameter `url_type == "imd"` will
override the returned data to IMD.


```r
NHSRpopulation::get_data(pcs_tb,
column = "pcs"
)
NHSRpopulation::get_data(tibble_postcodes,
url_type = "imd")
#> ℹ The following postcodes are terminated:
#> HD1 2UT
#> and have been replaced with these current postcodes:
Expand All @@ -216,39 +261,48 @@ NHSRpopulation::get_data(pcs_tb,
#> 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…
#> Joining with `by = join_by(postcode)`
#> # A tibble: 3 × 105
#> postcode new_postcode result_type quality eastings northings country nhs_ha longitude latitude european_electoral_r…¹ primary_care_trust region lsoa msoa incode
#> <chr> <chr> <chr> <int> <int> <int> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 HD1 2UT HD1 2RD terminated 1 414639 416430 England Yorkshi… -1.78 53.6 Yorkshire and The Hum… Kirklees Yorks… Kirk… Kirk… 2RD
#> 2 HD1 2UU HD1 2UU valid 1 414433 416422 England Yorkshi… -1.78 53.6 Yorkshire and The Hum… Kirklees Yorks… Kirk… Kirk… 2UU
#> 3 HD1 2UV HD1 2UD autocompleted 1 414371 416317 England Yorkshi… -1.78 53.6 Yorkshire and The Hum… Kirklees Yorks… Kirk… Kirk… 2UD
#> # 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>
#> # ℹ 89 more variables: 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>, fid <int>, lsoa11nm <chr>, lsoa11nmw <chr>, st_areasha <dbl>, st_lengths <dbl>,
#> # imd_rank <int>, imd_decile <int>, lsoa01nm <chr>, la_dcd <chr>, la_dnm <chr>, imd_score <dbl>, imd_rank0 <int>, imd_dec0 <int>, 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>, …
```


Note that the postcode data is still validated.


```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>
NHSRpopulation::get_data(tibble_postcodes,
url_type = "imd",
fix_invalid = FALSE)
#> 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 × 105
#> postcode new_postcode result_type quality eastings northings country nhs_ha longitude latitude european_electoral_r…¹ primary_care_trust region lsoa msoa incode
#> <chr> <chr> <chr> <int> <int> <int> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 HD1 2UT <NA> <NA> NA NA NA <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 HD1 2UU HD1 2UU valid 1 414433 416422 England Yorkshire… -1.78 53.6 Yorkshire and The Hum… Kirklees Yorks… Kirk… Kirk… 2UU
#> 3 HD1 2UV <NA> <NA> NA NA NA <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
#> # ℹ abbreviated name: ¹​european_electoral_region
#> # ℹ 89 more variables: 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>, fid <int>, lsoa11nm <chr>, lsoa11nmw <chr>, st_areasha <dbl>, st_lengths <dbl>,
#> # imd_rank <int>, imd_decile <int>, lsoa01nm <chr>, la_dcd <chr>, la_dnm <chr>, imd_score <dbl>, imd_rank0 <int>, imd_dec0 <int>, 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>, …
```

38 changes: 28 additions & 10 deletions vignettes/NHSRpopulation.Rmd.orig
View file
Original file line number Diff line number Diff line change
Expand Up @@ -107,15 +107,16 @@ NHSRpopulation::get_data(tibble_imd, url_type = "imd") |>

Data can be either vectors or data frames.

No corrections are made to incorrect LSOA codes and the current join to the API
is on `lsoa11` data.
No corrections are made to incorrect LSOA codes.

# Column names

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:

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

```{r}
# Create datasets
pcs_tb <- dplyr::tibble(
Expand All @@ -124,24 +125,41 @@ pcs_tb <- dplyr::tibble(

pcs_tb

NHSRpopulation::get_data(pcs_tb,
column = "pcs"
)
```

```{r}

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

lsoa_tb

NHSRpopulation::get_data(lsoa_tb,
column = "lower_soa"
)
```

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

## Getting IMD data from postcodes

If the data has postcodes (which automatically connects to the postcode API) and
IMD information is wanted, the argument/parameter `url_type == "imd"` will
override the returned data to IMD.

```{r}
NHSRpopulation::get_data(pcs_tb,
column = "pcs"
)
NHSRpopulation::get_data(tibble_postcodes,
url_type = "imd")
```


Note that the postcode data is still validated.

```{r}
NHSRpopulation::get_data(lsoa_tb,
column = "lower_soa"
)
NHSRpopulation::get_data(tibble_postcodes,
url_type = "imd",
fix_invalid = FALSE)
```

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