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Move adjusted Fig 3 into appendix #117

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Jan 31, 2025
Merged

Move adjusted Fig 3 into appendix #117

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2 changes: 1 addition & 1 deletion lib/functions/combine_os_nhsbsa_validation_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -76,4 +76,4 @@ df_os_validation_total <- bind_rows(
ungroup()

# Combine NHS BSA and OpenSAFELY data
pf_validation <- bind_rows(df_bsa_validation_total, df_os_validation_total)
pf_validation <- bind_rows(df_bsa_validation_total, df_os_validation_total)
153 changes: 130 additions & 23 deletions reports/create_results_manuscript.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ fig_pf_grouped_consultations_count
ggsave(
filename = here("released_output", "results", "manuscript", "fig1_pf_consultation_count_total.png"),
fig_pf_grouped_consultations_count,
height = 4,
height = 3.5,
width = 8
)
```
Expand Down Expand Up @@ -180,6 +180,8 @@ fig_pf_med_condition_linkage <- ggplot(df_pf_descriptive_stats, aes(
text = element_text(size = 14)
)

fig_pf_med_condition_linkage

ggsave(
filename = here("released_output", "results", "manuscript", "fig2_pf_med_condition.png"),
fig_pf_med_condition_linkage,
Expand Down Expand Up @@ -217,6 +219,118 @@ df_results_pf_linkage %>%
# But this file uses datasets created further down so it easiest to load it here
source(here("lib", "functions", "combine_os_nhsbsa_validation_data.R"))

# Pharmacy First Consultations
# Instead of only using the count of PF consultations in OS with a clinical
# condition we are using all PF consultations with a consultation id
df_pf_consultation_validatio_plot <- pf_validation |>
filter(
(data_source == "opensafely" &
data_desc == "pf_consultation" &
count_desc == "consultation_id") |
(data_source == "nhs_bsa" &
data_desc == "pf_consultation" &
count_desc == "consultation_type")
)

# Pivot wider to calculate ratio
df_pf_consultation_validatio_plot <- df_pf_consultation_validatio_plot |>
select(date, data_source, count_method, count_total) |>
pivot_wider(names_from = c(data_source, count_method), values_from = count_total) |>
mutate(ratio = opensafely_opensafely_tpp / nhs_bsa_count_40pct)

# Select colours for groups
# Group 1: #CF4446FF
colour_group_1 <- paletteer_c("viridis::inferno", n = 10)[6]
# Group 1: #1B0C42FF
colour_group_2 <- paletteer_c("viridis::inferno", n = 10)[2]

# Create consultation validation plot
pf_validatio_consultation_plot <- df_pf_consultation_validatio_plot |>
ggplot(aes(x = date)) +
geom_point(
aes(
y = nhs_bsa_count_40pct,
colour = "NHS BSA (40%)",
shape = "NHS BSA (40%)"
),
size = 2.6
) +
geom_line(
aes(y = nhs_bsa_count_40pct, colour = "NHS BSA (40%)"),
alpha = .3,
size = .5
) +
geom_point(
aes(
y = opensafely_opensafely_tpp,
colour = "OpenSAFELY-TPP",
shape = "OpenSAFELY-TPP"
),
size = 2.6
) +
geom_line(
aes(
y = opensafely_opensafely_tpp,
colour = "OpenSAFELY-TPP"
),
alpha = .3,
size = .5
) +
geom_label(
aes(
y = opensafely_opensafely_tpp,
label = scales::percent(ratio, accuracy = .1),
),
colour = colour_group_2,
vjust = -.5,
size = 3.5
) +
scale_y_continuous(labels = scales::number) +
scale_x_date(
date_breaks = "1 month",
labels = scales::label_date_short()
) +
scale_colour_manual(
values = c(
"NHS BSA (40%)" = colour_group_1,
"OpenSAFELY-TPP" = colour_group_2
),
name = NULL
) +
scale_shape_manual(
values = c(
"NHS BSA (40%)" = 15,
"OpenSAFELY-TPP" = 16
),
name = NULL
) +
labs(
x = NULL,
y = NULL,
colour = NULL,
shape = NULL
) +
theme(
panel.background = element_blank(),
axis.line = element_line(colour = "grey50"),
legend.position = "bottom",
text = element_text(size = 14)
)

ggsave(
filename = here("released_output", "results", "manuscript", "fig3_pf_os_nhsbsa_comparison.png"),
pf_validatio_consultation_plot,
height = 4,
width = 8
)
```
# Appendix

## Data comparison adjusted for % linkage

### Consultation

```{r, message=FALSE, warning=FALSE, echo = FALSE}
# Pharmacy First Consultations
# Instead of only using the count of PF consultations in OS with a clinical
# condition we are using all PF consultations with a consultation id
Expand Down Expand Up @@ -244,7 +358,7 @@ join_ratio <- df_pf_descriptive_stats |>
ungroup() |>
select(date, ratio_consultation_type_in_os)

df_pf_consultation_validation_plot <- df_pf_consultation_validation_plot |>
df_pf_consultation_validation_adjusted_plot <- df_pf_consultation_validation_plot |>
left_join(join_ratio) |>
mutate(
os_tpp_adjusted = round((opensafely_opensafely_tpp / (ratio_consultation_type_in_os * 100)) * 100, 0),
Expand All @@ -260,7 +374,7 @@ colour_group_2 <- paletteer_c("viridis::inferno", n = 10)[2]
colour_group_3 <- paletteer_c("viridis::inferno", n = 10)[4]

# Create consultation validation plot
pf_validation_consultation_plot <- df_pf_consultation_validation_plot |>
pf_validation_consultation_adjusted_plot <- df_pf_consultation_validation_adjusted_plot |>
ggplot(aes(x = date)) +
geom_point(
aes(
Expand Down Expand Up @@ -342,7 +456,7 @@ pf_validation_consultation_plot <- df_pf_consultation_validation_plot |>
values = c(
"NHS BSA (40%)" = 15,
"OpenSAFELY-TPP" = 16,
"OpenSAFELY-TPP (Adjusted)" = 16
"OpenSAFELY-TPP (Adjusted)" = 17
),
name = NULL
) +
Expand All @@ -359,15 +473,10 @@ pf_validation_consultation_plot <- df_pf_consultation_validation_plot |>
text = element_text(size = 14)
) +
ggtitle("A. Pharmacy First Consultations")

ggsave(
filename = here("released_output", "results", "manuscript", "fig3_pf_os_nhsbsa_comparison.png"),
pf_validation_consultation_plot,
height = 4,
width = 8
)
```

### Medications

```{r, message=FALSE, warning=FALSE, echo = FALSE}
df_pf_medication_validation <- pf_validation |>
filter(
Expand All @@ -393,15 +502,15 @@ linked_ratio <- df_pf_descriptive_stats |>
select(date, ratio_medication_in_os)


df_pf_medication_validation_plot <- df_pf_medication_validation_plot |>
df_pf_medication_validation_adjusted_plot <- df_pf_medication_validation_plot |>
left_join(linked_ratio) |>
mutate(
os_tpp_adjusted = round((opensafely_opensafely_tpp / (ratio_medication_in_os * 100)) * 100, 0),
ratio_adjusted = os_tpp_adjusted / nhs_bsa_count_40pct
)

# Create consultation validation plot
pf_medication_validation_plot <- df_pf_medication_validation_plot |>
pf_medication_validation_adjusted_plot <- df_pf_medication_validation_adjusted_plot |>
ggplot(aes(x = date)) +
geom_point(
aes(
Expand Down Expand Up @@ -483,7 +592,7 @@ pf_medication_validation_plot <- df_pf_medication_validation_plot |>
values = c(
"NHS BSA (40%)" = 15,
"OpenSAFELY-TPP" = 16,
"OpenSAFELY-TPP (Adjusted)" = 16
"OpenSAFELY-TPP (Adjusted)" = 17
),
name = NULL
) +
Expand All @@ -500,19 +609,17 @@ pf_medication_validation_plot <- df_pf_medication_validation_plot |>
text = element_text(size = 14)
) +
ggtitle("B. Pharmacy First Medications")
```

ggsave(
filename = here("released_output", "results", "manuscript", "fig3_pfmed_os_nhsbsa_comparison.png"),
pf_medication_validation_plot,
height = 4,
width = 8
)
```{r}
# Combine plots
validation_combined_adjusted_plot <- pf_validation_consultation_adjusted_plot / pf_medication_validation_adjusted_plot + plot_layout(guides = "collect") & theme(legend.position = "bottom")

validation_combined_plot <- pf_validation_consultation_plot / pf_medication_validation_plot + plot_layout(guides = "collect") & theme(legend.position = "bottom")
validation_combined_adjusted_plot

ggsave(
filename = here("released_output", "results", "manuscript", "fig3_pf_combined_os_nhsbsa_comparison.png"),
validation_combined_plot,
filename = here("released_output", "results", "manuscript", "figX_pf_os_nhsbsa_adjusted_comparison.png"),
validation_combined_adjusted_plot,
height = 8,
width = 10
)
Expand Down