Skip to content

Update fn-exclude_zero_consultation.R #75

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ZoeMZou merged 2 commits into from
Sep 23, 2026
Merged

Update fn-exclude_zero_consultation.R #75

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3acee4f
Update fn-exclude_zero_consultation.R
ZoeMZou Sep 22, 2026
0e2678e
Only include practices starting to use TPP 1year before Oct for each …
ZoeMZou Sep 22, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions analysis/dataset_clean_sensitivity/fn-exclude_zero_consultation.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,21 +15,21 @@ exclude_zero_consultation <- function(input, flow) {

# Filter out practices with zero consultation rates ----------------------------
input <- input %>%
filter(is.na(cons_mean) | cons_mean != 0)
filter(is.na(cons_mean) | cons_mean > 0.005)

n_after <- n_distinct(input$practice_id)

# Append the number of remaining practices to the flow table ------------------
flow <- bind_rows(
flow,
data.frame(
Description = "Sensitivity analysis: exclude practices with average monthly consultation rates = 0",
Description = "Sensitivity analysis: exclude practices with average monthly consultation rates <= 0.005",
N = n_after,
stringsAsFactors = FALSE
)
)

message("Practices excluded with zero consultation rates: ", n_before - n_after)
message("Practices excluded with consultation rates <= 0.005: ", n_before - n_after)
message("Practices remaining for sensitivity analysis: ", n_after)
print(flow[nrow(flow), ])

Expand Down
2 changes: 1 addition & 1 deletion analysis/dataset_definition/measures_cohorts.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@

# Import longitudinal variables (focusing on time period)
from variables_longitudinal import generate_variables
variables_dynamic = generate_variables(INTERVAL.start_date, INTERVAL.end_date)
variables_dynamic = generate_variables(INTERVAL.start_date, INTERVAL.end_date, start_cohort - months(12))
# Extract variables from the dictionary so they can be directly used
globals().update(variables_dynamic)

Expand Down
13 changes: 9 additions & 4 deletions analysis/dataset_definition/variables_longitudinal.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,14 +8,19 @@
)

# Define generate variables function
def generate_variables(interval_start, interval_end):
def generate_variables(interval_start, interval_end, start_cohort):
## Inclusion/exclusion criteria-------------------------------------------------------------------------

### Registered throughout the study period (for longitudinal measures, i.e. consultation rate/hospital admission)
inex_bin_reg_long = (practice_registrations.spanning_with_systmone(
inex_bin_reg_long = (
practice_registrations.spanning_with_systmone(
interval_start, interval_end
)).exists_for_patient()

).where(
practice_registrations.practice_systmone_go_live_date <= start_cohort
)
.exists_for_patient()
)

## Exposure---------------------------------------------------------------------------------------------

### Consultation rate during follow-up of exposure
Expand Down
Loading