Skip to content

Commit

Permalink
Merge pull request #9 from milanwiedemann/milanwiedemann/add-solution…
Browse files Browse the repository at this point in the history 
…s-session-1

Add solutions for Session 1
  • Loading branch information
@milanwiedemann
milanwiedemann authored Jan 19, 2024
2 parents 130c8fe + dc1295c commit 12aaa44
Show file tree
Hide file tree
Showing 5 changed files with 165 additions and 160 deletions.
1 change: 1 addition & 0 deletions .Rbuildignore
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
^LICENSE\.md$
21 changes: 21 additions & 0 deletions LICENSE.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
# MIT License

Copyright (c) 2024 phc-coding-club authors

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
255 changes: 124 additions & 131 deletions scripts/create_dummy_data.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,153 +9,146 @@ library(here)
# Addresses
# NOTE: Boolean T and F need to be specified as strings here
addresses <- tribble(
~patient_id, ~address_id, ~start_date, ~end_date, ~address_type, ~rural_urban_classification, ~imd_rounded, ~msoa_code, ~has_postcode, ~care_home_is_potential_match, ~care_home_requires_nursing, ~care_home_does_not_require_nursing,
1, 1, "1900-01-01", NA, 1, 1, 32400, "E02000010", "T", "T", "F", "T",
2, 1, "1950-01-01", NA, 1, 1, 22400, "E02000011", "T", "F", NA, NA,
3, 1, "1960-01-01", "2020-01-01", 1, 1, 12400, "E02000012", "T", "F", NA, NA,
3, 1, "2020-01-02", NA, 1, 1, 12400, "E02000013", "T", "T", "F", "T",
4, 1, "1970-01-01", NA, 1, 1, 2400, "E02000013", "T", "F", NA, NA,
5, 1, "1980-01-01", NA, 1, 1, 400, "E02000014", "T", "F", NA, NA,
6, 1, "1990-01-01", NA, 1, 1, 1400, "E02000014", "T", "F", NA, NA,
7, 1, "2000-01-01", NA, 1, 1, 2400, "E02000015", "T", "F", NA, NA,
8, 1, "2000-01-01", NA, 1, 1, 3400, "E02000015", "T", "F", NA, NA,
9, 1, "2021-01-01", NA, 1, 1, 4400, "E02000015", "T", "F", NA, NA,
11, 1, "2000-01-01", NA, 1, 1, 4400, "E02000015", "T", "F", NA, NA,
~patient_id, ~address_id, ~start_date, ~end_date, ~address_type, ~rural_urban_classification, ~imd_rounded, ~msoa_code, ~has_postcode, ~care_home_is_potential_match, ~care_home_requires_nursing, ~care_home_does_not_require_nursing,
1, 1, "1900-01-01", NA, 1, 1, 32400, "E02000010", "T", "T", "F", "T",
2, 1, "1950-01-01", NA, 1, 1, 22400, "E02000011", "T", "F", NA, NA,
3, 1, "1960-01-01", "2020-01-01", 1, 1, 12400, "E02000012", "T", "F", NA, NA,
3, 1, "2020-01-02", NA, 1, 1, 12400, "E02000013", "T", "T", "F", "T",
4, 1, "1970-01-01", NA, 1, 1, 2400, "E02000013", "T", "F", NA, NA,
5, 1, "1980-01-01", NA, 1, 1, 400, "E02000014", "T", "F", NA, NA,
6, 1, "1990-01-01", NA, 1, 1, 1400, "E02000014", "T", "F", NA, NA,
7, 1, "2000-01-01", NA, 1, 1, 2400, "E02000015", "T", "F", NA, NA,
8, 1, "2000-01-01", NA, 1, 1, 3400, "E02000015", "T", "F", NA, NA,
9, 1, "2021-01-01", NA, 1, 1, 4400, "E02000015", "T", "F", NA, NA,
11, 1, "2000-01-01", NA, 1, 1, 4400, "E02000015", "T", "F", NA, NA,
)

write_csv(addresses, here("dummy_data", "addresses.csv"), na= "")
write_csv(addresses, here("dummy_data", "addresses.csv"), na = "")

# Clinical events
clinical_events = tribble(
~patient_id, ~date, ~snomedct_code, ~ctv3_code, ~numeric_value ,
2, "2018-10-01", 111552007, NA, NA,
2, "2018-11-01", 112991000000101, NA, NA,
2, "2020-05-20", 11530004, NA, NA,
2, "2021-06-01", 1066911000000100, NA, NA,
2, "2021-07-01", 1066921000000106, NA, NA,
2, "2021-08-01", 1066931000000108, NA, NA,
2, "2022-06-01", 127014009, NA, NA,
2, "2022-06-01", 127014009, NA, NA,
2, "2022-06-01", 127014009, NA, NA,
2, "2022-06-01", 127014009, NA, NA,
2, "2022-01-01", 116471000119100, NA, NA,
2, "2022-01-02", 407569005, NA, NA,
2, "2022-01-03", 716031000000106, NA, NA,
2, "2022-02-03", 925791000000100, NA, NA,
2, "2022-01-04", 1049301000000100, NA, 53,
2, "2022-01-05", 717421000000100, NA, NA,
2, "2022-01-06", 925791000000100, NA, NA,
2, "2022-01-15", 925861000000102, NA, NA,
2, "2022-02-01", 925831000000107, NA, NA,
2, "2022-01-01", 1006751000000102, NA, NA,
2, "2022-12-01", 315051004, NA, NA,

3, "2022-01-04", 1049301000000100, NA, 80,
3, "2019-10-01", 1481000119100, NA, NA,
3, "2019-11-01", 190372001, NA, NA,
3, "2022-02-20", 230577008, NA, NA,
3, "2022-12-01", 237601000, NA, NA,
3, "2017-06-01", 1066911000000100, NA, NA,
3, "2021-06-01", 1066911000000100, NA, NA,
3, "2021-06-04", 1066921000000106, NA, NA,
3, "2021-06-09", 1066921000000106, NA, NA,
3, "2021-07-01", 1066921000000106, NA, NA,
3, "2021-08-01", 1066931000000108, NA, NA,
3, "2020-12-12", 315051004, NA, NA,
3, "2022-02-03", 925791000000100, NA, NA,

4, "2001-12-12", 1481000119100, NA, NA,
4, "2021-01-01", 315051004, NA, NA,
4, "2022-02-03", 925791000000100, NA, NA,

5, "2021-01-01", 190372001, NA, NA,

6, "2000-01-01", 190372001, NA, NA,
6, "2020-12-12", 315051004, NA, NA,

7, "1980-01-01", 190372001, NA, NA,
7, "2020-01-01", 315051004, NA, NA,

8, "2018-10-01", 111552007, NA, NA,
8, "2018-11-01", 112991000000101, NA, NA,
8, "2020-05-20", 11530004, NA, NA,
8, "2021-06-01", 1066911000000100, NA, NA,
8, "2022-06-01", 127014009, NA, NA,
8, "2022-06-01", 127014009, NA, NA,
8, "2022-06-01", 127014009, NA, NA,
8, "2022-06-01", 127014009, NA, NA,
8, "2020-01-01", 116471000119100, NA, NA,
8, "2020-01-02", 407569005, NA, NA,
8, "2020-01-03", 716031000000106, NA, NA,
8, "2022-02-03", 925791000000100, NA, NA,
8, "2022-01-04", 1049301000000100, NA, 80,
8, "2020-01-05", 717421000000100, NA, NA,
8, "2022-01-06", 925791000000100, NA, NA,
8, "2022-01-15", 925861000000102, NA, NA,
8, "2022-02-01", 925831000000107, NA, NA,
8, "2022-01-01", 1006751000000102, NA, NA,
8, "2022-12-01", 315051004, NA, NA,

11, "2018-10-01", 111552007, NA, NA,
11, "2018-11-01", 112991000000101, NA, NA,
11, "2020-05-20", 11530004, NA, NA,
11, "2021-06-01", 1066911000000100, NA, NA,
11, "2021-07-01", 1066921000000106, NA, NA,
11, "2022-06-01", 127014009, NA, NA,
11, "2022-06-01", 127014009, NA, NA,
11, "2022-06-01", 127014009, NA, NA,
11, "2022-06-01", 127014009, NA, NA,
11, "2020-01-01", 116471000119100, NA, NA,
11, "2022-01-02", 407569005, NA, NA,
11, "2020-01-03", 716031000000106, NA, NA,
11, "2022-02-03", 925791000000100, NA, NA,
11, "2021-05-04", 1049301000000100, NA, 74,
11, "2020-01-05", 717421000000100, NA, NA,
11, "2022-01-06", 925791000000100, NA, NA,
11, "2022-01-15", 925861000000102, NA, NA,
11, "2022-02-01", 925831000000107, NA, NA,
11, "2022-01-01", 1006751000000102, NA, NA,
11, "2022-12-01", 315051004, NA, NA,
clinical_events <- tribble(
~patient_id, ~date, ~snomedct_code, ~ctv3_code, ~numeric_value,
2, "2018-10-01", 111552007, NA, NA,
2, "2018-11-01", 112991000000101, NA, NA,
2, "2020-05-20", 11530004, NA, NA,
2, "2021-06-01", 1066911000000100, NA, NA,
2, "2021-07-01", 1066921000000106, NA, NA,
2, "2021-08-01", 1066931000000108, NA, NA,
2, "2022-06-01", 127014009, NA, NA,
2, "2022-06-01", 127014009, NA, NA,
2, "2022-06-01", 127014009, NA, NA,
2, "2022-06-01", 127014009, NA, NA,
2, "2022-01-01", 116471000119100, NA, NA,
2, "2022-01-02", 407569005, NA, NA,
2, "2022-01-03", 716031000000106, NA, NA,
2, "2022-02-03", 925791000000100, NA, NA,
2, "2022-01-04", 1049301000000100, NA, 53,
2, "2022-01-05", 717421000000100, NA, NA,
2, "2022-01-06", 925791000000100, NA, NA,
2, "2022-01-15", 925861000000102, NA, NA,
2, "2022-02-01", 925831000000107, NA, NA,
2, "2022-01-01", 1006751000000102, NA, NA,
2, "2022-12-01", 315051004, NA, NA,
3, "2022-01-04", 1049301000000100, NA, 80,
3, "2019-10-01", 1481000119100, NA, NA,
3, "2019-11-01", 190372001, NA, NA,
3, "2022-02-20", 230577008, NA, NA,
3, "2022-12-01", 237601000, NA, NA,
3, "2017-06-01", 1066911000000100, NA, NA,
3, "2021-06-01", 1066911000000100, NA, NA,
3, "2021-06-04", 1066921000000106, NA, NA,
3, "2021-06-09", 1066921000000106, NA, NA,
3, "2021-07-01", 1066921000000106, NA, NA,
3, "2021-08-01", 1066931000000108, NA, NA,
3, "2020-12-12", 315051004, NA, NA,
3, "2022-02-03", 925791000000100, NA, NA,
4, "2001-12-12", 1481000119100, NA, NA,
4, "2021-01-01", 315051004, NA, NA,
4, "2022-02-03", 925791000000100, NA, NA,
5, "2021-01-01", 190372001, NA, NA,
6, "2000-01-01", 190372001, NA, NA,
6, "2020-12-12", 315051004, NA, NA,
7, "1980-01-01", 190372001, NA, NA,
7, "2020-01-01", 315051004, NA, NA,
8, "2018-10-01", 111552007, NA, NA,
8, "2018-11-01", 112991000000101, NA, NA,
8, "2020-05-20", 11530004, NA, NA,
8, "2021-06-01", 1066911000000100, NA, NA,
8, "2022-06-01", 127014009, NA, NA,
8, "2022-06-01", 127014009, NA, NA,
8, "2022-06-01", 127014009, NA, NA,
8, "2022-06-01", 127014009, NA, NA,
8, "2020-01-01", 116471000119100, NA, NA,
8, "2020-01-02", 407569005, NA, NA,
8, "2020-01-03", 716031000000106, NA, NA,
8, "2022-02-03", 925791000000100, NA, NA,
8, "2022-01-04", 1049301000000100, NA, 80,
8, "2020-01-05", 717421000000100, NA, NA,
8, "2022-01-06", 925791000000100, NA, NA,
8, "2022-01-15", 925861000000102, NA, NA,
8, "2022-02-01", 925831000000107, NA, NA,
8, "2022-01-01", 1006751000000102, NA, NA,
8, "2022-12-01", 315051004, NA, NA,
11, "2018-10-01", 111552007, NA, NA,
11, "2018-11-01", 112991000000101, NA, NA,
11, "2020-05-20", 11530004, NA, NA,
11, "2021-06-01", 1066911000000100, NA, NA,
11, "2021-07-01", 1066921000000106, NA, NA,
11, "2022-06-01", 127014009, NA, NA,
11, "2022-06-01", 127014009, NA, NA,
11, "2022-06-01", 127014009, NA, NA,
11, "2022-06-01", 127014009, NA, NA,
11, "2020-01-01", 116471000119100, NA, NA,
11, "2022-01-02", 407569005, NA, NA,
11, "2020-01-03", 716031000000106, NA, NA,
11, "2022-02-03", 925791000000100, NA, NA,
11, "2021-05-04", 1049301000000100, NA, 74,
11, "2020-01-05", 717421000000100, NA, NA,
11, "2022-01-06", 925791000000100, NA, NA,
11, "2022-01-15", 925861000000102, NA, NA,
11, "2022-02-01", 925831000000107, NA, NA,
11, "2022-01-01", 1006751000000102, NA, NA,
11, "2022-12-01", 315051004, NA, NA,
)

write_csv(clinical_events, here("dummy_data", "clinical_events.csv"), na = "")

# Patients
patients <- tribble(
~patient_id, ~date_of_birth, ~sex, ~date_of_death,
1, "1900-01-01", "female", NA,
2, "1950-01-01", "female", "2022-10-01",
3, "1960-01-01", "female", NA,
4, "1970-01-01", NA, NA,
5, "1980-01-01", NA, NA,
6, "1990-01-01", "unknown", NA,
7, "2000-01-01", "male", NA,
8, "2000-01-01", "male", NA,
9, "2021-01-01", "male", NA,
10, "1930-01-01", "female", "2022-01-01",
11, "2000-01-01", "male", NA,
~patient_id, ~date_of_birth, ~sex, ~date_of_death,
1, "1900-01-01", "female", NA,
2, "1950-01-01", "female", "2022-10-01",
3, "1960-01-01", "female", NA,
4, "1970-01-01", NA, NA,
5, "1980-01-01", NA, NA,
6, "1990-01-01", "unknown", NA,
7, "2000-01-01", "male", NA,
8, "2000-01-01", "male", NA,
9, "2021-01-01", "male", NA,
10, "1930-01-01", "female", "2022-01-01",
11, "2000-01-01", "male", NA,
)

write_csv(patients, here("dummy_data", "patients.csv"), na = "")

# Practice registrations
practice_registrations <- tribble(
~patient_id, ~start_date, ~end_date, ~practice_pseudo_id, ~practice_stp, ~practice_nuts1_region_name,
1, "2018-01-01", NA, 1, 1, "region_practice1",
2, "2010-01-01", "2012-01-01", 1, 1, "region_practice1",
2, "2012-02-01", "2018-01-01", 2, 1, "region_practice2",
2, "2018-01-02", NA, 3, 1, "region_practice3",
3, "2000-01-01", "2019-01-01", 2, 2, "region_practice2",
3, "2019-02-01", "2023-01-01", 3, 2, "region_practice3",
3, "2023-01-02", NA, 4, 2, "region_practice4",
4, "2018-01-01", NA, 2, 2, "region_practice2",
5, "2018-01-01", NA, 2, 2, "region_practice2",
6, "2018-01-01", NA, 3, 3, "region_practice3",
7, "2018-01-01", NA, 3, 3, "region_practice3",
8, "2018-01-01", NA, 3, 3, "region_practice3",
9, "2018-01-01", NA, 3, 3, "region_practice3",
10, "2018-01-01", NA, 3, 3, "region_practice3",
11, "2018-01-01", NA, 3, 3, "region_practice3",
~patient_id, ~start_date, ~end_date, ~practice_pseudo_id, ~practice_stp, ~practice_nuts1_region_name,
1, "2018-01-01", NA, 1, 1, "region_practice1",
2, "2010-01-01", "2012-01-01", 1, 1, "region_practice1",
2, "2012-02-01", "2018-01-01", 2, 1, "region_practice2",
2, "2018-01-02", NA, 3, 1, "region_practice3",
3, "2000-01-01", "2019-01-01", 2, 2, "region_practice2",
3, "2019-02-01", "2023-01-01", 3, 2, "region_practice3",
3, "2023-01-02", NA, 4, 2, "region_practice4",
4, "2018-01-01", NA, 2, 2, "region_practice2",
5, "2018-01-01", NA, 2, 2, "region_practice2",
6, "2018-01-01", NA, 3, 3, "region_practice3",
7, "2018-01-01", NA, 3, 3, "region_practice3",
8, "2018-01-01", NA, 3, 3, "region_practice3",
9, "2018-01-01", NA, 3, 3, "region_practice3",
10, "2018-01-01", NA, 3, 3, "region_practice3",
11, "2018-01-01", NA, 3, 3, "region_practice3",
)

write_csv(practice_registrations, here("dummy_data", "practice_registrations.csv"), na = "")
Expand Down
11 changes: 3 additions & 8 deletions scripts/load_data.R
View file
Original file line number Diff line number Diff line change
@@ -1,17 +1,12 @@
# Load packages
library(readr)

# Delete everything in current global environment
rm(list = ls())

# Set working directory
setwd("~/Code/milanwiedemann/phc-coding-club/")
library(here)

# Load data
patients <- read_csv("dummy_data/patients.csv",
patients <- read_csv(here("dummy_data", "patients.csv"),
col_types = list(patient_id = "c")
)

clinical_events <- read_csv("dummy_data/clinical_events.csv",
clinical_events <- read_csv(here("dummy_data", "clinical_events.csv"),
col_types = list(patient_id = "c", snomedct_code = "c", ctv3_code = "c")
)
37 changes: 16 additions & 21 deletions scripts/summarise_patients.R
View file
Original file line number Diff line number Diff line change
@@ -1,36 +1,31 @@
# Load packages
library(dplyr)
library(readr)
library(lubridate)
library(here)
library(fs)
library(readr)
library(lubridate)
library(here)
library(fs)

# First run the script "scripts/load_data.R"

# Summarise patients data
patients_summary <- patients |>
mutate(age= year(as.period( interval(date_of_birth, today())))) |>
mutate(age = year(as.period(interval(date_of_birth, today())))) |>
summarise(
age_min = min(age,na.rm =TRUE),
age_max = max(age, na.rm = TRUE) ,
n_sex_female = sum(sex == "female", na.rm = TRUE),
n_sex_male = sum(sex == "male", na.rm = TRUE),
age_min = min(age, na.rm = TRUE),
age_max = max(age, na.rm = TRUE),
n_sex_female = sum(sex == "female", na.rm = TRUE),
n_sex_male = sum(sex == "male", na.rm = TRUE),
n_sex_na = sum(is.na(sex))
)

# Create folder for results
dir_create(here("results"))

# Write results
write_csv(patients_summary,
here( "results",






"patients_summary.csv"
)
)

write_csv(
patients_summary,
here(
"results",
"patients_summary.csv"
)
)

0 comments on commit 12aaa44

Please sign in to comment.