Demo.R
In zongyf02/INORMUS: Functions for the INORMUS Project
# Last Updated: Sept 2, 2021
# Run this if you want to restart R
# .rs.restartR()
# Remove all variables in the environment
rm(list = ls())
# Install tidyverse, only needs to run for first time setup
# install.packages("tidyverse")
# Import and tidyverse
library(tidyverse)
# Install devtools, one time setup
# install.packages("devtools")
# Import devtools, only required to update INORMUS
# library(devtools)
# Unimport INORMUS, run before you update the package
# detach("package:INORMUS", unload = TRUE)
# (Re)Install INORMUS package, run this regularly to keep it updated
# install_github("zongyf02/INORMUS")
# Import INORMUS
library(INORMUS)
# Change if needed
setwd("../Data")
# Read in all forms
form1.1 <- read_form1.1("1.1.csv")
# form1.1_raw <- read_form1.1("1.1.csv", raw = TRUE)
form2.1 <- read_form2.1("2.1.csv")
# form2.1_raw <- read_form2.1("2.1.csv", raw = TRUE)
form2.2 <- read_form2.2("2.2.csv")
# form2.2_raw <- read_form2.2("2.2.csv", raw = TRUE)
form3.1 <- read_form3.1("3.1.csv")
# form3.1_raw <- read_form3.1("3.1.csv", raw = TRUE)
form3.2 <- read_form3.2("3.2.csv")
# form3.2_raw <- read_form3.2("3.2.csv", raw = TRUE)
form3.3 <- read_form3.3("3.3.csv")
# form3.3_raw <- read_form3.3("3.3.csv", raw = TRUE)
form4.1 <- read_form4.1("4.1.csv")
# form4.1_raw <- read_form4.1("4.1.csv", raw = TRUE)
form5.1 <- read_form5.1("5.1.csv")
# form5.1_raw <- read_form5.1("5.1.csv", raw = TRUE)
form5.2 <- read_form5.2("5.2.csv")
# form5.2_raw <- read_form5.2("5.2.csv", raw = TRUE)
form5.3 <- read_form5.3("5.3.csv")
# form5.3_raw <- read_form5.3("5.3.csv", raw = TRUE)
form5.4 <- read_form5.4("5.4.csv")
# form5.4_raw <- read_form5.4("5.4.csv", raw = TRUE)
form5.5 <- read_form5.5("5.5.csv")
# form5.5_raw <- read_form5.5("5.5.csv", raw = TRUE)
form5.6 <- read_form5.6("5.6.csv")
# form5.6_raw <- read_form5.6("5.6.csv", raw = TRUE)
form5.7 <- read_form5.7("5.7.csv")
# form5.7_raw <- read_form5.7("5.7.csv", raw = TRUE)
form5.8 <- read_form5.8("5.8.csv")
# form5.8_raw <- read_form5.8("5.8.csv", raw = TRUE)
form5.9 <- read_form5.9("5.9.csv")
# form5.9_raw <- read_form5.9("5.9.csv", raw = TRUE)
form5.10 <- read_form5.10("5.10.csv")
# form5.10_raw <- read_form5.10("5.10.csv", raw = TRUE)
form5.11 <- read_form5.11("5.11.csv")
# form5.11_raw <- read_form5.11("5.11.csv", raw = TRUE)
form5.12 <- read_form5.12("5.12.csv")
# form5.12_raw <- read_form5.12("5.12.csv", raw = TRUE)
form5.13 <- read_form5.13("5.13.csv")
# form5.13_raw <- read_form5.13("5.13.csv", raw = TRUE)
form5.14 <- read_form5.14("5.14.csv")
# form5.14_raw <- read_form5.14("5.14.csv", raw = TRUE)
form6.1 <- read_form6.1("6.1.csv")
# form6.1_raw <- read_form6.1("6.1.csv", raw = TRUE)
form7.1 <- read_form7.1("7.1.csv")
# form7.1_raw <- read_form7.1("7.1.csv", raw = TRUE)
form7.2 <- read_form7.2("7.2.csv")
# form7.2_raw <- read_form7.2("7.2.csv", raw = TRUE)
form7.3 <- read_form7.3("7.3.csv")
# form7.3_raw <- read_form7.3("7.3.csv", raw = TRUE)
form7.4 <- read_form7.4("7.4.csv")
# form7.4_raw <- read_form7.4("7.4.csv", raw = TRUE)
# Create a list of all forms
forms <- list(form1.1, form2.1, form2.2, form3.1, form3.2, form3.3, form4.1,
form5.1, form5.2, form5.3, form5.4, form5.5, form5.6, form5.7,
form5.8, form5.9, form5.10, form5.11, form5.12, form5.13,
form5.14, form6.1, form7.1, form7.2, form7.3, form7.4)
# Merge all forms
form <- merge_forms(forms)
# Select the precovid forms and export them as "precovid_data"
precovid_form <- filter_precovid(form)
write_csv(precovid_form, "precovid_data.csv")
# Select the forms with hip fractures and export them as "hip_data"
hip_only_form <- filter_hip(form)
write_csv(hip_only_form, "hip_data.csv")
# View the structure of all columns of form
str(form, list.len = ncol(form))
################################################################################
# Create a table with region, site, studyid, and sex columns
select(form, c(region, site, studyid, sex))
# Create a table with all columns between region and ptinit
select(form, region:ptinit)
# Create a table without columns between region and ptinit
select(form, !(region:ptinit))
# Create a table with columns starting with "pneu"
select(form, starts_with("pneu"))
################################################################################
# Create a table with only male patients
filter(form, sex == 1)
# Create a table with only male patients who are participating
filter(form, sex == 1 & ptstatus == 1)
# Create a table with only admitted patients, grouped by sex
filter(form, ptstatus == 1) %>%
group_by(sex)
################################################################################
# Replace 1, 0 in ptstatus by "Admitted", "Not Admitted"
mutate(form, ptstatus = if_else(ptstatus == 1, "Admitted", "Not Admitted"))
# Compress the range of the income column
mutate(form, income = case_when(income == 0 ~ 0,
income == 1 | income == 2 ~ 1,
income == 3 | income == 4 ~ 2,
income == 5 | income == 6 ~ 3,
income == 7 | income == 8 ~ 4,
income == 9 ~ 5,
income == 10 ~ 6,
income == 11 ~ 7))
################################################################################
# Create a summary table of number of patients in each region
form %>% group_by(region) %>%
summarize(n = n())
# equivalently use the library function
summarize_form(form, "studyid", region)
# Create a summary table of number of admitted patients in each region
form %>% group_by(region) %>%
summarize(nAdmitted = sum(ptstatus == 1, na.rm = TRUE))
# equivalently, use the library function
summarize_form(form, "ptstatus", region)
# Create a summary table of patient consent date grouped by region and site
form %>% group_by(region, site) %>%
summarize(minDate = min(parse_dmY(condate), na.rm = TRUE),
maxDate = max(parse_dmY(condate), na.rm = TRUE))
# equivalently
summarize_form(form, "condate", region, site)
# Create a summary table of patient age grouped by region and site
form %>% group_by(region, site) %>%
summarize(minAge = min(age, na.rm = TRUE),
maxAge = max(age, na.rm = TRUE),
meanAge = mean(age, na.rm = TRUE),
sdAge = sd(age, na.rm = TRUE))
# equivalently
summarize_form(form, "age", region, site)
# Create a summary table of admitted patients' sex grouped by region and site
form %>% group_by(region, site) %>% filter(ptstatus == 1) %>%
summarize(male = sum(sex == 1, na.rm = TRUE),
percentMale = mean(sex == 1, na.rm = TRUE),
female = sum(sex ==2, na.rm = TRUE),
percentFemale = mean(sex ==2, na.rm = TRUE),
other = sum(sex != 1 && sex != 2),
percentOther = mean(sex != 1 && sex != 2))
#equivalently
summarize_form(filter(form, ptstatus == 1), "sex", region, site)
# Create summary table of the first 11 columns grouped by region
# Note the first two omitted. The function will throw an error if asked
# to summarize a column used for grouping
summarize_form(form, colnames(form)[3:11], region)
################################################################################
# Check that text field and coding box is filled if and only if "other" is chosen
problems_form2.1_box5 <- check_form2.1_box5(form)
problems_form2.2_box10 <- check_form2.2_box10(form)
problems_form3.1_box4 <- check_form3.1_box4(form)
problems_form3.2_box5 <- check_form3.2_box5(form)
problems_form3.2_box6 <- check_form3.2_box6(form)
problems_form3.2_box7_chest <- check_form3.2_box7_chest(form)
problems_form3.2_box7_abdo <- check_form3.2_box7_abdo(form)
problems_form3.2_box7_hn <- check_form3.2_box7_hn(form)
problems_form3.3_p50dist <- check_form3.3_p50dist(form)
problems_form3.3_p50city <- check_form3.3_p50city(form)
problems_form4.1_box2 <- check_form4.1_box2(form)
problems_form4.1_box3 <- check_form4.1_box3(form)
problems_form4.1_box5 <- check_form4.1_box5(form)
problems_form5.1_box1 <- check_form5.1x_box1(form, 1)
problems_form5.5_box1 <- check_form5.1x_box1(form, 2)
problems_form5.9_box1 <- check_form5.1x_box1(form, 3)
problems_form5.2_box2 <- check_form5.2x_box2(form, 1)
problems_form5.6_box2 <- check_form5.2x_box2(form, 2)
problems_form5.10_box2 <- check_form5.2x_box2(form, 3)
problems_form5.2_box3a <- check_form5.2x_box3a(form, 1)
problems_form5.6_box3a <- check_form5.2x_box3a(form, 2)
problems_form5.10_box3a <- check_form5.2x_box3a(form, 3)
problems_form5.2_box3b <- check_form5.2x_box3b(form, 1)
problems_form5.6_box3b <- check_form5.2x_box3b(form, 2)
problems_form5.10_box3b <- check_form5.2x_box3b(form, 3)
problems_form5.2_box4 <- check_form5.2x_box4(form, 1)
problems_form5.6_box4 <- check_form5.2x_box4(form, 2)
problems_form5.10_box4 <- check_form5.2x_box4(form, 3)
problems_form5.3_box5a <- check_form5.3x_box5a(form, 1)
problems_form5.7_box5a <- check_form5.3x_box5a(form, 2)
problems_form5.11_box5a <- check_form5.3x_box5a(form, 3)
problems_form5.3_box5b <- check_form5.3x_box5b(form, 1)
problems_form5.7_box5b <- check_form5.3x_box5b(form, 2)
problems_form5.11_box5b <- check_form5.3x_box5b(form, 3)
problems_form5.4_box7a <- check_form5.4x_box7a(form, 1)
problems_form5.8_box7a <- check_form5.4x_box7a(form, 2)
problems_form5.12_box7a <- check_form5.4x_box7a(form, 3)
problems_form5.4_box7b <- check_form5.4x_box7b(form, 1)
problems_form5.8_box7b <- check_form5.4x_box7b(form, 2)
problems_form5.12_box7b <- check_form5.4x_box7b(form, 3)
problems_form5.4_box8 <- check_form5.4x_box8(form, 1)
problems_form5.8_box8 <- check_form5.4x_box8(form, 2)
problems_form5.12_box8 <- check_form5.4x_box8(form, 3)
problems_form5.4_box9 <- check_form5.4x_box9(form, 1)
problems_form5.8_box9 <- check_form5.4x_box9(form, 2)
problems_form5.12_box9 <- check_form5.4x_box9(form, 3)
problems_form5.14_box1a <- check_form5.14_box1a(form)
problems_form5.14_box1b <- check_form5.14_box1b(form)
problems_form5.14_box2 <- check_form5.14_box2(form)
problems_form5.14_box3 <- check_form5.14_box3(form)
problems_form6.1_box1a <- check_form6.1_box1a(form)
problems_form6.1_box1b <- check_form6.1_box1b(form)
problems_form6.1_box2a <- check_form6.1_box2a(form)
problems_form6.1_box2b <- check_form6.1_box2b(form)
problems_form6.1_box4 <- check_form6.1_box4(form)
problems_form7.1_box3 <- check_form7.x_box3(form, 1)
problems_form7.2_box3 <- check_form7.x_box3(form, 2)
problems_form7.3_box3 <- check_form7.x_box3(form, 3)
problems_form7.4_box3 <- check_form7.x_box3(form, 4)
problems_form7.1_box4a <- check_form7.x_box4a(form, 1)
problems_form7.2_box4a <- check_form7.x_box4a(form, 2)
problems_form7.3_box4a <- check_form7.x_box4a(form, 3)
problems_form7.4_box4a <- check_form7.x_box4a(form, 4)
problems_form7.1_box4b <- check_form7.x_box4b(form, 1)
problems_form7.2_box4b <- check_form7.x_box4b(form, 2)
problems_form7.3_box4b <- check_form7.x_box4b(form, 3)
problems_form7.4_box4b <- check_form7.x_box4b(form, 4)
problems_form7.1_box4c <- check_form7.x_box4c(form, 1)
problems_form7.2_box4c <- check_form7.x_box4c(form, 2)
problems_form7.3_box4c <- check_form7.x_box4c(form, 3)
problems_form7.4_box4c <- check_form7.x_box4c(form, 4)
# Check that consent date should be on the same day, or after the date of injury
# Check 1
problems_condate_injdate <- check_condate_injdate(form)
# Check that hospital admission date should be on the same day, or after the date of injury
# Check 2
problems_hspdate_injdate <- check_hspdate_injdate(form)
# Check that consent date should be 0 - 30 days after hospital admission date
# Check 3
problems_condate_hspdate <- check_condate_hspdate(form)
# Check that the number of orthopedic injuries stated on form 3.2 is consistent with the number of sets of injury forms and form5.14
# Check 4
problems_northinj_form5.x <- check_northinj_form5.x(form)
problems_northinj_form5.14 <- check_northinj_form5.14(form)
# Check that time from injury to hsp admission should be within +/- 24 hrs range of difference between injdate and hspdate
# Check 5
problems_injdate_hspdate <- check_injdate_hspdate(form)
# The time from injury to hospital admission should be within 24 hours if the patient is coming from the Accident/Injury Site
# Check 6
problems_admfrom_ihunits <- check_admfrom_ihunits(form)
# Check that for antibiotics first administered at the injury scene, time from injury to antibiotics administration is at most 5 hours before time from injury to hospital admission
# Check 7
problems_locabx <- check_locabx(form)
# Check that the location of fracture and the location of dislocation in one set of form5.x are related
# Also ensures only 1 fracture per set of form
# Checks 8 and 9
problems_fracwith_diswith_1 <- check_fracwith_diswith(form, 1)
problems_fracwith_diswith_2 <- check_fracwith_diswith(form, 2)
problems_fracwith_diswith_3 <- check_fracwith_diswith(form, 3)
# Check that the response to I&D is consistent with whether the fracture is open or closed
# Check 11
problems_openclos_iandd_1 <- check_openclos_iandd(form, 1)
problems_openclos_iandd_2 <- check_openclos_iandd(form, 2)
problems_openclos_iandd_3 <- check_openclos_iandd(form, 3)
# Check that details on the patient's surgery is consistent
# Check 12
problems_operat_failsurg_delsurg_1 <- check_operat_failsurg_delsurg(form, 1)
problems_operat_failsurg_delsurg_2 <- check_operat_failsurg_delsurg(form, 2)
problems_operat_failsurg_delsurg_3 <- check_operat_failsurg_delsurg(form, 3)
# Check that closed fracture injuries have have NA selected in form5.14
# Check 13
problems_openclos_NA <- check_openclos_NA(form)
# Check that he time difference between the time from injury to hsp admission and the time from injury to prep solution in ER is within +/- 24 hr range
# Check 14
problems_ihunits_ipunits <- check_ihunits_ipunits(form)
#' Check that date of follow-up is 30 or more days after hospital admission
#' Check 16
problems_formdate_ocrecyes <- check_formdate_ocrecyes(form)
#' Check that consent date is before discharge date
#' Check 17
problems_condate_hdcdate_dthdate <- check_condate_hdcdate_dthdate(form)
# Check for invalid/missing entries in form1.1
problems_invalid_form1.1 <- check_invalid_form1.1(form)
# Check for invalid/missing entries in form2.1
problems_invalid_form2.1 <- check_invalid_form2.1(form)
# Check for invalid/missing entries in form2.2
problems_invalid_form2.2 <- check_invalid_form2.2(form)
# Check for invalid/missing entries in form3.1, do not check question 4.1, intent of injury
problems_invalid_form3.1 <- check_invalid_form3.1(form, checkIntent = FALSE)
# Check for invalid/missing entries in form3.2
problems_invalid_form3.2 <- check_invalid_form3.2(form)
# Check for invalid/missing entries in form4.1
problems_invalid_form4.1 <- check_invalid_form4.1(form)
# Check for invalid/missing entries in form5.2
problems_invalid_form5.2x <- check_invalid_form5.2x(form, 1)
problems_invalid_form5.2x <- check_invalid_form5.2x(form, 2)
problems_invalid_form5.2x <- check_invalid_form5.2x(form, 3)
# Check initials
problems_initials <- check_initials(forms)
zongyf02/INORMUS documentation built on Dec. 28, 2021, 8:49 a.m.
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# Last Updated: Sept 2, 2021
# Run this if you want to restart R
# .rs.restartR()
# Remove all variables in the environment
rm(list = ls())
# Install tidyverse, only needs to run for first time setup
# install.packages("tidyverse")
# Import and tidyverse
library(tidyverse)
# Install devtools, one time setup
# install.packages("devtools")
# Import devtools, only required to update INORMUS
# library(devtools)
# Unimport INORMUS, run before you update the package
# detach("package:INORMUS", unload = TRUE)
# (Re)Install INORMUS package, run this regularly to keep it updated
# install_github("zongyf02/INORMUS")
# Import INORMUS
library(INORMUS)
# Change if needed
setwd("../Data")
# Read in all forms
form1.1 <- read_form1.1("1.1.csv")
# form1.1_raw <- read_form1.1("1.1.csv", raw = TRUE)
form2.1 <- read_form2.1("2.1.csv")
# form2.1_raw <- read_form2.1("2.1.csv", raw = TRUE)
form2.2 <- read_form2.2("2.2.csv")
# form2.2_raw <- read_form2.2("2.2.csv", raw = TRUE)
form3.1 <- read_form3.1("3.1.csv")
# form3.1_raw <- read_form3.1("3.1.csv", raw = TRUE)
form3.2 <- read_form3.2("3.2.csv")
# form3.2_raw <- read_form3.2("3.2.csv", raw = TRUE)
form3.3 <- read_form3.3("3.3.csv")
# form3.3_raw <- read_form3.3("3.3.csv", raw = TRUE)
form4.1 <- read_form4.1("4.1.csv")
# form4.1_raw <- read_form4.1("4.1.csv", raw = TRUE)
form5.1 <- read_form5.1("5.1.csv")
# form5.1_raw <- read_form5.1("5.1.csv", raw = TRUE)
form5.2 <- read_form5.2("5.2.csv")
# form5.2_raw <- read_form5.2("5.2.csv", raw = TRUE)
form5.3 <- read_form5.3("5.3.csv")
# form5.3_raw <- read_form5.3("5.3.csv", raw = TRUE)
form5.4 <- read_form5.4("5.4.csv")
# form5.4_raw <- read_form5.4("5.4.csv", raw = TRUE)
form5.5 <- read_form5.5("5.5.csv")
# form5.5_raw <- read_form5.5("5.5.csv", raw = TRUE)
form5.6 <- read_form5.6("5.6.csv")
# form5.6_raw <- read_form5.6("5.6.csv", raw = TRUE)
form5.7 <- read_form5.7("5.7.csv")
# form5.7_raw <- read_form5.7("5.7.csv", raw = TRUE)
form5.8 <- read_form5.8("5.8.csv")
# form5.8_raw <- read_form5.8("5.8.csv", raw = TRUE)
form5.9 <- read_form5.9("5.9.csv")
# form5.9_raw <- read_form5.9("5.9.csv", raw = TRUE)
form5.10 <- read_form5.10("5.10.csv")
# form5.10_raw <- read_form5.10("5.10.csv", raw = TRUE)
form5.11 <- read_form5.11("5.11.csv")
# form5.11_raw <- read_form5.11("5.11.csv", raw = TRUE)
form5.12 <- read_form5.12("5.12.csv")
# form5.12_raw <- read_form5.12("5.12.csv", raw = TRUE)
form5.13 <- read_form5.13("5.13.csv")
# form5.13_raw <- read_form5.13("5.13.csv", raw = TRUE)
form5.14 <- read_form5.14("5.14.csv")
# form5.14_raw <- read_form5.14("5.14.csv", raw = TRUE)
form6.1 <- read_form6.1("6.1.csv")
# form6.1_raw <- read_form6.1("6.1.csv", raw = TRUE)
form7.1 <- read_form7.1("7.1.csv")
# form7.1_raw <- read_form7.1("7.1.csv", raw = TRUE)
form7.2 <- read_form7.2("7.2.csv")
# form7.2_raw <- read_form7.2("7.2.csv", raw = TRUE)
form7.3 <- read_form7.3("7.3.csv")
# form7.3_raw <- read_form7.3("7.3.csv", raw = TRUE)
form7.4 <- read_form7.4("7.4.csv")
# form7.4_raw <- read_form7.4("7.4.csv", raw = TRUE)
# Create a list of all forms
forms <- list(form1.1, form2.1, form2.2, form3.1, form3.2, form3.3, form4.1,
form5.1, form5.2, form5.3, form5.4, form5.5, form5.6, form5.7,
form5.8, form5.9, form5.10, form5.11, form5.12, form5.13,
form5.14, form6.1, form7.1, form7.2, form7.3, form7.4)
# Merge all forms
form <- merge_forms(forms)
# Select the precovid forms and export them as "precovid_data"
precovid_form <- filter_precovid(form)
write_csv(precovid_form, "precovid_data.csv")
# Select the forms with hip fractures and export them as "hip_data"
hip_only_form <- filter_hip(form)
write_csv(hip_only_form, "hip_data.csv")
# View the structure of all columns of form
str(form, list.len = ncol(form))
################################################################################
# Create a table with region, site, studyid, and sex columns
select(form, c(region, site, studyid, sex))
# Create a table with all columns between region and ptinit
select(form, region:ptinit)
# Create a table without columns between region and ptinit
select(form, !(region:ptinit))
# Create a table with columns starting with "pneu"
select(form, starts_with("pneu"))
################################################################################
# Create a table with only male patients
filter(form, sex == 1)
# Create a table with only male patients who are participating
filter(form, sex == 1 & ptstatus == 1)
# Create a table with only admitted patients, grouped by sex
filter(form, ptstatus == 1) %>%
group_by(sex)
################################################################################
# Replace 1, 0 in ptstatus by "Admitted", "Not Admitted"
mutate(form, ptstatus = if_else(ptstatus == 1, "Admitted", "Not Admitted"))
# Compress the range of the income column
mutate(form, income = case_when(income == 0 ~ 0,
income == 1 | income == 2 ~ 1,
income == 3 | income == 4 ~ 2,
income == 5 | income == 6 ~ 3,
income == 7 | income == 8 ~ 4,
income == 9 ~ 5,
income == 10 ~ 6,
income == 11 ~ 7))
################################################################################
# Create a summary table of number of patients in each region
form %>% group_by(region) %>%
summarize(n = n())
# equivalently use the library function
summarize_form(form, "studyid", region)
# Create a summary table of number of admitted patients in each region
form %>% group_by(region) %>%
summarize(nAdmitted = sum(ptstatus == 1, na.rm = TRUE))
# equivalently, use the library function
summarize_form(form, "ptstatus", region)
# Create a summary table of patient consent date grouped by region and site
form %>% group_by(region, site) %>%
summarize(minDate = min(parse_dmY(condate), na.rm = TRUE),
maxDate = max(parse_dmY(condate), na.rm = TRUE))
# equivalently
summarize_form(form, "condate", region, site)
# Create a summary table of patient age grouped by region and site
form %>% group_by(region, site) %>%
summarize(minAge = min(age, na.rm = TRUE),
maxAge = max(age, na.rm = TRUE),
meanAge = mean(age, na.rm = TRUE),
sdAge = sd(age, na.rm = TRUE))
# equivalently
summarize_form(form, "age", region, site)
# Create a summary table of admitted patients' sex grouped by region and site
form %>% group_by(region, site) %>% filter(ptstatus == 1) %>%
summarize(male = sum(sex == 1, na.rm = TRUE),
percentMale = mean(sex == 1, na.rm = TRUE),
female = sum(sex ==2, na.rm = TRUE),
percentFemale = mean(sex ==2, na.rm = TRUE),
other = sum(sex != 1 && sex != 2),
percentOther = mean(sex != 1 && sex != 2))
#equivalently
summarize_form(filter(form, ptstatus == 1), "sex", region, site)
# Create summary table of the first 11 columns grouped by region
# Note the first two omitted. The function will throw an error if asked
# to summarize a column used for grouping
summarize_form(form, colnames(form)[3:11], region)
################################################################################
# Check that text field and coding box is filled if and only if "other" is chosen
problems_form2.1_box5 <- check_form2.1_box5(form)
problems_form2.2_box10 <- check_form2.2_box10(form)
problems_form3.1_box4 <- check_form3.1_box4(form)
problems_form3.2_box5 <- check_form3.2_box5(form)
problems_form3.2_box6 <- check_form3.2_box6(form)
problems_form3.2_box7_chest <- check_form3.2_box7_chest(form)
problems_form3.2_box7_abdo <- check_form3.2_box7_abdo(form)
problems_form3.2_box7_hn <- check_form3.2_box7_hn(form)
problems_form3.3_p50dist <- check_form3.3_p50dist(form)
problems_form3.3_p50city <- check_form3.3_p50city(form)
problems_form4.1_box2 <- check_form4.1_box2(form)
problems_form4.1_box3 <- check_form4.1_box3(form)
problems_form4.1_box5 <- check_form4.1_box5(form)
problems_form5.1_box1 <- check_form5.1x_box1(form, 1)
problems_form5.5_box1 <- check_form5.1x_box1(form, 2)
problems_form5.9_box1 <- check_form5.1x_box1(form, 3)
problems_form5.2_box2 <- check_form5.2x_box2(form, 1)
problems_form5.6_box2 <- check_form5.2x_box2(form, 2)
problems_form5.10_box2 <- check_form5.2x_box2(form, 3)
problems_form5.2_box3a <- check_form5.2x_box3a(form, 1)
problems_form5.6_box3a <- check_form5.2x_box3a(form, 2)
problems_form5.10_box3a <- check_form5.2x_box3a(form, 3)
problems_form5.2_box3b <- check_form5.2x_box3b(form, 1)
problems_form5.6_box3b <- check_form5.2x_box3b(form, 2)
problems_form5.10_box3b <- check_form5.2x_box3b(form, 3)
problems_form5.2_box4 <- check_form5.2x_box4(form, 1)
problems_form5.6_box4 <- check_form5.2x_box4(form, 2)
problems_form5.10_box4 <- check_form5.2x_box4(form, 3)
problems_form5.3_box5a <- check_form5.3x_box5a(form, 1)
problems_form5.7_box5a <- check_form5.3x_box5a(form, 2)
problems_form5.11_box5a <- check_form5.3x_box5a(form, 3)
problems_form5.3_box5b <- check_form5.3x_box5b(form, 1)
problems_form5.7_box5b <- check_form5.3x_box5b(form, 2)
problems_form5.11_box5b <- check_form5.3x_box5b(form, 3)
problems_form5.4_box7a <- check_form5.4x_box7a(form, 1)
problems_form5.8_box7a <- check_form5.4x_box7a(form, 2)
problems_form5.12_box7a <- check_form5.4x_box7a(form, 3)
problems_form5.4_box7b <- check_form5.4x_box7b(form, 1)
problems_form5.8_box7b <- check_form5.4x_box7b(form, 2)
problems_form5.12_box7b <- check_form5.4x_box7b(form, 3)
problems_form5.4_box8 <- check_form5.4x_box8(form, 1)
problems_form5.8_box8 <- check_form5.4x_box8(form, 2)
problems_form5.12_box8 <- check_form5.4x_box8(form, 3)
problems_form5.4_box9 <- check_form5.4x_box9(form, 1)
problems_form5.8_box9 <- check_form5.4x_box9(form, 2)
problems_form5.12_box9 <- check_form5.4x_box9(form, 3)
problems_form5.14_box1a <- check_form5.14_box1a(form)
problems_form5.14_box1b <- check_form5.14_box1b(form)
problems_form5.14_box2 <- check_form5.14_box2(form)
problems_form5.14_box3 <- check_form5.14_box3(form)
problems_form6.1_box1a <- check_form6.1_box1a(form)
problems_form6.1_box1b <- check_form6.1_box1b(form)
problems_form6.1_box2a <- check_form6.1_box2a(form)
problems_form6.1_box2b <- check_form6.1_box2b(form)
problems_form6.1_box4 <- check_form6.1_box4(form)
problems_form7.1_box3 <- check_form7.x_box3(form, 1)
problems_form7.2_box3 <- check_form7.x_box3(form, 2)
problems_form7.3_box3 <- check_form7.x_box3(form, 3)
problems_form7.4_box3 <- check_form7.x_box3(form, 4)
problems_form7.1_box4a <- check_form7.x_box4a(form, 1)
problems_form7.2_box4a <- check_form7.x_box4a(form, 2)
problems_form7.3_box4a <- check_form7.x_box4a(form, 3)
problems_form7.4_box4a <- check_form7.x_box4a(form, 4)
problems_form7.1_box4b <- check_form7.x_box4b(form, 1)
problems_form7.2_box4b <- check_form7.x_box4b(form, 2)
problems_form7.3_box4b <- check_form7.x_box4b(form, 3)
problems_form7.4_box4b <- check_form7.x_box4b(form, 4)
problems_form7.1_box4c <- check_form7.x_box4c(form, 1)
problems_form7.2_box4c <- check_form7.x_box4c(form, 2)
problems_form7.3_box4c <- check_form7.x_box4c(form, 3)
problems_form7.4_box4c <- check_form7.x_box4c(form, 4)
# Check that consent date should be on the same day, or after the date of injury
# Check 1
problems_condate_injdate <- check_condate_injdate(form)
# Check that hospital admission date should be on the same day, or after the date of injury
# Check 2
problems_hspdate_injdate <- check_hspdate_injdate(form)
# Check that consent date should be 0 - 30 days after hospital admission date
# Check 3
problems_condate_hspdate <- check_condate_hspdate(form)
# Check that the number of orthopedic injuries stated on form 3.2 is consistent with the number of sets of injury forms and form5.14
# Check 4
problems_northinj_form5.x <- check_northinj_form5.x(form)
problems_northinj_form5.14 <- check_northinj_form5.14(form)
# Check that time from injury to hsp admission should be within +/- 24 hrs range of difference between injdate and hspdate
# Check 5
problems_injdate_hspdate <- check_injdate_hspdate(form)
# The time from injury to hospital admission should be within 24 hours if the patient is coming from the Accident/Injury Site
# Check 6
problems_admfrom_ihunits <- check_admfrom_ihunits(form)
# Check that for antibiotics first administered at the injury scene, time from injury to antibiotics administration is at most 5 hours before time from injury to hospital admission
# Check 7
problems_locabx <- check_locabx(form)
# Check that the location of fracture and the location of dislocation in one set of form5.x are related
# Also ensures only 1 fracture per set of form
# Checks 8 and 9
problems_fracwith_diswith_1 <- check_fracwith_diswith(form, 1)
problems_fracwith_diswith_2 <- check_fracwith_diswith(form, 2)
problems_fracwith_diswith_3 <- check_fracwith_diswith(form, 3)
# Check that the response to I&D is consistent with whether the fracture is open or closed
# Check 11
problems_openclos_iandd_1 <- check_openclos_iandd(form, 1)
problems_openclos_iandd_2 <- check_openclos_iandd(form, 2)
problems_openclos_iandd_3 <- check_openclos_iandd(form, 3)
# Check that details on the patient's surgery is consistent
# Check 12
problems_operat_failsurg_delsurg_1 <- check_operat_failsurg_delsurg(form, 1)
problems_operat_failsurg_delsurg_2 <- check_operat_failsurg_delsurg(form, 2)
problems_operat_failsurg_delsurg_3 <- check_operat_failsurg_delsurg(form, 3)
# Check that closed fracture injuries have have NA selected in form5.14
# Check 13
problems_openclos_NA <- check_openclos_NA(form)
# Check that he time difference between the time from injury to hsp admission and the time from injury to prep solution in ER is within +/- 24 hr range
# Check 14
problems_ihunits_ipunits <- check_ihunits_ipunits(form)
#' Check that date of follow-up is 30 or more days after hospital admission
#' Check 16
problems_formdate_ocrecyes <- check_formdate_ocrecyes(form)
#' Check that consent date is before discharge date
#' Check 17
problems_condate_hdcdate_dthdate <- check_condate_hdcdate_dthdate(form)
# Check for invalid/missing entries in form1.1
problems_invalid_form1.1 <- check_invalid_form1.1(form)
# Check for invalid/missing entries in form2.1
problems_invalid_form2.1 <- check_invalid_form2.1(form)
# Check for invalid/missing entries in form2.2
problems_invalid_form2.2 <- check_invalid_form2.2(form)
# Check for invalid/missing entries in form3.1, do not check question 4.1, intent of injury
problems_invalid_form3.1 <- check_invalid_form3.1(form, checkIntent = FALSE)
# Check for invalid/missing entries in form3.2
problems_invalid_form3.2 <- check_invalid_form3.2(form)
# Check for invalid/missing entries in form4.1
problems_invalid_form4.1 <- check_invalid_form4.1(form)
# Check for invalid/missing entries in form5.2
problems_invalid_form5.2x <- check_invalid_form5.2x(form, 1)
problems_invalid_form5.2x <- check_invalid_form5.2x(form, 2)
problems_invalid_form5.2x <- check_invalid_form5.2x(form, 3)
# Check initials
problems_initials <- check_initials(forms)
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