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sendout.R
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sendout.R
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# LSQ SENDOUT
## Prepping libraries to be used ===================================================================
library('pacman')
p_load(pacman, RODBC, RDCOMClient, openxlsx)
# Pacman: package manager, allows you to load multiple packages
# RODBC: allows you to reach into Access database for patient information
# RDCOMClient: sends emails to participants, me, Kim
## Modified redcap_read_oneshot from REDCapR library ===============================================
redcap_read_oneshot <- function (redcap_uri,
token,
records = NULL,
records_collapsed = "",
fields = NULL,
fields_collapsed = "",
events = NULL,
events_collapsed = "",
export_data_access_groups = FALSE,
raw_or_label = "raw",
verbose = TRUE,
config_options = NULL)
{
start_time <- Sys.time()
if (missing(redcap_uri))
stop("The required parameter `redcap_uri` was missing from the call to `redcap_read_oneshot()`.")
if (missing(token))
stop("The required parameter `token` was missing from the call to `redcap_read_oneshot()`.")
if (all(nchar(records_collapsed) == 0))
records_collapsed <- ifelse(is.null(records), "", paste0(records,
collapse = ","))
if ((length(fields_collapsed) == 0L) | is.null(fields_collapsed) |
all(nchar(fields_collapsed) == 0L))
fields_collapsed <- ifelse(is.null(fields), "", paste0(fields,
collapse = ","))
if (all(nchar(events_collapsed) == 0))
events_collapsed <- ifelse(is.null(events), "", paste0(events,
collapse = ","))
export_data_access_groups_string <- ifelse(export_data_access_groups,
"true", "false")
post_body <- list(token = token, content = "record", format = "csv",
type = "flat", rawOrLabel = raw_or_label, exportDataAccessGroups = export_data_access_groups_string,
records = records_collapsed, fields = fields_collapsed,
events = events_collapsed, exportSurveyFields = "true")
result <- httr::POST(url = redcap_uri, body = post_body,
config = config_options)
status_code <- result$status
LSQdownload <<- status_code
success <- (status_code == 200L)
raw_text <- httr::content(result, "text")
elapsed_seconds <- as.numeric(difftime(Sys.time(), start_time,
units = "secs"))
regex_cannot_connect <- "^The hostname \\((.+)\\) / username \\((.+)\\) / password \\((.+)\\) combination could not connect.+"
if (any(grepl(regex_cannot_connect, raw_text)))
success <- FALSE
if (success) {
try({
ds <- utils::read.csv(text = raw_text, stringsAsFactors = FALSE)
}, silent = TRUE)
if (exists("ds") & (class(ds) == "data.frame")) {
outcome_message <- paste0(format(nrow(ds), big.mark = ",",
scientific = FALSE, trim = TRUE), " records and ",
format(length(ds), big.mark = ",", scientific = FALSE,
trim = TRUE), " columns were read from REDCap in ",
round(elapsed_seconds, 1), " seconds. The http status code was ",
status_code, ".")
raw_text <- ""
}
else {
success <- FALSE
ds <- data.frame()
outcome_message <- paste0("The REDCap read failed. The http status code was ",
status_code, ". The 'raw_text' returned was '",
raw_text, "'.")
}
}
else {
ds <- data.frame()
outcome_message <- paste0("The REDCapR read/export operation was not successful. The error message was:\n",
raw_text)
}
if (verbose)
message(outcome_message)
return(list(data = ds, success = success, status_code = status_code,
outcome_message = outcome_message, records_collapsed = records_collapsed,
fields_collapsed = fields_collapsed, events_collapsed = events_collapsed,
elapsed_seconds = elapsed_seconds, raw_text = raw_text))
}
## First Reach into accdb, to check which LSQs have been completed, and by who =====================
myconnection <- odbcDriverConnect("Driver={Microsoft Access Driver (*.mdb, *.accdb)};
DBQ= filepath")
enrolment <- sqlFetch(myconnection, "OBS Enrolment Log")
followup <- sqlFetch(myconnection, "OBS Followup Log")
close(myconnection)
enrolment <- enrolment[, c("OBSEnrolmentID", "EDC")]
total <- merge(enrolment, followup, by="OBSEnrolmentID")
total$OBSVisitDate <- as.Date(total$OBSVisitDate)
total$DeliveryDate <- as.Date(total$DeliveryDate)
total$EDC <- as.Date(total$EDC)
#drop all subjects who have delivered more than 14 weeks ago
total <- total[total$EDC >= as.Date("05/30/16", "%m/%d/%y"), ]
total <- total[!is.na(total$OBSEnrolmentID), ]
OBSID <- as.character(unique(total$OBSEnrolmentID))
#function to see if patient gave consent or didn't withdrawl
invisible(sapply(OBSID, function(OBSEnrolmentID){
enrol_table <- total[total$OBSEnrolmentID == OBSEnrolmentID, ]
if(sum(enrol_table$OBSPatientWithdrawl) > 0 |
sum(enrol_table[, "Fetal Demise/Termination"]) > 0 |
sum(enrol_table[, "Neonatal death"]) > 0 ){ #add more variables which may eliminate subjects
OBSID <<- OBSID[!OBSID %in% c(OBSEnrolmentID)]
}
}))
## Creates check_if_completed data frame + fills it with OBS ids and associated LSQs not completed=========
check_if_completed_1 <- c()
check_if_completed_2 <- c()
check_if_completed_3 <- c()
invisible(sapply(OBSID, function(enrolmentID){
enrol_table <- total[total$OBSEnrolmentID == enrolmentID, ]
if(sum(enrol_table[, "LSQ(1)Given"]) > 0 &
sum(enrol_table[, "LSQ(1)Returned"]) == 0) {
check_if_completed_1 <<- c(check_if_completed_1, enrolmentID)
}
if(sum(enrol_table[, "LSQ(2)Given"]) > 0 &
sum(enrol_table[, "LSQ(2)Returned"]) == 0) {
check_if_completed_2 <<- c(check_if_completed_2, enrolmentID)
}
if(sum(enrol_table[, "LSQ(3)Given"]) > 0 &
sum(enrol_table[, "LSQ(3)Returned"]) == 0) {
check_if_completed_3 <<- c(check_if_completed_3, enrolmentID)
}
}))
repeat{
## Use the API to check if surveys have been completed (REDCapR) =============================================
# LSQ1
secret_token <- "token"
api_url <- "api link"
LSQ1complete <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_1_timestamp",
"lifestyle_questionnaire_1_complete"))$data
LSQ1download <- LSQdownload
LSQ1complete$lifestyle_questionnaire_1_timestamp <- as.Date(LSQ1complete$lifestyle_questionnaire_1_timestamp,
"%Y-%m-%d")
LSQ1complete <- LSQ1complete[LSQ1complete[, "lifestyle_questionnaire_1_complete"] == 2, ]
secret_token <- "token"
api_url <- "api link"
LSQ1complete2 <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_1_timestamp",
"lifestyle_questionnaire_1_complete"))$data
LSQ1download2 <- LSQdownload
LSQ1complete2$lifestyle_questionnaire_1_timestamp <- as.Date(LSQ1complete2$lifestyle_questionnaire_1_timestamp,
"%Y-%m-%d")
LSQ1complete2 <- LSQ1complete2[LSQ1complete2[, "lifestyle_questionnaire_1_complete"] == 2, ]
LSQ1complete <- rbind(LSQ1complete, LSQ1complete2)
# LSQ2
secret_token <- "token"
api_url <- "api link"
LSQ2complete <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_2_timestamp",
"lifestyle_questionnaire_2_complete"))$data
LSQ2download <- LSQdownload
LSQ2complete$lifestyle_questionnaire_2_timestamp <- as.Date(LSQ2complete$lifestyle_questionnaire_2_timestamp,
"%Y-%m-%d")
LSQ2complete <- LSQ2complete[LSQ2complete[, "lifestyle_questionnaire_2_complete"] == 2, ]
secret_token <- "token"
api_url <- "api link"
LSQ2complete2 <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_2_timestamp",
"lifestyle_questionnaire_2_complete"))$data
LSQ2download2 <- LSQdownload
LSQ2complete2$lifestyle_questionnaire_2_timestamp <- as.Date(LSQ2complete2$lifestyle_questionnaire_2_timestamp,
"%Y-%m-%d")
LSQ2complete2 <- LSQ2complete2[LSQ2complete2[, "lifestyle_questionnaire_2_complete"] == 2, ]
LSQ2complete <- rbind(LSQ2complete, LSQ2complete2)
# LSQ3
secret_token <- "token"
api_url <- "api link"
LSQ3complete <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_3_timestamp",
"lifestyle_questionnaire_3_complete"))$data
LSQ3complete <- LSQ3complete[LSQ3complete$obs_study_id < 91600000, ] #because I added SMH to MSH survey; eventually need to delete when cleaned up
LSQ3complete$lifestyle_questionnaire_3_timestamp <- as.Date(LSQ3complete$lifestyle_questionnaire_3_timestamp,
"%Y-%m-%d")
LSQ3download <- LSQdownload
LSQ3complete <- LSQ3complete[LSQ3complete[, "lifestyle_questionnaire_3_complete"] == 2, ]
secret_token <- "token"
api_url <- "api link"
LSQ3complete2 <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_3_timestamp",
"lifestyle_questionnaire_3_complete"))$data
LSQ3complete2 <- LSQ3complete2[LSQ3complete2$obs_study_id < 91600000, ]
LSQ3complete2$lifestyle_questionnaire_3_timestamp <- as.Date(LSQ3complete2$lifestyle_questionnaire_3_timestamp,
"%Y-%m-%d")
LSQ3download2 <- LSQdownload
LSQ3complete2 <- LSQ3complete2[LSQ3complete2[, "lifestyle_questionnaire_3_complete"] == 2, ]
LSQ3complete <- rbind(LSQ3complete, LSQ3complete2)
if(LSQ1download == 200 & LSQ2download == 200 & LSQ3download == 200 & LSQ1download2 == 200 & LSQ2download2 == 200 & LSQ3download2 == 200){
break
} else {
Sys.sleep(1800)
}
}
## Completed LSQs, format change so things work with access ========================================
completed_1 <- LSQ1complete[LSQ1complete$obs_study_id %in% as.integer(gsub("-", "", check_if_completed_1)), c("obs_study_id", "lifestyle_questionnaire_1_timestamp")]
names(completed_1) <- c("OBSID", "DateComplete")
completed_1$OBSID <- gsub("^912", "912-", as.character(completed_1$OBSID))
completed_1$emailstatus <- rep("LSQ(1)Returned", nrow(completed_1))
rownames(completed_1 ) <- NULL
completed_2 <- LSQ2complete[LSQ2complete$obs_study_id %in% as.integer(gsub("-", "", check_if_completed_2)), c("obs_study_id", "lifestyle_questionnaire_2_timestamp")]
names(completed_2) <- c("OBSID", "DateComplete")
completed_2$OBSID <- gsub("^912", "912-", as.character(completed_2$OBSID))
completed_2$emailstatus <- rep("LSQ(2)Returned", nrow(completed_2))
rownames(completed_2 ) <- NULL
completed_3 <- LSQ3complete[LSQ3complete$obs_study_id %in% as.integer(gsub("-", "", check_if_completed_3)), c("obs_study_id", "lifestyle_questionnaire_3_timestamp")]
names(completed_3) <- c("OBSID", "DateComplete")
completed_3$OBSID <- gsub("^912", "912-", as.character(completed_3$OBSID))
completed_3$emailstatus <- rep("LSQ(3)Returned", nrow(completed_3))
rownames(completed_3 ) <- NULL
## LSQ completion entries in database ==============================================================
myconnection <- odbcDriverConnect("Driver={Microsoft Access Driver (*.mdb, *.accdb)};
DBQ= filepath")
enrolment <- sqlFetch(myconnection, "OBS Enrolment Log")
if(nrow(completed_1) > 0){
invisible(sapply(completed_1$OBSID, function(obsid){
PatientID <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientID"]
OBSEnrolmentID <- obsid
PatientFirstName <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientFirstName"]
PatientSurname <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientSurname"]
PatientSurname <- gsub("'", "''", PatientSurname)
DateComplete <- completed_1[which(completed_1$OBSID == obsid), ][1, "DateComplete"]
emailstatus <- "LSQ(1)Returned"
sqlQuery(myconnection, paste0("INSERT INTO OBSFollowupLog (PatientID,",
" OBSEnrolmentID, PatientFirstName,",
" PatientSurname, OBSVisitDate, \"",
emailstatus,"\") VALUES ('", PatientID,"', '",
OBSEnrolmentID,"', '", PatientFirstName,"', '",
PatientSurname,"', '", DateComplete,
"', 1)"))
}))
}
if(nrow(completed_2) > 0){
invisible(sapply(completed_2$OBSID, function(obsid){
PatientID <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientID"]
OBSEnrolmentID <- obsid
PatientFirstName <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientFirstName"]
PatientSurname <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientSurname"]
PatientSurname <- gsub("'", "''", PatientSurname)
DateComplete <- completed_2[which(completed_2$OBSID == obsid), ][1, "DateComplete"]
emailstatus <- "LSQ(2)Returned"
sqlQuery(myconnection, paste0("INSERT INTO OBSFollowupLog (PatientID,",
" OBSEnrolmentID, PatientFirstName,",
" PatientSurname, OBSVisitDate, \"",
emailstatus,"\") VALUES ('", PatientID,"', '",
OBSEnrolmentID,"', '", PatientFirstName,"', '",
PatientSurname,"', '", DateComplete,
"', 1)"))
}))
}
if(nrow(completed_3) > 0){
invisible(sapply(completed_3$OBSID, function(obsid){
PatientID <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientID"]
OBSEnrolmentID <- obsid
PatientFirstName <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientFirstName"]
PatientSurname <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientSurname"]
PatientSurname <- gsub("'", "''", PatientSurname)
DateComplete <- completed_3[which(completed_3$OBSID == obsid), ][1, "DateComplete"]
emailstatus <- "LSQ(3)Returned"
sqlQuery(myconnection, paste0("INSERT INTO OBSFollowupLog (PatientID,",
" OBSEnrolmentID, PatientFirstName,",
" PatientSurname, OBSVisitDate, \"",
emailstatus,"\") VALUES ('", PatientID,"', '",
OBSEnrolmentID,"', '", PatientFirstName,"', '",
PatientSurname,"', '", DateComplete,
"', 1)"))
}))
}
close(myconnection)
## Connecting to accdb to determine new patients ===================================================
myconnection <- odbcDriverConnect("Driver={Microsoft Access Driver (*.mdb, *.accdb)};
DBQ= filepath")
enrolment <- sqlFetch(myconnection, "OBS Enrolment Log")
followup <- sqlFetch(myconnection, "OBS Followup Log")
close(myconnection)
enrolment <- enrolment[, c("OBSEnrolmentID", "EDC", "DIPLateEntry", "DIPCurEnrol")]
total <- merge(enrolment, followup, by="OBSEnrolmentID")
total$OBSVisitDate <- as.Date(total$OBSVisitDate)
total$DeliveryDate <- as.Date(total$DeliveryDate)
total$EDC <- as.Date(total$EDC)
#drop all subjects who have delivered more than 14 weeks ago
total <- total[total$EDC >= as.Date("05/30/16", "%m/%d/%y"), ]
total <- total[!is.na(total$OBSEnrolmentID), ]
OBSID <- as.character(unique(total$OBSEnrolmentID))
#function to see if patient gave consent or didn't withdrawl
invisible(sapply(OBSID, function(OBSEnrolmentID){
enrol_table <- total[total$OBSEnrolmentID == OBSEnrolmentID, ]
if(sum(enrol_table$OBSPatientWithdrawl) > 0 |
sum(enrol_table[, "Fetal Demise/Termination"]) > 0 |
sum(enrol_table[, "Neonatal death"]) > 0 ){ #add more variables which may eliminate subjects
OBSID <<- OBSID[!OBSID %in% c(OBSEnrolmentID)]
}
}))
LSQ_send_list <- data.frame(obsid = character(),
emailstatus = character(),
stringsAsFactors = FALSE)
statuses <- c("LSQ(1)Given", "LSQ(1)Followup1", "LSQ(1)Followup2", "LSQ(1)Followup3")
LSQselection <- function(enrol_table){
for(i in 2:4){
if(sum(enrol_table[, statuses[i]]) == 0) { #TOOK OUT LENGHT_TO_STOP argument; need to replace it, if not, delete length_to_stop
if((enrol_table[enrol_table[, statuses[(i - 1)]] == 1, "OBSVisitDate"] + 13) <= Sys.Date()){ #has it been 14 days since the LSQ was last sent out?
LSQ_send_list[nrow(LSQ_send_list) + 1, "obsid"] <<- enrolmentID
LSQ_send_list[nrow(LSQ_send_list), "emailstatus"] <<- statuses[i]
# obsid <<- c(obsid, enrolmentID)
# emailstatus <<- c(emailstatus, statuses[i])
break
} else {
break
}
}
}
}
# creates 2 vectors (obsid, emailstatus) for people who need to be sent LSQs based on Access DB
invisible(sapply(OBSID, function(enrolmentID){
enrol_table <- total[total$OBSEnrolmentID == enrolmentID, ]
enrolmentID <<- enrolmentID
print(enrolmentID)
if(sum(enrol_table[, "LSQ(1)Returned"], enrol_table[, "LSQ(1)Followup3"],
enrol_table[, "LSQ1Refused"], enrol_table[, "Paper LSQ1"]) < 1) { # add LSQ1refusal here?
if(sum(enrol_table[, "LSQ(1)Given"]) == 0){
if(enrol_table[1, "EDC"] -(40*7) + (11*7) <= Sys.Date ()) {
LSQ_send_list[nrow(LSQ_send_list) + 1, "obsid"] <<- enrolmentID
LSQ_send_list[nrow(LSQ_send_list), "emailstatus"] <<- "LSQ(1)Given"
}
} else if(sum(enrol_table[, "LSQ(1)Given"]) == 1){
statuses <<- gsub("\\([2-3]\\)", "(1)", statuses)
LSQselection(enrol_table)
}
} else if((sum(enrol_table[, "LSQ(2)Returned"], enrol_table[, "LSQ(2)Followup3"],
enrol_table[, "LSQ2Refused"], enrol_table[, "Paper LSQ2"]) < 1)) {
if(sum(enrol_table[, "LSQ(2)Given"]) == 0){
if((enrol_table[1, "EDC"] - (40*7) + (26*7) <= Sys.Date ()) |
((sum(enrol_table[, "DIPLateEntry"]) > 0) ) # check if this makes sense
){
LSQ_send_list[nrow(LSQ_send_list) + 1, "obsid"] <<- enrolmentID
LSQ_send_list[nrow(LSQ_send_list), "emailstatus"] <<- "LSQ(2)Given"
}
} else if(sum(enrol_table[, "LSQ(2)Given"]) == 1) {
statuses <<- gsub("\\([1|3]\\)", "(2)", statuses)
LSQselection(enrol_table)
}
} else if((sum(enrol_table[, "LSQ(3)Returned"], enrol_table[, "LSQ(3)Followup3"],
enrol_table[, "LSQ3Refused"], enrol_table[, "Paper LSQ3"]) < 1)){
if(sum(enrol_table[, "LSQ(3)Given"]) == 0){
if(sum(!is.na(enrol_table$DeliveryDate)) == 1){
if(enrol_table$DeliveryDate[!is.na(enrol_table$DeliveryDate)] + (5*7) <= Sys.Date()){ #checks recorded delivery date; send after 5 weeks
LSQ_send_list[nrow(LSQ_send_list) + 1, "obsid"] <<- enrolmentID
LSQ_send_list[nrow(LSQ_send_list), "emailstatus"] <<- "LSQ(3)Given"
}
} else if(sum(!is.na(enrol_table$DeliveryDate)) == 0){ #### if no deliver date, send LSQ3 based on EDC
if(enrol_table[1, "EDC"] + (6*7) <= Sys.Date()){
LSQ_send_list[nrow(LSQ_send_list) + 1, "obsid"] <<- enrolmentID
LSQ_send_list[nrow(LSQ_send_list), "emailstatus"] <<- "LSQ(3)Given"
}
} else {
print(paste0(enrolmentID, " has more than one delivery date"))
}
} else if(sum(enrol_table[, "LSQ(3)Given"]) == 1) {
statuses <<- gsub("\\([1-2]\\)", "(3)", statuses)
LSQselection(enrol_table)
}
}
}))
## Accessing patient contact information from drive ================================================
dir.create("T:temporary folder)
file.copy("T:/Patient contact information.xlsx",
"T:/Patient contact information.xlsx")
# connect to "Patient contact information" to get email addresses
repeat{
tryCatch({
myconnection <- odbcConnectExcel2007("T:Patient contact information.xlsx")
emails <<- sqlFetch(myconnection, "Sheet1$")
close(myconnection)
break
}, warning=function(w) {
Sys.sleep(1800)
})
}
unlink("Patient contact information/Temp", recursive = TRUE)
emails <- emails[, c("OBSID", "E-mail")]
names(emails) <- c("OBSID", "email")
emails <- emails[complete.cases(emails), ]
emails$OBSID <- sapply(emails$OBSID, function(x){
toString(paste0("912-", sprintf("%05.0f", x)))
})
# Validation for emails: presence of an '@' sign
emails <- emails[grepl("@", emails$email), ]
emails <- emails[emails$OBSID %in% as.character(LSQ_send_list$obsid), ]
emails <- merge(LSQ_send_list, emails, by.x = "obsid", by.y = "OBSID", all = TRUE)
emails <- emails[!is.na(emails$emailstatus), ]
emails$email <- gsub(" ", "", emails$email)
emails <- emails[!is.na(emails$email), ]
# check if email address has '@' and domain'
if (sum(!grepl("^[A-z0-9.]+@[A-z0-9]+\\.[A-z0-9]+", emails$email)) > 0){
emailIssues <- emails[, "obsid"][!grepl("^[A-z0-9.]+@[A-z0-9]+\\.[A-z0-9]+", emails$email)]
## Email Coworker about corrections that need to be made ================================================
OutApp <- COMCreate("Outlook.Application")
outMail <- OutApp$CreateItem(0)
outMail[["To"]] <- as.character("email")
outMail[["SentOnBehalfofName"]] <- "email"
outMail[["subject"]] <- "OBS Email Issues; check contact info"
outMail[["body"]] <- paste0("Hey, these patients have errors in their email addresses on the Patient Contat Information file: \n\n",
as.character(emailIssues))
outMail$Send()
emails <- emails[grepl("^[A-z0-9.]+@[A-z0-9]+\\.[A-z0-9]+", emails$email), ]
}
## Email patients LSQ Emails (initial, follow up 1, follow up 2) ===================================
pwlist <- read.csv("T:/file with questionnaire links and passwords.xlsx", nrow = 10000)
emailsubjects <- function(obsid){
OutApp <- COMCreate("Outlook.Application")
outMail <- OutApp$CreateItem(0)
outMail[["To"]] <- as.character(emails$email[emails$obsid == obsid])
outMail[["SentOnBehalfofName"]] <- "studyemail@organization.ca"
if(emails$emailstatus[emails$obsid == obsid] == "LSQ(1)Given"){
link <- pwlist$lsq1_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Subject Content"
outMail[["body"]] <- paste0("Here is a link\n\n",
link,
"\n\n
Your password will be in a separate email. ")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(1)Followup1"){
link <- pwlist$lsq1_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Follow-up 1"
outMail[["body"]] <- paste0("Reminder:\n\n",
link,
"\n\nYour password will be in a separate email. ")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(1)Followup2" | emails$emailstatus[emails$obsid == obsid] == "LSQ(1)Followup3"){
link <- pwlist$lsq1_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Follow-up 2"
outMail[["body"]] <- paste0("Reminder:\n\n",
link,
"\n\nYour password will be in a separate email. ")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(2)Given"){
link <- pwlist$lsq2_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Subject Content"
outMail[["body"]] <- paste0("Here is a link:\n\n",
link,
"\n\nYour password will be in a separate email ")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(2)Followup1"){
link <- pwlist$lsq2_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Folloq up 1"
outMail[["body"]] <- paste0("Here is a link ",
link,
"\n\nYour password will follow in a separate email ")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(2)Followup2" | emails$emailstatus[emails$obsid == obsid] == "LSQ(2)Followup3"){
link <- pwlist$lsq2_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Follow Up 2"
outMail[["body"]] <- paste0("Here is a link",
link,
"\n\nYour password will follow in a separate email ")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(3)Given"){
link <- pwlist$lsq3_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Subject Content "
outMail[["body"]] <- paste0("Here is a link:\n\n",
link,
"\n\nYour password will follow in a separate email ")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(3)Followup1"){
link <- pwlist$lsq3_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Follow up 2"
outMail[["body"]] <- paste0("Here is a link:\n\n",
link,
"\n\nYour password will follow in a separate email ")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(3)Followup2" | emails$emailstatus[emails$obsid == obsid] == "LSQ(3)Followup3"){
link <- pwlist$lsq3_website[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Follow up 2"
outMail[["body"]] <- paste0("Here is a link\n\n",
link,
"\n\nYour password will follow in a separate email.")
}
outMail$Send()
Sys.sleep(5)
}
## Email subjects passwords ====================================================================
invisible(sapply(emails$obsid, emailsubjects))
emailsubjectspw <- function(obsid){
OutApp <- COMCreate("Outlook.Application")
outMail <- OutApp$CreateItem(0)
outMail[["To"]] <- as.character(emails$email[emails$obsid == obsid])
outMail[["SentOnBehalfofName"]] <- "studyemail@organization.ca"
if(emails$emailstatus[emails$obsid == obsid] == "LSQ(1)Given" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(1)Followup1" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(1)Followup2" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(1)Followup3"){
pw <- pwlist$lsq1_password[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Password"
outMail[["body"]] <- paste0("Here is your password:\n\n",
pw,
"\n\nPlease click the link provided in the previous email and enter the above password to access your personal Lifestyle Questionnaire.")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(2)Given" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(2)Followup1" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(2)Followup2" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(2)Followup3"){
pw <- pwlist$lsq2_password[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Password"
outMail[["body"]] <- paste0("Here is your password:\n\n",
pw,
"\n\nPlease click the link provided in the previous email and enter the above password to access your personal Lifestyle Questionnaire.")
} else if(emails$emailstatus[emails$obsid == obsid] == "LSQ(3)Given" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(3)Followup1" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(3)Followup2" |
emails$emailstatus[emails$obsid == obsid] == "LSQ(3)Followup3"){
pw <- pwlist$lsq3_password[pwlist$obs_subject_id == toString(obsid)]
outMail[["subject"]] <- "Password"
outMail[["body"]] <- paste0("Here is your password:\n\n",
pw,
"\n\nPlease click the link provided in the previous email and enter the above password to access your personal Lifestyle Questionnaire.")
}
outMail$Send()
Sys.sleep(5)
}
invisible(sapply(emails$obsid, emailsubjectspw))
## Updating accdb with information on who has been emailed or not ==================================
myconnection <- odbcDriverConnect("Driver={Microsoft Access Driver (*.mdb, *.accdb)};
DBQ= filepath")
updateaccess <- function(obsid){
PatientID <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientID"]
OBSEnrolmentID <- obsid
PatientFirstName <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientFirstName"]
PatientSurname <- followup[which(followup$OBSEnrolmentID == obsid), ][1, "PatientSurname"]
PatientSurname <- gsub("'", "''", PatientSurname) # to compensate for people with apostrophes in their last name
emailstatus <- emails[which(emails$obsid == obsid), ][1, "emailstatus"]
sqlQuery(myconnection, paste0("INSERT INTO OBSFollowupLog (PatientID,",
" OBSEnrolmentID, PatientFirstName,",
" PatientSurname, OBSVisitDate, \"",
emailstatus,"\") VALUES ('", PatientID,"', '",
OBSEnrolmentID,"', '", PatientFirstName,"', '",
PatientSurname,"', '", as.character(Sys.Date()),
"', 1)"))
}
invisible(sapply(as.character(emails$obsid), updateaccess))
close(myconnection)
## Email Coworker + myself a success message and completions ============================================================
OutApp <- COMCreate("Outlook.Application")
outMail <- OutApp$CreateItem(0)
outMail[["To"]] <- as.character("justin@organization.ca; coworker@organization.ca)
outMail[["SentOnBehalfofName"]] <- "studyemail@organization.ca"
outMail[["subject"]] <- paste0(as.character(Sys.Date()), " LSQ Distribution")
outMail[["body"]] <- paste0("Total Number of LSQs sent for the week of ",
as.character(Sys.Date()), ": ", nrow(emails),
"\n\nLSQ 1 Completed for the week: ", length(completed_1$OBSID),
"\n\nLSQ 2 completed for the week: ", length(completed_2$OBSID),
"\n\nLSQ 3 completed for the week: ", length(completed_3$OBSID))
outMail$Send()
outMail$Send()
## Checking LSQ2 + LSQ3 completion for EPDS analysis ======================================================
repeat{
secret_token <- "F5F5DF07561C69F942A351DF702A25DF"
api_url <- "https://redcap.smh.ca/redcap/api/"
LSQ2complete <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_2_timestamp",
"lifestyle_questionnaire_2_complete",
"lwk_funny",
"lwk_lookfo",
"lwk_blame",
"lwk_anxio",
"lwk_scare",
"lwk_top",
"lwk_sleep",
"lwk_miser",
"lwk_cryin",
"lwk_harm"))$data
LSQ2download <- LSQdownload
LSQ2complete$lifestyle_questionnaire_2_timestamp <- as.Date(LSQ2complete$lifestyle_questionnaire_2_timestamp, "%Y-%m-%d")
LSQ2complete <- LSQ2complete[LSQ2complete[, "lifestyle_questionnaire_2_complete"] == 2, ]
secret_token <- "81B266259963503578E01CA69255E8A8"
api_url <- "https://redcap.smh.ca/redcap/api/"
LSQ2complete2 <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_2_timestamp",
"lifestyle_questionnaire_2_complete",
"lwk_funny",
"lwk_lookfo",
"lwk_blame",
"lwk_anxio",
"lwk_scare",
"lwk_top",
"lwk_sleep",
"lwk_miser",
"lwk_cryin",
"lwk_harm"))$data
LSQ2download2 <- LSQdownload
LSQ2complete2$lifestyle_questionnaire_2_timestamp <- as.Date(LSQ2complete2$lifestyle_questionnaire_2_timestamp, "%Y-%m-%d")
LSQ2complete2 <- LSQ2complete2[LSQ2complete2[, "lifestyle_questionnaire_2_complete"] == 2, ]
LSQ2complete <- rbind(LSQ2complete, LSQ2complete2)
secret_token <- "5A8058DBF425BDD1284B504B893AA711"
api_url <- "https://redcap.smh.ca/redcap/api/"
LSQ3complete <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_3_timestamp",
"lifestyle_questionnaire_3_complete",
"lweek_laugh",
"lweek_enjoy",
"lweek_blame",
"lweek_anxious",
"lweek_panic",
"lweek_top",
"lweek_unhappy",
"lweek_miserable",
"lweek_crying",
"lweek_harming"))$data
LSQ3complete <- LSQ3complete[LSQ3complete$obs_study_id < 91600000, ] #because I added SMH to MSH survey; eventually need to delete when cleaned up
LSQ3complete$lifestyle_questionnaire_3_timestamp <- as.Date(LSQ3complete$lifestyle_questionnaire_3_timestamp, "%Y-%m-%d")
LSQ3download <- LSQdownload
LSQ3complete <- LSQ3complete[LSQ3complete[, "lifestyle_questionnaire_3_complete"] == 2, ]
secret_token <- "637FBFC0C50DCC153C37AE7942481534"
api_url <- "https://redcap.smh.ca/redcap/api/"
LSQ3complete2 <- redcap_read_oneshot(redcap_uri = api_url,
token = secret_token,
fields = c("obs_study_id",
"lifestyle_questionnaire_3_timestamp",
"lifestyle_questionnaire_3_complete",
"lweek_laugh",
"lweek_enjoy",
"lweek_blame",
"lweek_anxious",
"lweek_panic",
"lweek_top",
"lweek_unhappy",
"lweek_miserable",
"lweek_crying",
"lweek_harming"))$data
LSQ3complete2 <- LSQ3complete2[LSQ3complete2$obs_study_id < 91600000, ] #because I added SMH to MSH survey; eventually need to delete when cleaned up
LSQ3complete2$lifestyle_questionnaire_3_timestamp <- as.Date(LSQ3complete2$lifestyle_questionnaire_3_timestamp, "%Y-%m-%d")
LSQ3download2 <- LSQdownload
LSQ3complete2 <- LSQ3complete2[LSQ3complete2[, "lifestyle_questionnaire_3_complete"] == 2, ]
LSQ3complete <- rbind(LSQ3complete, LSQ3complete2)
if(LSQ2download == 200 & LSQ3download == 200 & LSQ2download2 == 200 & LSQ3download2 == 200){
break
} else {
Sys.sleep(1800)
}
}
# subset only those who have completed since last check
LSQ2complete <- LSQ2complete[LSQ2complete$obs_study_id %in% as.numeric(gsub("-", "", completed_2$OBSID)), ]
LSQ3complete <- LSQ3complete[LSQ3complete$obs_study_id %in% as.numeric(gsub("-", "", completed_3$OBSID)), ]
## EDPS Conversion scales ==========================================================================
# EPDS conversion, LSQ2
LSQ2complete$lwk_funny <- LSQ2complete$lwk_funny - 1
LSQ2complete$lwk_lookfo <- LSQ2complete$lwk_lookfo - 1
LSQ2complete$lwk_blame[LSQ2complete$lwk_blame == 2] <- "Yes, most of the time"
LSQ2complete$lwk_blame[LSQ2complete$lwk_blame == 3] <- "Yes, some of the time"
LSQ2complete$lwk_blame[LSQ2complete$lwk_blame == 1] <- "Not very often"
LSQ2complete$lwk_blame[LSQ2complete$lwk_blame == 4] <- "No, never"
LSQ2complete$lwk_blame[LSQ2complete$lwk_blame == "Yes, most of the time"] <- 3
LSQ2complete$lwk_blame[LSQ2complete$lwk_blame == "Yes, some of the time"] <- 2
LSQ2complete$lwk_blame[LSQ2complete$lwk_blame == "Not very often"] <- 1
LSQ2complete$lwk_blame[LSQ2complete$lwk_blame == "No, never"] <- 0
LSQ2complete$lwk_blame <- as.numeric(LSQ2complete$lwk_blame)
LSQ2complete$lwk_anxio[LSQ2complete$lwk_anxio == 2] <- "No, not at all"
LSQ2complete$lwk_anxio[LSQ2complete$lwk_anxio == 1] <- "Hardly ever"
LSQ2complete$lwk_anxio[LSQ2complete$lwk_anxio == 3] <- "Yes, sometimes"
LSQ2complete$lwk_anxio[LSQ2complete$lwk_anxio == 4] <- "Yes, very often"
LSQ2complete$lwk_anxio[LSQ2complete$lwk_anxio == "No, not at all"] <- 0
LSQ2complete$lwk_anxio[LSQ2complete$lwk_anxio == "Hardly ever"] <- 1
LSQ2complete$lwk_anxio[LSQ2complete$lwk_anxio == "Yes, sometimes"] <- 2
LSQ2complete$lwk_anxio[LSQ2complete$lwk_anxio == "Yes, very often"] <- 3
LSQ2complete$lwk_anxio <- as.numeric(LSQ2complete$lwk_anxio)
LSQ2complete$lwk_scare[LSQ2complete$lwk_scare == 1] <- "Yes, quite a lot"
LSQ2complete$lwk_scare[LSQ2complete$lwk_scare == 2] <- "Yes, sometimes"
LSQ2complete$lwk_scare[LSQ2complete$lwk_scare == 3] <- "No, not much"
LSQ2complete$lwk_scare[LSQ2complete$lwk_scare == 4] <- "No, not at all"
LSQ2complete$lwk_scare[LSQ2complete$lwk_scare == "Yes, quite a lot"] <- 3
LSQ2complete$lwk_scare[LSQ2complete$lwk_scare == "Yes, sometimes"] <- 2
LSQ2complete$lwk_scare[LSQ2complete$lwk_scare == "No, not much"] <- 1
LSQ2complete$lwk_scare[LSQ2complete$lwk_scare == "No, not at all"] <- 0
LSQ2complete$lwk_scare <- as.numeric(LSQ2complete$lwk_scare)
LSQ2complete$lwk_top[LSQ2complete$lwk_top == 1] <- "Yes, most of the time I haven't been able to cope at all"
LSQ2complete$lwk_top[LSQ2complete$lwk_top == 2] <- "Yes, sometimes I haven't been coping as well as usual"
LSQ2complete$lwk_top[LSQ2complete$lwk_top == 3] <- "No, most of the time I have copied quite well"
LSQ2complete$lwk_top[LSQ2complete$lwk_top == 4] <- "No, I have been coping as well as ever"
LSQ2complete$lwk_top[LSQ2complete$lwk_top == "Yes, most of the time I haven't been able to cope at all"] <- 3
LSQ2complete$lwk_top[LSQ2complete$lwk_top == "Yes, sometimes I haven't been coping as well as usual"] <- 2
LSQ2complete$lwk_top[LSQ2complete$lwk_top == "No, most of the time I have copied quite well"] <- 1
LSQ2complete$lwk_top[LSQ2complete$lwk_top == "No, I have been coping as well as ever"] <- 0
LSQ2complete$lwk_top <- as.numeric(LSQ2complete$lwk_top)
LSQ2complete$lwk_sleep[LSQ2complete$lwk_sleep == 1] <- "Yes, most of the time"
LSQ2complete$lwk_sleep[LSQ2complete$lwk_sleep == 2] <- "Yes, sometimes"
LSQ2complete$lwk_sleep[LSQ2complete$lwk_sleep == 3] <- "Not very often"
LSQ2complete$lwk_sleep[LSQ2complete$lwk_sleep == 4] <- "No, not at all"
LSQ2complete$lwk_sleep[LSQ2complete$lwk_sleep == "Yes, most of the time"] <- 3
LSQ2complete$lwk_sleep[LSQ2complete$lwk_sleep == "Yes, sometimes"] <- 2
LSQ2complete$lwk_sleep[LSQ2complete$lwk_sleep == "Not very often"] <- 1
LSQ2complete$lwk_sleep[LSQ2complete$lwk_sleep == "No, not at all"] <- 0
LSQ2complete$lwk_sleep <- as.numeric(LSQ2complete$lwk_sleep)
LSQ2complete$lwk_miser[LSQ2complete$lwk_miser == 2] <- "Yes, most of the time"
LSQ2complete$lwk_miser[LSQ2complete$lwk_miser == 3] <- "Yes, quite often"
LSQ2complete$lwk_miser[LSQ2complete$lwk_miser == 1] <- "Not very often"
LSQ2complete$lwk_miser[LSQ2complete$lwk_miser == 4] <- "No, not at all"
LSQ2complete$lwk_miser[LSQ2complete$lwk_miser == "Yes, most of the time"] <- 3
LSQ2complete$lwk_miser[LSQ2complete$lwk_miser == "Yes, quite often"] <- 2
LSQ2complete$lwk_miser[LSQ2complete$lwk_miser == "Not very often"] <- 1
LSQ2complete$lwk_miser[LSQ2complete$lwk_miser == "No, not at all"] <- 0
LSQ2complete$lwk_miser <- as.numeric(LSQ2complete$lwk_miser)
LSQ2complete$lwk_cryin[LSQ2complete$lwk_cryin == 1] <- "Yes, most of the time"
LSQ2complete$lwk_cryin[LSQ2complete$lwk_cryin == 2] <- "Yes, quite often"
LSQ2complete$lwk_cryin[LSQ2complete$lwk_cryin == 3] <- "Only occasionally"
LSQ2complete$lwk_cryin[LSQ2complete$lwk_cryin == 4] <- "No, never"
LSQ2complete$lwk_cryin[LSQ2complete$lwk_cryin == "Yes, most of the time"] <- 3
LSQ2complete$lwk_cryin[LSQ2complete$lwk_cryin == "Yes, quite often"] <- 2
LSQ2complete$lwk_cryin[LSQ2complete$lwk_cryin == "Only occasionally"] <- 1
LSQ2complete$lwk_cryin[LSQ2complete$lwk_cryin == "No, never"] <- 0
LSQ2complete$lwk_cryin <- as.numeric(LSQ2complete$lwk_cryin)
LSQ2complete$lwk_harm[LSQ2complete$lwk_harm == 1] <- "Yes, quite often"
LSQ2complete$lwk_harm[LSQ2complete$lwk_harm == 2] <- "Sometimes"
LSQ2complete$lwk_harm[LSQ2complete$lwk_harm == 3] <- "Hardly ever"
LSQ2complete$lwk_harm[LSQ2complete$lwk_harm == 4] <- "Never"
LSQ2complete$lwk_harm[LSQ2complete$lwk_harm == "Yes, quite often"] <- 3
LSQ2complete$lwk_harm[LSQ2complete$lwk_harm == "Sometimes"] <- 2
LSQ2complete$lwk_harm[LSQ2complete$lwk_harm == "Hardly ever"] <- 1
LSQ2complete$lwk_harm[LSQ2complete$lwk_harm == "Never"] <- 0
LSQ2complete$lwk_harm <- as.numeric(LSQ2complete$lwk_harm)
LSQ2complete$EPDS <- rowSums(LSQ2complete[, c("lwk_funny",
"lwk_lookfo",
"lwk_blame",
"lwk_anxio",
"lwk_scare",
"lwk_top",
"lwk_sleep",
"lwk_miser",
"lwk_cryin",
"lwk_harm")], na.rm = TRUE)
LSQ2EPDSreview <- LSQ2complete$obs_study_id[LSQ2complete$EPDS >= 13 |
LSQ2complete$lwk_harm == 3 |
LSQ2complete$lwk_harm == 2 |
LSQ2complete$lwk_harm == 1]
LSQ2EPDSreview <- LSQ2EPDSreview[!is.na(LSQ2EPDSreview)]
LSQ2EPDSreviewscore <- LSQ2complete$EPDS[LSQ2complete$obs_study_id %in% LSQ2EPDSreview]
LSQ2EPDSreviewharm <- LSQ2complete$lwk_harm[LSQ2complete$obs_study_id %in% LSQ2EPDSreview]
# EPDS conversion, LSQ3
LSQ3complete$lweek_laugh[LSQ3complete$lweek_laugh == 1] <- "As much as I always could"
LSQ3complete$lweek_laugh[LSQ3complete$lweek_laugh == 2] <- "Not quite so much now"
LSQ3complete$lweek_laugh[LSQ3complete$lweek_laugh == 3] <- "Definitely not so much now"
LSQ3complete$lweek_laugh[LSQ3complete$lweek_laugh == 4] <- "Not at all"
LSQ3complete$lweek_laugh[LSQ3complete$lweek_laugh == "As much as I always could"] <- 0
LSQ3complete$lweek_laugh[LSQ3complete$lweek_laugh == "Not quite so much now"] <- 1
LSQ3complete$lweek_laugh[LSQ3complete$lweek_laugh == "Definitely not so much now"] <- 2
LSQ3complete$lweek_laugh[LSQ3complete$lweek_laugh == "Not at all"] <- 3
LSQ3complete$lweek_laugh <- as.numeric(LSQ3complete$lweek_laugh)
LSQ3complete$lweek_enjoy[LSQ3complete$lweek_enjoy == 1] <- "As much as I ever did"
LSQ3complete$lweek_enjoy[LSQ3complete$lweek_enjoy == 2] <- "Rather less than I used to"
LSQ3complete$lweek_enjoy[LSQ3complete$lweek_enjoy == 3] <- "Definitely less than I used to"
LSQ3complete$lweek_enjoy[LSQ3complete$lweek_enjoy == 4] <- "Hardly at all"
LSQ3complete$lweek_enjoy[LSQ3complete$lweek_enjoy == "As much as I ever did"] <- 0
LSQ3complete$lweek_enjoy[LSQ3complete$lweek_enjoy == "Rather less than I used to"] <- 1
LSQ3complete$lweek_enjoy[LSQ3complete$lweek_enjoy == "Definitely less than I used to"] <- 2
LSQ3complete$lweek_enjoy[LSQ3complete$lweek_enjoy == "Hardly at all"] <- 3
LSQ3complete$lweek_enjoy <- as.numeric(LSQ3complete$lweek_enjoy)
LSQ3complete$lweek_blame[LSQ3complete$lweek_blame == 2] <- "Yes, most of the time"
LSQ3complete$lweek_blame[LSQ3complete$lweek_blame == 3] <- "Yes, some of the time"
LSQ3complete$lweek_blame[LSQ3complete$lweek_blame == 1] <- "Not very often"
LSQ3complete$lweek_blame[LSQ3complete$lweek_blame == 4] <- "No, never"
LSQ3complete$lweek_blame[LSQ3complete$lweek_blame == "Yes, most of the time"] <- 3
LSQ3complete$lweek_blame[LSQ3complete$lweek_blame == "Yes, some of the time"] <- 2
LSQ3complete$lweek_blame[LSQ3complete$lweek_blame == "Not very often"] <- 1
LSQ3complete$lweek_blame[LSQ3complete$lweek_blame == "No, never"] <- 0
LSQ3complete$lweek_blame <- as.numeric(LSQ3complete$lweek_blame)
LSQ3complete$lweek_anxious[LSQ3complete$lweek_anxious == 1] <- "No, not at all"
LSQ3complete$lweek_anxious[LSQ3complete$lweek_anxious == 2] <- "Hardly ever"
LSQ3complete$lweek_anxious[LSQ3complete$lweek_anxious == 3] <- "Yes, sometimes"
LSQ3complete$lweek_anxious[LSQ3complete$lweek_anxious == 4] <- "Yes, very often"
LSQ3complete$lweek_anxious[LSQ3complete$lweek_anxious == "No, not at all"] <- 0
LSQ3complete$lweek_anxious[LSQ3complete$lweek_anxious == "Hardly ever"] <- 1
LSQ3complete$lweek_anxious[LSQ3complete$lweek_anxious == "Yes, sometimes"] <- 2
LSQ3complete$lweek_anxious[LSQ3complete$lweek_anxious == "Yes, very often"] <- 3
LSQ3complete$lweek_anxious <- as.numeric(LSQ3complete$lweek_anxious)
LSQ3complete$lweek_panic[LSQ3complete$lweek_panic == 1] <- "Yes, quite a lot"
LSQ3complete$lweek_panic[LSQ3complete$lweek_panic == 2] <- "Yes, sometimes"
LSQ3complete$lweek_panic[LSQ3complete$lweek_panic == 3] <- "No, not much"
LSQ3complete$lweek_panic[LSQ3complete$lweek_panic == 4] <- "No, not at all"
LSQ3complete$lweek_panic[LSQ3complete$lweek_panic == "Yes, quite a lot"] <- 3
LSQ3complete$lweek_panic[LSQ3complete$lweek_panic == "Yes, sometimes"] <- 2
LSQ3complete$lweek_panic[LSQ3complete$lweek_panic == "No, not much"] <- 1
LSQ3complete$lweek_panic[LSQ3complete$lweek_panic == "No, not at all"] <- 0
LSQ3complete$lweek_panic <- as.numeric(LSQ3complete$lweek_panic)
LSQ3complete$lweek_top[LSQ3complete$lweek_top == 1] <- "Yes, most of the time I haven't been able to cope at all"
LSQ3complete$lweek_top[LSQ3complete$lweek_top == 2] <- "Yes, sometimes I haven't been coping as well as usual"
LSQ3complete$lweek_top[LSQ3complete$lweek_top == 3] <- "No, most of the time I have coped quite well"
LSQ3complete$lweek_top[LSQ3complete$lweek_top == 4] <- "No, I have been coping as well as ever"
LSQ3complete$lweek_top[LSQ3complete$lweek_top == "Yes, most of the time I haven't been able to cope at all"] <- 3
LSQ3complete$lweek_top[LSQ3complete$lweek_top == "Yes, sometimes I haven't been coping as well as usual"] <- 2
LSQ3complete$lweek_top[LSQ3complete$lweek_top == "No, most of the time I have coped quite well"] <- 1
LSQ3complete$lweek_top[LSQ3complete$lweek_top == "No, I have been coping as well as ever"] <- 0
LSQ3complete$lweek_top <- as.numeric(LSQ3complete$lweek_top)
LSQ3complete$lweek_unhappy[LSQ3complete$lweek_unhappy == 1] <- "Yes, most of the time"
LSQ3complete$lweek_unhappy[LSQ3complete$lweek_unhappy == 2] <- "Yes, sometimes"
LSQ3complete$lweek_unhappy[LSQ3complete$lweek_unhappy == 3] <- "Not very often"
LSQ3complete$lweek_unhappy[LSQ3complete$lweek_unhappy == 4] <- "No, not at all"
LSQ3complete$lweek_unhappy[LSQ3complete$lweek_unhappy == "Yes, most of the time"] <- 3
LSQ3complete$lweek_unhappy[LSQ3complete$lweek_unhappy == "Yes, sometimes"] <- 2
LSQ3complete$lweek_unhappy[LSQ3complete$lweek_unhappy == "Not very often"] <- 1
LSQ3complete$lweek_unhappy[LSQ3complete$lweek_unhappy == "No, not at all"] <- 0
LSQ3complete$lweek_unhappy <- as.numeric(LSQ3complete$lweek_unhappy)
LSQ3complete$lweek_miserable[LSQ3complete$lweek_miserable == 1] <- "Yes, most of the time"
LSQ3complete$lweek_miserable[LSQ3complete$lweek_miserable == 2] <- "Yes, quite often"
LSQ3complete$lweek_miserable[LSQ3complete$lweek_miserable == 3] <- "Not very often"
LSQ3complete$lweek_miserable[LSQ3complete$lweek_miserable == 4] <- "No, not at all"
LSQ3complete$lweek_miserable[LSQ3complete$lweek_miserable == "Yes, most of the time"] <- 3
LSQ3complete$lweek_miserable[LSQ3complete$lweek_miserable == "Yes, quite often"] <- 2
LSQ3complete$lweek_miserable[LSQ3complete$lweek_miserable == "Not very often"] <- 1
LSQ3complete$lweek_miserable[LSQ3complete$lweek_miserable == "No, not at all"] <- 0
LSQ3complete$lweek_miserable <- as.numeric(LSQ3complete$lweek_miserable)
LSQ3complete$lweek_crying[LSQ3complete$lweek_crying == 1] <- "Yes, most of the time"
LSQ3complete$lweek_crying[LSQ3complete$lweek_crying == 2] <- "Yes, quite often"
LSQ3complete$lweek_crying[LSQ3complete$lweek_crying == 3] <- "Only occasionally"
LSQ3complete$lweek_crying[LSQ3complete$lweek_crying == 4] <- "No, never"
LSQ3complete$lweek_crying[LSQ3complete$lweek_crying == "Yes, most of the time"] <- 3
LSQ3complete$lweek_crying[LSQ3complete$lweek_crying == "Yes, quite often"] <- 2
LSQ3complete$lweek_crying[LSQ3complete$lweek_crying == "Only occasionally"] <- 1
LSQ3complete$lweek_crying[LSQ3complete$lweek_crying == "No, never"] <- 0
LSQ3complete$lweek_crying <- as.numeric(LSQ3complete$lweek_crying)
LSQ3complete$lweek_harming[LSQ3complete$lweek_harming == 4] <- "Yes, quite often"
LSQ3complete$lweek_harming[LSQ3complete$lweek_harming == 5] <- "Sometimes"
LSQ3complete$lweek_harming[LSQ3complete$lweek_harming == 6] <- "Hardly ever"
LSQ3complete$lweek_harming[LSQ3complete$lweek_harming == 7] <- "Never"