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myFun_readTransPairs.R
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myFun_readTransPairs.R
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## Prepare calendar day -> No. of days since 2020/01/01
Get_calndr_str <- function(days_vec, tar_mth_str, tar_yr_str) {
tar_date_str = sapply(
days_vec,
function (tar_date, mth, yr) paste(yr, mth, toString(tar_date), sep = "/"),
mth = tar_mth_str,
yr = tar_yr_str
)
return( tar_date_str );
}
Get_ndays_from_20200101 <- function( tar_yr_str ) {
# Jan 01 to Jan 31
days_vec1 = seq(1, 31);
date_mth1 = Get_calndr_str(days_vec1, "1", tar_yr_str);
# Feb 01 to Feb 29
days_vec2 = seq(1, 29);
date_mth2 = Get_calndr_str(days_vec2, "2", tar_yr_str);
days_vec2 = days_vec2 + 31;
df_uniq_date = tibble(
nday = c(days_vec1, days_vec2),
str = as.Date( c(date_mth1, date_mth2) )
)
return( df_uniq_date )
}
Get_onset_day <- function(onset_date, df_uniq_date) {
tar_vec = sapply(
onset_date,
function (tar_date, df_uniq_date) {
if (str_detect(tar_date, "unknown")) {
tar_nday = 1000000;
} else if (str_detect(tar_date, "local")) {
tar_nday = 200000;
} else {
tar_nday = df_uniq_date$nday[ df_uniq_date$str == as.Date(tar_date) ];
}
return(tar_nday)
},
df_uniq_date = df_uniq_date
)
return(tar_vec)
}
Set_uniq_caseID <- function( tarID_vec ) {
result_vec = unname( sapply( tarID_vec, function (tar_id) paste0("-", tar_id, "-") ) );
return(result_vec)
}
#### Read raw transmission pair data ####
## Transform into "linelist" and "contacts" as package "epicontacts" (http://www.repidemicsconsortium.org/epicontacts/)
Read_TransPairs <- function( file_name ) {
df_uniq_date = Get_ndays_from_20200101( "2020" ); # Calender dates -> No. of days since 2020/01/01
raw_linelist <- read_csv( file_name );
raw_linelist$infector_id <- Set_uniq_caseID( raw_linelist$infector_id );
raw_linelist$infectee_id <- Set_uniq_caseID( raw_linelist$infectee_id );
tar_linelist <- raw_linelist %>% filter(
!str_detect(raw_linelist$infector_onsetDate, "unknown" ) &
!str_detect(raw_linelist$infectee_onsetDate, "unknown" )
)
tar_linelist_p1 <- tar_linelist
## Get onset times (days) of infector and infectee -----------------------------
tar_linelist_p1$infector_onsetDate <- unname( Get_onset_day(tar_linelist_p1$infector_onsetDate, df_uniq_date) );
tar_linelist_p1$infectee_onsetDate <- unname( Get_onset_day(tar_linelist_p1$infectee_onsetDate, df_uniq_date) );
# infectors' onset between 9 Jan 2020 and 13 Feb 2020
tar_linelist = tar_linelist_p1 %>% filter( infector_onsetDate >= 9 & infector_onsetDate < 45 );
## Isolation delay: time delay from onset to isolation of infector --------------------------
tar_linelist$infector_isolateDate_beforeSymptom <- unname( Get_onset_day( tar_linelist$infector_isolateDate_beforeSymptom, df_uniq_date ) );
tar_linelist$infector_isolateDate_afterSymptom <- unname( Get_onset_day( tar_linelist$infector_isolateDate_afterSymptom, df_uniq_date ) );
tar_linelist$infector_firstHospitalVisit <- unname( Get_onset_day( tar_linelist$infector_firstHospitalVisit, df_uniq_date ) );
tar_linelist$infector_labConfirmDate <- unname( Get_onset_day( tar_linelist$infector_labConfirmDate, df_uniq_date ) );
date_isol_vec = mapply(
function (A, B) min(A, B),
A = tar_linelist$infector_isolateDate_beforeSymptom,
B = tar_linelist$infector_isolateDate_afterSymptom
)
tar_linelist <- tar_linelist %>% mutate(
infector_isolateDelay = date_isol_vec - tar_linelist$infector_onsetDate
)
## Isolation delay: time delay from onset to isolation of infectee --------------------------
tar_linelist$infectee_isolateDate_beforeSymptom <- unname( Get_onset_day( tar_linelist$infectee_isolateDate_beforeSymptom, df_uniq_date ) );
tar_linelist$infectee_isolateDate_afterSymptom <- unname( Get_onset_day( tar_linelist$infectee_isolateDate_afterSymptom, df_uniq_date ) );
tar_linelist$infectee_firstHospitalVisit <- unname( Get_onset_day( tar_linelist$infectee_firstHospitalVisit, df_uniq_date ) );
date2_isol_vec = mapply(
function (A, B) min(A, B),
A = tar_linelist$infectee_isolateDate_beforeSymptom,
B = tar_linelist$infectee_isolateDate_afterSymptom
)
tar_linelist <- tar_linelist %>% mutate(
infectee_isolateDelay = date2_isol_vec - tar_linelist$infectee_onsetDate
)
#### Transform to linelist and contacts for "epicontact" ####
linelist = data.frame(
id = c( tar_linelist$infector_id, tar_linelist$infectee_id ),
age = c( tar_linelist$infector_age, tar_linelist$infectee_age ),
sex = c( tar_linelist$infector_sex, tar_linelist$infectee_sex ),
city_report = c( tar_linelist$infector_reportCity, tar_linelist$infectee_reportCity ),
city_infect = c( tar_linelist$infector_infectCity, tar_linelist$infectee_infectCity ),
date_onset = c( tar_linelist$infector_onsetDate, tar_linelist$infectee_onsetDate ),
delay_isol = c( tar_linelist$infector_isolateDelay, tar_linelist$infectee_isolateDelay )
)
linelist_uniq = distinct(linelist, id, .keep_all = T)
contacts = data.frame(
from = tar_linelist$infector_id,
to = tar_linelist$infectee_id,
date_onset_infector = tar_linelist$infector_onsetDate,
date_onset_infectee = tar_linelist$infectee_onsetDate,
serialInterval = tar_linelist$infectee_onsetDate - tar_linelist$infector_onsetDate,
is_household = tar_linelist$isHousehold,
delayIsol_infector = tar_linelist$infector_isolateDelay,
delayIsol_infectee = tar_linelist$infectee_isolateDelay
)
newlist = list(
"tar_linelist" = tar_linelist,
"linelist" = linelist_uniq,
"contacts" = contacts
)
return( newlist )
}