Reported by Bertrand Sudre during his time with the analytics cell of the EOC, DRC:
library(outbreaks)
library(epicontacts)
attach(mers_korea_2015)
str(mers_korea_2015)
#> List of 2
#> $ linelist:'data.frame': 162 obs. of 15 variables:
#> ..$ id : chr [1:162] "SK_1" "SK_2" "SK_3" "SK_4" ...
#> ..$ age : int [1:162] 68 63 76 46 50 71 28 46 56 44 ...
#> ..$ age_class : chr [1:162] "60-69" "60-69" "70-79" "40-49" ...
#> ..$ sex : Factor w/ 2 levels "F","M": 2 1 2 1 2 2 1 1 2 2 ...
#> ..$ place_infect : Factor w/ 2 levels "Middle East",..: 1 2 2 2 2 2 2 2 2 2 ...
#> ..$ reporting_ctry: Factor w/ 2 levels "China","South Korea": 2 2 2 2 2 2 2 2 2 1 ...
#> ..$ loc_hosp : Factor w/ 13 levels "365 Yeollin Clinic, Seoul",..: 10 10 10 10 1 10 10 13 10 10 ...
#> ..$ dt_onset : Date[1:162], format: "2015-05-11" "2015-05-18" ...
#> ..$ dt_report : Date[1:162], format: "2015-05-19" "2015-05-20" ...
#> ..$ week_report : Factor w/ 5 levels "2015_21","2015_22",..: 1 1 1 2 2 2 2 2 2 2 ...
#> ..$ dt_start_exp : Date[1:162], format: "2015-04-18" "2015-05-15" ...
#> ..$ dt_end_exp : Date[1:162], format: "2015-05-04" "2015-05-20" ...
#> ..$ dt_diag : Date[1:162], format: "2015-05-20" "2015-05-20" ...
#> ..$ outcome : Factor w/ 2 levels "Alive","Dead": 1 1 2 1 1 2 1 1 1 1 ...
#> ..$ dt_death : Date[1:162], format: NA NA ...
#> $ contacts:'data.frame': 98 obs. of 4 variables:
#> ..$ from : chr [1:98] "SK_14" "SK_14" "SK_14" "SK_14" ...
#> ..$ to : chr [1:98] "SK_113" "SK_116" "SK_41" "SK_112" ...
#> ..$ exposure : Factor w/ 5 levels "Contact with HCW",..: 2 2 2 2 2 2 2 2 2 2 ...
#> ..$ diff_dt_onset: int [1:98] 10 13 14 14 15 15 15 16 16 16 ...
x <- make_epicontacts(linelist = mers_korea_2015$linelist,
contacts = mers_korea_2015$contacts,
directed = TRUE)
str(x)
#> List of 3
#> $ linelist:'data.frame': 162 obs. of 15 variables:
#> ..$ id : chr [1:162] "SK_1" "SK_2" "SK_3" "SK_4" ...
#> ..$ age : int [1:162] 68 63 76 46 50 71 28 46 56 44 ...
#> ..$ age_class : chr [1:162] "60-69" "60-69" "70-79" "40-49" ...
#> ..$ sex : Factor w/ 2 levels "F","M": 2 1 2 1 2 2 1 1 2 2 ...
#> ..$ place_infect : Factor w/ 2 levels "Middle East",..: 1 2 2 2 2 2 2 2 2 2 ...
#> ..$ reporting_ctry: Factor w/ 2 levels "China","South Korea": 2 2 2 2 2 2 2 2 2 1 ...
#> ..$ loc_hosp : Factor w/ 13 levels "365 Yeollin Clinic, Seoul",..: 10 10 10 10 1 10 10 13 10 10 ...
#> ..$ dt_onset : Date[1:162], format: "2015-05-11" "2015-05-18" ...
#> ..$ dt_report : Date[1:162], format: "2015-05-19" "2015-05-20" ...
#> ..$ week_report : Factor w/ 5 levels "2015_21","2015_22",..: 1 1 1 2 2 2 2 2 2 2 ...
#> ..$ dt_start_exp : Date[1:162], format: "2015-04-18" "2015-05-15" ...
#> ..$ dt_end_exp : Date[1:162], format: "2015-05-04" "2015-05-20" ...
#> ..$ dt_diag : Date[1:162], format: "2015-05-20" "2015-05-20" ...
#> ..$ outcome : Factor w/ 2 levels "Alive","Dead": 1 1 2 1 1 2 1 1 1 1 ...
#> ..$ dt_death : Date[1:162], format: NA NA ...
#> $ contacts:'data.frame': 98 obs. of 4 variables:
#> ..$ from : chr [1:98] "SK_14" "SK_14" "SK_14" "SK_14" ...
#> ..$ to : chr [1:98] "SK_113" "SK_116" "SK_41" "SK_112" ...
#> ..$ exposure : Factor w/ 5 levels "Contact with HCW",..: 2 2 2 2 2 2 2 2 2 2 ...
#> ..$ diff_dt_onset: int [1:98] 10 13 14 14 15 15 15 16 16 16 ...
#> $ directed: logi TRUE
#> - attr(*, "class")= chr "epicontacts"
## this does not work
test <- as.igraph(x)
#> Error in as.igraph(x): could not find function "as.igraph"
test <- epicontacts::as.igraph.epicontacts(x)
#> Error: 'as.igraph.epicontacts' is not an exported object from 'namespace:epicontacts'
## this works
test <- epicontacts:::as.igraph.epicontacts(x)Created on 2019-12-10 by the reprex package (v0.3.0)
It would be good to ensure the conversion function is exported and documented.
Reported by Bertrand Sudre during his time with the analytics cell of the EOC, DRC:
Created on 2019-12-10 by the reprex package (v0.3.0)
It would be good to ensure the conversion function is exported and documented.