export as.igraph

[thibautjombart]

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.

[zkamvar]

This is a duplicate of #98. This issue exists because of weird S3 caveats: #98 (comment)

[thibautjombart]

It did sound familiar, and weirdly enough I managed not to find the other issue. Thanks.