Fix 104 2

[finlaycampbell]

• no longer going from epicontacts -> igraph -> epicontacts which was causing a bunch of issues
• using the native square bracket subsetting instead and keeping all linelist and contact elements associated with a given cluster
• using 'either' not 'both' so that all contact elements of interested are returned, even if one of them is not in the linelist
• added functional tests to ensure the correct clusters are being returned

[zkamvar]

Note that this will fix #104 and #100

[zkamvar]

The tests work now and it is much easier to follow the logic of the tests for subsetting.

It should note that this also fixes #100:

library(epicontacts)
library(outbreaks)

x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
                      id="case_id", to="case_id", from="infector",
                      directed=TRUE)


x
#> 
#> /// Epidemiological Contacts //
#> 
#>   // class: epicontacts
#>   // 5,888 cases in linelist; 3,800 contacts;  directed 
#> 
#>   // linelist
#> 
#> # A tibble: 5,888 x 11
#>    id    generation date_of_infecti… date_of_onset date_of_hospita…
#>    <chr>      <int> <date>           <date>        <date>          
#>  1 d1fa…          0 NA               2014-04-07    2014-04-17      
#>  2 5337…          1 2014-04-09       2014-04-15    2014-04-20      
#>  3 f5c3…          1 2014-04-18       2014-04-21    2014-04-25      
#>  4 6c28…          2 NA               2014-04-27    2014-04-27      
#>  5 0f58…          2 2014-04-22       2014-04-26    2014-04-29      
#>  6 4973…          0 2014-03-19       2014-04-25    2014-05-02      
#>  7 f914…          3 NA               2014-05-03    2014-05-04      
#>  8 881b…          3 2014-04-26       2014-05-01    2014-05-05      
#>  9 e66f…          2 NA               2014-04-21    2014-05-06      
#> 10 20b6…          3 NA               2014-05-05    2014-05-06      
#> # … with 5,878 more rows, and 6 more variables: date_of_outcome <date>,
#> #   outcome <fct>, gender <fct>, hospital <fct>, lon <dbl>, lat <dbl>
#> 
#>   // contacts
#> 
#> # A tibble: 3,800 x 3
#>    from   to     source 
#>    <chr>  <chr>  <fct>  
#>  1 d1fafd 53371b other  
#>  2 cac51e f5c3d8 funeral
#>  3 f5c3d8 0f58c4 other  
#>  4 0f58c4 881bd4 other  
#>  5 8508df 40ae5f other  
#>  6 127d83 f547d6 funeral
#>  7 f5c3d8 d58402 other  
#>  8 20b688 d8a13d other  
#>  9 2ae019 a3c8b8 other  
#> 10 20b688 974bc1 other  
#> # … with 3,790 more rows
id <- "cac51e" ## it can be a vector of id as well


## subset based on cluster to which "cac51e" belongs
x_subset <- subset_clusters_by_id(x, id)
x_subset
#> 
#> /// Epidemiological Contacts //
#> 
#>   // class: epicontacts
#>   // 5 cases in linelist; 5 contacts;  directed 
#> 
#>   // linelist
#> 
#> # A tibble: 5 x 11
#>   id    generation date_of_infecti… date_of_onset date_of_hospita…
#>   <chr>      <int> <date>           <date>        <date>          
#> 1 f5c3…          1 2014-04-18       2014-04-21    2014-04-25      
#> 2 0f58…          2 2014-04-22       2014-04-26    2014-04-29      
#> 3 881b…          3 2014-04-26       2014-05-01    2014-05-05      
#> 4 d584…          2 2014-04-23       2014-05-01    2014-05-10      
#> 5 9000…          3 2014-05-09       2014-05-14    2014-05-17      
#> # … with 6 more variables: date_of_outcome <date>, outcome <fct>,
#> #   gender <fct>, hospital <fct>, lon <dbl>, lat <dbl>
#> 
#>   // contacts
#> 
#> # A tibble: 5 x 3
#>   from   to     source 
#>   <chr>  <chr>  <fct>  
#> 1 cac51e f5c3d8 funeral
#> 2 f5c3d8 0f58c4 other  
#> 3 0f58c4 881bd4 other  
#> 4 f5c3d8 d58402 other  
#> 5 d58402 900021 other

^{Created on 2019-06-06 by the reprex package (v0.3.0)}

[nistara]

Hi, I'm in the middle of hosting a workshop right now, so please go ahead and make the changes you think will fix things. This bug may/may not be related as well: #97 which I'd worked on fixing a while ago.

[zkamvar]

@finlaycampbell, merge when ready.