epicontacts: Manipulation, Visualisation and Analysis of Epidemiological Contact Data

Introduction

epicontacts aims to facilitate manipulation, visualisation and analysis of epidemiological contact data. Such datasets inherently have network components, in which nodes are typically cases and reported contacts or exposures are (directed or undirected) edges. This package provides a convenient data structure as well as functionality specific to handle these data.

library(outbreaks)
library(epicontacts)

Loading Data

epicontacts provides a convenient structure to store heterogeneous epidemiological contact network data (i.e. nodes and edges) in a single object. The epicontacts class must contain two components: a line list and a contact dataset.

Each row of the line list should represent unique observations of cases, and each row of the contact list should represent unique pairs of contacts. Each can include arbitrary features, but both datasets should share an identification scheme.

Example Dataset

The example that follows will use the mers_korea_2015, which is a dataset (in list format) distributed in the outbreaks package.

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 ...

What features are in the line list?

colnames((mers_korea_2015$linelist))

##  [1] "id"             "age"            "age_class"      "sex"           
##  [5] "place_infect"   "reporting_ctry" "loc_hosp"       "dt_onset"      
##  [9] "dt_report"      "week_report"    "dt_start_exp"   "dt_end_exp"    
## [13] "dt_diag"        "outcome"        "dt_death"

What about the contact dataset?

colnames((mers_korea_2015$contacts))

## [1] "from"          "to"            "exposure"      "diff_dt_onset"

Creating `epicontacts` Object

In order to create the epicontacts object, both the line list and contact data frames must be passed to make_epicontacts(). This function accommodates instances when the respective identifiers are not the first columns of these data frames (see the “id”, “from” and “to” arguments). make_epicontacts() can also account for contact networks that have a direction (see “directed” argument).

merskor15 <- make_epicontacts(linelist = mers_korea_2015$linelist,
                              contacts = mers_korea_2015$contacts, 
                              directed = FALSE)
class(merskor15)

## [1] "epicontacts"

summary(merskor15)

## 
## /// Overview //
##   // number of unique IDs in linelist: 162
##   // number of unique IDs in contacts: 97
##   // number of unique IDs in both: 97
##   // number of contacts: 98
##   // contacts with both cases in linelist: 100 %
## 
## /// Degrees of the network //
##   // in-degree summary:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   1.000   1.000   1.000   2.021   1.000  39.000 
## 
##   // out-degree summary:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   1.000   1.000   1.000   2.021   1.000  39.000 
## 
##   // in and out degree summary:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   1.000   1.000   1.000   2.021   1.000  39.000 
## 
## /// Attributes //
##   // attributes in linelist:
##  age age_class sex place_infect reporting_ctry loc_hosp dt_onset dt_report week_report dt_start_exp dt_end_exp dt_diag outcome dt_death
## 
##   // attributes in contacts:
##  exposure diff_dt_onset

Data Manipulation

Access Unique Identifiers

The summary() method above provided counts for the number unique cases in both the contact and line list. The get_id() function retrieves similar information but as vectors of identifiers. This can be parameterized as follows:

linelist: IDs in the line list data
contacts: IDs in the contact dataset (“from” and “to” combined)
from: IDs in the “from” column of contact datset
to IDs in the “to” column of contact dataset
all: IDs that appear anywhere in either dataset
common: IDs that appear in both contacts dataset and line list

What are the first ten IDs in the contacts dataset?

contacts_ids <- get_id(merskor15, "contacts")
head(contacts_ids, n = 10)

##  [1] "SK_14"  "SK_16"  "SK_6"   "SK_87"  "SK_1"   "SK_15"  "SK_76"  "SK_11" 
##  [9] "SK_12"  "SK_118"

How many IDs are common to both?

length(get_id(merskor15, "common"))

## [1] 97

Subsetting

The subset() method for epicontacts objects allows for, among other things, pruning of networks based on values of node and edge attributes. These values must be passed as named lists to the respective argument.

subset(merskor15, node_attribute = list("outcome" = "Dead", "sex" = "M"), 
       edge_attribute = list("exposure" = "Emergency room"))

## 
## /// Epidemiological Contacts //
## 
##   // class: epicontacts
##   // 14 cases in linelist; 33 contacts;  non directed 
## 
##   // linelist
## 
## # A tibble: 14 × 15
##    id       age age_class sex   place_infect  reporting_ctry loc_hosp dt_onset  
##    <chr>  <int> <chr>     <fct> <fct>         <fct>          <fct>    <date>    
##  1 SK_3      76 70-79     M     Outside Midd… South Korea    Pyeongt… 2015-05-20
##  2 SK_6      71 70-79     M     Outside Midd… South Korea    Pyeongt… 2015-05-24
##  3 SK_23     73 70-79     M     Outside Midd… South Korea    Konyang… 2015-05-31
##  4 SK_24     78 70-79     M     Outside Midd… South Korea    Konyang… 2015-05-31
##  5 SK_28     58 50-59     M     Outside Midd… South Korea    Pyeongt… 2015-05-29
##  6 SK_36     82 80-89     M     Outside Midd… South Korea    Konyang… NA        
##  7 SK_38     49 40-49     M     Outside Midd… South Korea    Dae Che… 2015-05-23
##  8 SK_64     75 70-79     M     Outside Midd… South Korea    Samsung… 2015-06-04
##  9 SK_81     62 60-69     M     Outside Midd… South Korea    Samsung… NA        
## 10 SK_83     65 60-69     M     Outside Midd… South Korea    Konyang… 2015-06-01
## 11 SK_84     80 80-89     M     Outside Midd… South Korea    Dae Che… 2015-06-05
## 12 SK_90     62 60-69     M     Outside Midd… South Korea    Samsung… NA        
## 13 SK_98     58 50-59     M     Outside Midd… South Korea    Samsung… 2015-06-04
## 14 SK_123    65 60-69     M     Outside Midd… South Korea    Samsung… 2015-06-07
## # ℹ 7 more variables: dt_report <date>, week_report <fct>, dt_start_exp <date>,
## #   dt_end_exp <date>, dt_diag <date>, outcome <fct>, dt_death <date>
## 
##   // contacts
## 
## # A tibble: 33 × 4
##    from  to     exposure       diff_dt_onset
##    <chr> <chr>  <fct>                  <int>
##  1 SK_14 SK_113 Emergency room            10
##  2 SK_14 SK_116 Emergency room            13
##  3 SK_14 SK_41  Emergency room            14
##  4 SK_14 SK_112 Emergency room            14
##  5 SK_14 SK_100 Emergency room            15
##  6 SK_14 SK_114 Emergency room            15
##  7 SK_14 SK_136 Emergency room            15
##  8 SK_14 SK_47  Emergency room            16
##  9 SK_14 SK_110 Emergency room            16
## 10 SK_14 SK_122 Emergency room            16
## # ℹ 23 more rows

In addition to subsetting by node and edge attributes, networks can be pruned to only include components that are connected to certain nodes. The “id” argument takes a vector of nodes and returns the line list of individuals that “touch” those IDs.

nodes <- c("SK_14","SK_145")                  
subset(merskor15, cluster_id = nodes)

## 
## /// Epidemiological Contacts //
## 
##   // class: epicontacts
##   // 97 cases in linelist; 98 contacts;  non directed 
## 
##   // linelist
## 
## # A tibble: 97 × 15
##    id      age age_class sex   place_infect   reporting_ctry loc_hosp dt_onset  
##    <chr> <int> <chr>     <fct> <fct>          <fct>          <fct>    <date>    
##  1 SK_1     68 60-69     M     Middle East    South Korea    Pyeongt… 2015-05-11
##  2 SK_2     63 60-69     F     Outside Middl… South Korea    Pyeongt… 2015-05-18
##  3 SK_3     76 70-79     M     Outside Middl… South Korea    Pyeongt… 2015-05-20
##  4 SK_4     46 40-49     F     Outside Middl… South Korea    Pyeongt… 2015-05-25
##  5 SK_5     50 50-59     M     Outside Middl… South Korea    365 Yeo… 2015-05-25
##  6 SK_6     71 70-79     M     Outside Middl… South Korea    Pyeongt… 2015-05-24
##  7 SK_7     28 20-29     F     Outside Middl… South Korea    Pyeongt… 2015-05-21
##  8 SK_8     46 40-49     F     Outside Middl… South Korea    Seoul C… 2015-05-26
##  9 SK_10    44 40-49     M     Outside Middl… China          Pyeongt… 2015-05-21
## 10 SK_11    79 70-79     F     Outside Middl… South Korea    Pyeongt… 2015-05-20
## # ℹ 87 more rows
## # ℹ 7 more variables: dt_report <date>, week_report <fct>, dt_start_exp <date>,
## #   dt_end_exp <date>, dt_diag <date>, outcome <fct>, dt_death <date>
## 
##   // contacts
## 
## # A tibble: 98 × 4
##    from  to     exposure       diff_dt_onset
##    <chr> <chr>  <fct>                  <int>
##  1 SK_14 SK_113 Emergency room            10
##  2 SK_14 SK_116 Emergency room            13
##  3 SK_14 SK_41  Emergency room            14
##  4 SK_14 SK_112 Emergency room            14
##  5 SK_14 SK_100 Emergency room            15
##  6 SK_14 SK_114 Emergency room            15
##  7 SK_14 SK_136 Emergency room            15
##  8 SK_14 SK_47  Emergency room            16
##  9 SK_14 SK_110 Emergency room            16
## 10 SK_14 SK_122 Emergency room            16
## # ℹ 88 more rows

The subset() method for epicontacts objects also accepts cluster size parameters (see “cs”, “cs_min” and “cs_max” arguments).

subset(merskor15, cs = 3)

## 
## /// Epidemiological Contacts //
## 
##   // class: epicontacts
##   // 3 cases in linelist; 2 contacts;  non directed 
## 
##   // linelist
## 
## # A tibble: 3 × 15
##   id       age age_class sex   place_infect   reporting_ctry loc_hosp dt_onset  
##   <chr>  <int> <chr>     <fct> <fct>          <fct>          <fct>    <date>    
## 1 SK_76     75 70-79     F     Outside Middl… South Korea    Samsung… 2015-06-05
## 2 SK_145    37 30-39     M     Outside Middl… South Korea    Samsung… 2015-06-10
## 3 SK_150    44 40-49     M     Outside Middl… South Korea    Konkuk … 2015-06-11
## # ℹ 7 more variables: dt_report <date>, week_report <fct>, dt_start_exp <date>,
## #   dt_end_exp <date>, dt_diag <date>, outcome <fct>, dt_death <date>
## 
##   // contacts
## 
## # A tibble: 2 × 4
##   from  to     exposure         diff_dt_onset
##   <chr> <chr>  <fct>                    <int>
## 1 SK_76 SK_145 Contact with HCW             5
## 2 SK_76 SK_150 Hospital room                6

subset(merskor15, cs_min = 10, cs_max = 100)

## 
## /// Epidemiological Contacts //
## 
##   // class: epicontacts
##   // 94 cases in linelist; 96 contacts;  non directed 
## 
##   // linelist
## 
## # A tibble: 94 × 15
##    id      age age_class sex   place_infect   reporting_ctry loc_hosp dt_onset  
##    <chr> <int> <chr>     <fct> <fct>          <fct>          <fct>    <date>    
##  1 SK_1     68 60-69     M     Middle East    South Korea    Pyeongt… 2015-05-11
##  2 SK_2     63 60-69     F     Outside Middl… South Korea    Pyeongt… 2015-05-18
##  3 SK_3     76 70-79     M     Outside Middl… South Korea    Pyeongt… 2015-05-20
##  4 SK_4     46 40-49     F     Outside Middl… South Korea    Pyeongt… 2015-05-25
##  5 SK_5     50 50-59     M     Outside Middl… South Korea    365 Yeo… 2015-05-25
##  6 SK_6     71 70-79     M     Outside Middl… South Korea    Pyeongt… 2015-05-24
##  7 SK_7     28 20-29     F     Outside Middl… South Korea    Pyeongt… 2015-05-21
##  8 SK_8     46 40-49     F     Outside Middl… South Korea    Seoul C… 2015-05-26
##  9 SK_10    44 40-49     M     Outside Middl… China          Pyeongt… 2015-05-21
## 10 SK_11    79 70-79     F     Outside Middl… South Korea    Pyeongt… 2015-05-20
## # ℹ 84 more rows
## # ℹ 7 more variables: dt_report <date>, week_report <fct>, dt_start_exp <date>,
## #   dt_end_exp <date>, dt_diag <date>, outcome <fct>, dt_death <date>
## 
##   // contacts
## 
## # A tibble: 96 × 4
##    from  to     exposure       diff_dt_onset
##    <chr> <chr>  <fct>                  <int>
##  1 SK_14 SK_113 Emergency room            10
##  2 SK_14 SK_116 Emergency room            13
##  3 SK_14 SK_41  Emergency room            14
##  4 SK_14 SK_112 Emergency room            14
##  5 SK_14 SK_100 Emergency room            15
##  6 SK_14 SK_114 Emergency room            15
##  7 SK_14 SK_136 Emergency room            15
##  8 SK_14 SK_47  Emergency room            16
##  9 SK_14 SK_110 Emergency room            16
## 10 SK_14 SK_122 Emergency room            16
## # ℹ 86 more rows

Visualisation

Default Plotting Method

One of the main features of epicontacts is its visualisation capabilities. As a default, the package uses interactive plotting based on the visNetwork package¹. This interactivity is particularly useful for visualising large datasets.

plot(merskor15)

The above is a generic method based on the vis_epicontacts() and accepts a number of arguments to customize the plot appearance and functionality. For a full list of options use ?vis_epicontacts(). For instance, one can customize nodes using colors and icons:

plot(merskor15, "place_infect", node_shape = "sex",
     shapes = c(M = "male", F = "female"))

See codeawesome to see available shapes.

Alternatively, the method used for plotting can be graph3D, in which case a 3-dimensional graph will be used (see below).

3D plots

epicontacts loads the threejs package to enable 3D visualisation tools with the graph3D() function².

graph3D(merskor15, node_color = "sex", g_title = "MERS Korea 2014")

To interact with the plot:

zoom: scrollwheel
rotate: left-mouse button + move
pan: right-mouse button + move
identify node by label: mouse over

Analysis

Extract Characteristics of Pairwise Nodes

The get_pairwise() function allows processing of variable(s) in the line list according to each pair in the contact dataset. For the following example, date of onset of disease is extracted from the line list in order to compute the difference between disease date of onset for each pair. The value that is produced from this comparison represents the serial interval (si).

si <- get_pairwise(merskor15, "dt_onset")   
summary(si)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    2.00   11.00   14.00   14.47   18.00   27.00

hist(si, col="grey", border="white", xlab="Days after symptoms",
     main="MERS Korea 2014\nSerial Interval")

The get_pairwise() will interpret the class of the column being used for comparison, and will adjust its method of comparing the values accordingly. For numbers and dates (like the si example above), the function will subtract the values. When applied to columns that are characters or categorical, get_pairwise() will paste values together. Because the function also allows for arbitrary processing (see “f” argument), these discrete combinations can be easily tabulated and analyzed.

head(get_pairwise(merskor15, "sex"), n = 10)

##  [1] "M - M" "M - F" "M - F" "M - M" "M - F" "M - M" "M - M" "M - F" "M - F"
## [10] "M - F"

get_pairwise(merskor15, "sex", f=table)

##            values.to
## values.from  F  M
##           F  2  4
##           M 38 54

fisher.test(get_pairwise(merskor15, "sex", f=table))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  get_pairwise(merskor15, "sex", f = table)
## p-value = 1
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##  0.06158088 5.26628732
## sample estimates:
## odds ratio 
##   0.712926

Identify Clusters

The get_clusters() function can be used for to identify connected components in an epicontacts object. Here, we illustrate its use to study contact patterns in a simulated Ebola outbreak. First, we use it to retrieve data.frame containing the cluster information:

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 × 11
##    id     generation date_of_infection date_of_onset date_of_hospitalisation
##    <chr>       <int> <date>            <date>        <date>                 
##  1 d1fafd          0 NA                2014-04-07    2014-04-17             
##  2 53371b          1 2014-04-09        2014-04-15    2014-04-20             
##  3 f5c3d8          1 2014-04-18        2014-04-21    2014-04-25             
##  4 6c286a          2 NA                2014-04-27    2014-04-27             
##  5 0f58c4          2 2014-04-22        2014-04-26    2014-04-29             
##  6 49731d          0 2014-03-19        2014-04-25    2014-05-02             
##  7 f9149b          3 NA                2014-05-03    2014-05-04             
##  8 881bd4          3 2014-04-26        2014-05-01    2014-05-05             
##  9 e66fa4          2 NA                2014-04-21    2014-05-06             
## 10 20b688          3 NA                2014-05-05    2014-05-06             
## # ℹ 5,878 more rows
## # ℹ 6 more variables: date_of_outcome <date>, outcome <fct>, gender <fct>,
## #   hospital <fct>, lon <dbl>, lat <dbl>
## 
##   // contacts
## 
## # A tibble: 3,800 × 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  
## # ℹ 3,790 more rows

clust <- get_clusters(x, output = "data.frame")
class(clust)

## [1] "data.frame"

dim(clust)

## [1] 7047    3

table(clust$cluster_size)

## 
##    1    2    3    4    5    6    7    8    9   10   11   12   13   14 
## 1536 1680 1182  784  545  342  308  208  171  100   99   24   26   42

barplot(table(clust$cluster_size),
        main = "Cluster size distribution",
    xlab = "Cluster size",
    ylab = "Frequency")

Let us look at the largest clusters. For this, we add cluster information to the epicontacts object, and then subset it:

x <- get_clusters(x)
x_14 <- subset(x, cs = 14)
plot(x_14, "cluster_member")

Calculate Degree

The degree of a node corresponds to its number of edges or connections to other nodes. get_degree() provides an easy method for calculating this value for epicontacts networks. A high degree in this context indicates an individual who was in contact with many others.

nb use of “type” argument depends on whether or not the network is directed.

deg_both <- get_degree(merskor15, "both", only_linelist = TRUE)

Which individuals have the ten most contacts?

head(sort(deg_both, decreasing = TRUE), 10)

## SK_14  SK_1 SK_16 SK_15  SK_6 SK_39 SK_11 SK_12 SK_76 SK_87 
##    39    26    22     5     3     3     2     2     2     2

What is the mean number of contacts?

mean(deg_both)

## [1] 1.209877

`epicontacts`: Manipulation, Visualisation and Analysis of Epidemiological Contact Data

Introduction

Loading Data

Example Dataset

Creating `epicontacts` Object

Data Manipulation

Access Unique Identifiers

Subsetting

Visualisation

Default Plotting Method

3D plots

Analysis

Extract Characteristics of Pairwise Nodes

Identify Clusters

Calculate Degree

References

epicontacts: Manipulation, Visualisation and Analysis of Epidemiological Contact Data

Introduction

Loading Data

Example Dataset

Creating epicontacts Object

Data Manipulation

Access Unique Identifiers

Subsetting

Visualisation

Default Plotting Method

3D plots

Analysis

Extract Characteristics of Pairwise Nodes

Identify Clusters

Calculate Degree

References

`epicontacts`: Manipulation, Visualisation and Analysis of Epidemiological Contact Data

Creating `epicontacts` Object