Datasets

This dataset household contains contact matrices measured in South Africa in November 2017, as part of the PHIRST-C project, in collaboration with SocioPatterns. Results from the analysis of this dataset are available at L. Dall’‘Amico et al., PLoS ONE 19(3), e0296810 (2024).

The data can be downloaded at this GitHub repository.

This dataset contains contact networks and demographic information for almost 500 participants in a large-scale SARS-CoV-2 household transmission carried out in South Africa in 2020-2021. The study was led by Jackie Kleynhans at NICD. Results from the analysis of this dataset are available at J. Kleynhans et al., eLife 12, e84753 (2023). Details about the main transmission study are available here.

The data can be downloaded at this GitHub repository.

The data set contains observational contact data collected for 86 individuals living in a village in rural Malawi. These data were analyzed and published in the paper Using wearable proximity sensors to characterize social contact patterns in a village of rural Malawi”.

The data set contains observational and wearable sensors data collected in a group of 20 Guinea baboons living in an enclosure of a Primate Center in France, between June 13th 2019 and July 10th 2019. These data were analyzed and published in the paper Measuring social networks in primates: wearable sensors vs. direct observations.

Observation Data

The file OBS_data.txt contains all the behavioral events registered by an observer, with 8 columns:

• DateTime = Time stamp of the event, namely the moment the observed behavior was registered. In case of STATE events (events with duration > 0), it refers to the beginning of the behavior;
• Actor = The name of the actor;
• Recipient = The name of the individual the Actor is acting upon;
• Behavior = The behavior the Actor. 14 types of behaviors are registered: ‘Resting’, ‘Grooming’, ‘Presenting’, ‘Playing with’, ‘Grunting-Lipsmacking’, ‘Supplanting’, ‘Threatening’, ‘Submission’, ‘Touching’, ‘Avoiding’, ‘Attacking’,’Carrying’, ‘Embracing’, ‘Mounting’, ‘Copulating’, ‘Chasing’. In addition two other categories were included: ‘Invisible’ and ‘Other’;
• Category = The classification of the behavior. It can be ‘Affiliative’, ‘Agonistic’, ‘Other’;
• Duration = Duration of the observed behavior. POINT events have no duration;
• Localisation = Zone of the enclosure where the observed behavior takes place;
• Point = indicates if the event is a POINT event (YES) or a STATE event (NO).

Proximity Sensors Data

The file RFID_data.txt contains contacts data recorded in the same period by the SocioPatterns infrastructure. The proximity sensors were worn by 13 of the 20 individuals cited above. The data file consists of 4 columns:

• t = time of the beginning of the contact in Epoch format (Unix timestamps);
• i = Name of the first individual;
• j = Name of the second individual;
• DateTime

We are releasing complementary data with respect to the face-to-face contact data released previously. For a series of cases, we consider, as described in the publication Can co-location be used as a proxy for face-to-face contacts?, the information on which RFID readers received information from the RFID tags. Namely, we define two individuals to be in co-presence if the same exact set of readers have received signals from both individuals during a 20s time window.

We release here 6 co-presence data sets. The contexts in which these data were collected are: a workplace, with data collected in two different years (InVS13, InVS15), a hospital (LH10), a primary school (LyonSchool), a scientific conference (SFHH) and a high school (Thiers13). In each case, the data on face-to-face contacts during the same timeframe has already been released. In all cases except SFHH, metadata is also available concerning the department, class or status of each individual.

All the data are also in Supplementary Material of the publication Can co-location be used as a proxy for face-to-face contacts?.

File format

• colocation.tar.gz contains all six co-presence networks. Both contacts and co-presence data are formatted as tij, i.e. each line represents a contact occurring at a time t between two nodes i and j.
• colocation_metadata.tar contains the lists of nodes, with the first column being the node identifier and the second the group affiliation, when available.

This data set describes the face-to-face interactions of 405 participants to the 2009 SFHH conference in Nice, France (June 4-5, 2009). It was first described in the publications Dynamics of Person-to-Person Interactions from Distributed RFID Sensor Networks and Simulation of an SEIR Infectious Disease Model on the Dynamic Contact Network of Conference Attendees. It was released as supplementary data set of the publication Can co-location be used as a proxy for face-to-face contacts?

The data file is in the usual format representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j”, where i and j are the anonymous IDs of the persons in contact, and the interval during which this contact was active is [ t – 20s, t ] (t is expressed in seconds).

This data set contains the temporal network of contacts between individuals measured in an office building in France in 2015. This network was described and analyzed in the publication Can co-location be used as a proxy for face-to-face contacts?

The data set comprises two files. The first one contains a space-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j”, where i and j are the anonymous IDs of the persons in contact, and the interval during which this contact was active is [ t – 20s, t ] (t is expressed in seconds). The second file contains a list of the form “i Di” where i is the anonymous ID of an individual and Di the name of his/her department in the workplace.

This data set contains the temporal network of contacts between individuals measured in an office building in France, from June 24 to July 3, 2013. This network was described and analyzed in the publication “Data on face-to-face contacts in an office building suggest a low-cost vaccination strategy based on community linkers” by M. Génois et al., published in Network Science 3, 326 (2015). The data set comprises two files. The first one contains a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j”, where i and j are the anonymous IDs of the persons in contact, and the interval during which this contact was active is [ t – 20s, t ] (t is expressed in seconds since the time origin taken as 0:00 on June 24, 2013). The second file contains a list of the form “i Di” where i is the anonymous ID of an individual and Di the name of his/her department in the workplace.

This dataset contains the full list of contacts measured between members of 5 households of rural Kenya between April 24  and May 12, 2012. Results from the analysis of this dataset have been published in M. Kiti et al., EPJ Data Science 5(1), 1-21 (2016).

Each file in the downloadable package contains a comma-separated list representing each measured contact between any two household members (member 1 and member 2) over three days of experiment. The first file stores the contacts recorded between members of the same household, the second file stores the contacts between members of different households. Each line has the form: “h1, m1, h2, m2, age1, age2, sex1, sex2, duration, day, hour”, where:

• h1 is the household of member 1; h1=[L, F, E, B, H]
• m1 is the anonymous ID number of member 1;
• h2 is the household of member 2; h2=[L, F, E, B, H]
• m2 is the anonymous ID number of member 2;
• age1 is the age of member 1; age1 = [0, 1, 2, 3, 4]
• age2 is the age of member 2; age2 = [0, 1, 2, 3, 4]
• sex1 is the gender of member 1; sex1 = [F, M]
• sex2 is the gender of member 2; sex2 = [F, M]
• duration is the duration of the contact event in seconds;
• day is the day of experiment; day = [1, 2, 3]
• hour is the day time of the contact event; hour = [7 - 20]

A more detailed description of the variables is available in the variable dictionary file.

This data set contains the temporal network of contacts between the children and teachers used in the study published in V. Gemmetto et al., BMC Infectious Diseases 2014, 14:695. The file contains a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j Ci Cj”, where i and j are the anonymous IDs of the persons in contact, Ci and Cj are their classes, and the interval during which this contact was active is [ t - 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds.

These data sets correspond to the contacts and friendship relations between students in a high school in Marseilles, France, in December 2013, as measured through several techniques.

• The first dataset gives the contacts of the students of nine classes during 5 days in Dec. 2013, as measured by the SocioPatterns infrastructure. The file contains a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j Ci Cj“, where i and j are the anonymous IDs of the persons in contact, Ci and Cj are their classes, and the interval during which this contact was active is [ t - 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds and expressed in UNIX ctime.

• The second dataset corresponds to the directed network of contacts between students as reported in contact diaries collected at the end of the fourth day of the data collection. Each line has the form “i j w”, meaning that student i reported contacts with student j of aggregate durations of (i) at most 5 min if w = 1, (ii) between 5 and 15 min if w = 2, (iii) between 15 min and 1 h if w = 3, (iv) more than 1 h if w = 4.

• The third dataset corresponds to the directed network of reported friendships. Each line has the form “i j”, meaning that student i reported a friendship with student j.

• The fourth dataset corresponds to the list of pairs of students for which the presence or absence of a Facebook friendship is known. Each line has the form “i j w”, where w=1 means that students i and j are linked on Facebook, while w=0 means that they are not.

• Finally the metadata file contains a tab-separated list in which each line of the form “i Ci Gi” gives class Ci and gender Gi of the person having ID i.

These datasets contain the temporal network of contacts between students in a high school in Marseilles, France. The first dataset gives the contacts of the students of three classes during 4 days in Dec. 2011, and the second corresponds to the contacts of the students of 5 classes during 7 days (from a Monday to the Tuesday of the following week) in Nov. 2012.

Each Contact list file contains a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j Ci Cj“, where i and j are the anonymous IDs of the persons in contact, Ci and Cj are their classes, and the interval during which this contact was active is [ t - 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds (for the 2012 data, it is expressed in UNIX ctime).

Each metadata file contains a tab-separated list in which each line of the form “i Ci Gi” gives class Ci and gender Gi of the person having ID i.

This dataset contains the temporal network of contacts between patients, patients and health-care workers (HCWs) and among HCWs in a hospital ward in Lyon, France, from Monday, December 6, 2010 at 1:00 pm to Friday, December 10, 2010 at 2:00 pm. The study included 46 HCWs and 29 patients.

The file contains a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j Si Sj“, where i and j are the anonymous IDs of the persons in contact, Si and Sj are their statuses (NUR=paramedical staff, i.e. nurses and nurses’ aides; PAT=Patient; MED=Medical doctor; ADM=administrative staff), and the interval during which this contact was active is [ t - 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds.

This dataset contains the daily dynamic contact networks collected during the Infectious SocioPatterns event that took place at the Science Gallery in Dublin, Ireland, during the art-science exhibition INFECTIOUS: STAY AWAY. Each file in the downloadable package contains a tab-separated list representing the active contacts during 20-second intervals of one day of data collection.  Each line has the form “t i j“, where i and j are the anonymous IDs of the persons in contact, and the interval during which this contact was active is [ t - 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds and expressed in UNIX ctime.

This dataset was collected during the ACM Hypertext 2009 conference, where the SocioPatterns project deployed the Live Social Semantics application. Conference attendees volunteered to wear radio badges that monitored their face-to-face proximity. The dataset published here represents the dynamical network of face-to-face proximity of ~110 conference attendees over about 2.5 days. No personal data are released here, and no metadata collected by the Live Social Semantics application are exposed. We provide two data files, described below.

Contact List. This is a tab-separated list representing the active contacts during 20-second intervals of the data collection. Each line has the form “t i j”, where i and j are the anonymous IDs of the persons in contact, and the interval during which this contact was active is [ t - 20s, t ]. If multiple contacts are active in a given interval, you will see multiple lines starting with the same value of t. Time is measured in seconds since 8am on Jun 29th 2009 (UNIX ctime 1246255200).

Contact Intervals. This file is in JSON format and contains a dictionary. Each key is a person ID and the corresponding value is a dictionary of neighbors of that person in the contact network. This dictionary of neighbors has person IDs as keys and, for each key, the value gives the list of time intervals during which the corresponding contact was active. Time is measured as above.

This dataset is part of our study of contact networks in a primary school, as reported in the paper High-Resolution Measurements of Face-to-Face Contact Patterns in a Primary School. The dataset comprises two weighted networks of  face-to-face proximity between students and teachers. For each day of the study, a daily contact network is provided: nodes are individuals and edges represent face-to-face interactions.  Nodes have two attributes: classname that indicates the school class and grade of the corresponding individual, and gender. Teachers are all assigned to the “Teachers” class. Edges between A and B have two weights associated with them: duration, which is the cumulative time spent by A and B in face-to-face proximity, over one day, measured in seconds (multiples of 20 seconds); and count, which is the number of times the A-B contact was established during the school day. The networks are provided as two GEXF files, one per day of the study, which can be loaded directly into Gephi. These GEXF files contain the same data provided in the supporting information of the paper above.

This first dataset contains the daily cumulated networks represented in the Infectious SocioPatterns visualization. The downloadable package contains one gml (Graph Modelling Language) file for each of the sixty-nine covered days. The nodes represent visitors of the Science Gallery while the edges represent close-range face-to-face proximity between the concerned persons. The weights associated with the edges are the number of 20 seconds intervals during which close-range face-to-face proximity has been detected. Note that the same node ids are used in successive days for simplicity, but they naturally correspond to different visitors as each visitor was present only on one day.

For more details on the data collection and processing please see our paper What’s in a crowd? Analysis of face-to-face behavioral networks.