Epidemics

Supplementary code for the paper Milton et al. - Spatial Analysis Made Easy with Linear Regression and Kernels (2019).

Excel data sheets for grey squirrel trapping field data and diagnostic viral testing results.

Data set made available contains data on the reporting delays for the submitted manuscript "Assessing reporting delays and the effective reproduction number: The 2018-19 Ebola epidemic in DRC, May 2018-January 2019". Data set contains 7 variables and 661 observations in total. Data has been extracted from the epidemic curves of the WHO situation reports and disease outbreak news using an online software, WebPlotDigitizer.

This is a set of contact-based adjacency matrix arrays (70 x 70) created from locational data of 70 feed lot cattle over 21 days. Data were processed according to 4 parameters, including Spatial Threshold(0.1665m-0.999m), temporal sampling window(called TempAgg here) (10-180 sec), and minimum sampling duration (1-4). Half the dataset includes contacts aggregated over days(array length 21), and half the dataset includes contacts aggregated over hours(array length 504).

This dataset contained the data that was used in the analysis of the manuscript entitled "Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections". The study was conducted in Sheema North Sub-District (South-West Uganda) between January and March 2014. Sixty clusters were randomly selected from the 215 villages and two small district towns (Kabwohe and Itendero) in the study area, proportionally to the population size of each village and town. In each cluster, from 29 or 30 individuals randomly sampled from different households for inclusion in a nasopharyngeal carriage study, a subset of 11 or 12 individuals were selected to answer questions about their social contacts and their history of respiratory illness in the last two weeks, in addition to having a nasopharyngeal swab taken. For the social contact questionnaire, participants were first asked to list all the individuals with whom they had a two-way conversational contact lasting for ≥5 minutes during a period of approximately 24 hours prior to the survey day (from wake up the previous day until wake up on the survey day). Such encounters were defined as ‘ordinary contacts’. For each reported ordinary contact, participants (or their parent/guardian) were asked to estimate the contact’s age (or estimated age), how long the encounter lasted for and whether it involved skin-to-skin touch or utensils passed from mouth to mouth (either of those defining ‘physical contacts’). For very short social encounters (<5 minutes), which were defined as ‘casual contacts’ (e.g. seeing someone on the way, encounter in a shop etc.), participants were asked to estimate the number of encounters based on pre-defined categories (<10 contacts, 10-19 contacts, 20-29 contacts, ≥30 contacts), but not to provide further details about each contact. Next, participants were asked about respiratory symptoms experienced in the two weeks prior to the survey, including any of the following: cough, runny nose, sneezing, sore throat, difficulty breathing. Finally, after the interview was completed, a nasopharyngeal swab was taken from each participant. The data dictionary for this dataset can be found in the corresponding manuscript files

SNP alignments of M. tuberculosis outbreak data sets.

Data and Matlab scripts to replicate our experimental results

Results (percent human infection reduction) from all simulations of all scenarios presented in the research article. Results from each simulation are in a different tab.

The main code is "surv.m," which references the other 2 files provided.