BernardoGG/ebov_SL_timtam

TimTam2 analysis of a data set describing the early EBOV epidemic in eastern Sierra Leone. # Sierra Leone EBOV analysis _Bernardo Gutierrez_ TimTam2 analysis of a data set describing the early EBOV epidemic in two eastern provinces in Sierra Leone, Kailahun and Kenema. This outbreak followed shortly after the introduction of the virus into the country and corresponds to a period where cases were growing exponentially, and where a portion of the cases were sequenced. This summary presents a detailed description of the data. From here, the current analysis focuses on the following: - Dataset B from the original analysis. - Data available from May 19 2014 to August 3 2014. ## Script inventory and usage - `TimTam_EBOV_DataWrangling.R`: Import case data, sequence data and metadata, and generate data frames to be further used for subsequent analyses. - `TimTam_EBOV_epi_plots.R`: Generate summary plot with numbers of cases and sequences per week in eastern Sierra Leone. - `TimTam_EBOV_slam_dataset.R`: Uses the TimTamSlam package to distribute weekly aggregated cases over days per epidemiological week. Also estimates disaster times and backward time for these. Remaining R scripts are not used on the main analysis pipeline, they were used for preliminary tests. ## Results - Sequencing was performed over the entirety of the study period. A larger proportion of cases were sequenced during June; epidemic growth continued through July with fewer numbers of sequences produced.