2.6 Community detection
In the state of SC, epidemiological surveillance and control units are
organized at various levels starting at the municipality-level. For that
reason, we aggregate the movements made by farms in each municipality,
considering the municipality to be a node. This analysis captured
spatial connectivity amongst different municipalities via animal
movements, including pairs of locations that shared common direct and
indirect connections within the network. Community detection was
performed using an algorithm based on the calculation of LinkRank, a
concept derived from Google’s PageRank (BRIN; PAGE, 1998) that takes
into account the incoming links of a given municipality and the incoming
links of its neighbors (GRISI-FILHO et al., 2013).
We also calculated modularity as a measure of the strength of community
structure, where values of 0.3 – 0.7 generally indicate moderate to
strong community structure (GRANOVETTER, 1973).
All analysis and data visualization were performed in R statistical
software (R CORE TEAM, 2017) version 2.4.2 using the packages: igraph
version 1.1.2 (NEPUSZ, 2006), rgdal version 1.2‐8 (KEITT et al., 2018),
circlize version 0.4.1 (GU et al., 2014), EpiContactTrace version 0.12.0
(NÖREMARK; WIDGREN, 2014), tidyverse (Hadley Wickham, 2017), sf
(PEBESMA, 2018), and the Illustrator CC5 software (GOLDING, 2017).
Shapefiles to produce the maps were obtained from the Instituto
Brasileiro de Geografia e Estatística(www.ibge.gov.br).
Results
Data
The movements included in this study compromised 99.9% of the total
available records. A small proportion of records were removed because
the number of animals was listed as zero animals or >20000,
which were considered errors. In this swine trade network, there were
11,606 premises, and 6,0645,853 pigs involved in 320,814 movements
during the period of study.
Data trade description
Within SC, the dominant trade flow
of animals originated from breeding-farms and CSBF and passed through
Nurseries to Finisher farms. Finishers received a significant amount of
movements from Nursery, Breeding and CSBF premises and, sent the largest
flow of movements to Slaughterhouses.
We illustrated the main movements within and between types of premises
in Figure 2; for visualization purposes, atypical movements representing
less than 1 % of the total of possible connections were excluded
(Figure 2). The full description is available in the supplementary table
1.