Pig production system drivers of antibiotic resistance in Uganda

There are three main datasets i.e A) House_Hold_PAIRS, B) HOUSE_HOLD_PAIRS_SHARED_MDR, C) E_COLI_MDR_SHARED, We also have a list of paired farmer and pig(HOUSE_HOLD_PAIRS), the multi-drug resistant(MDR) strains they share (HOUSE_HOLD_PAIRS_MDR_SHARED), and the MDR patterns carried by E.coli recovered from the paired farmer and pig(E_COLI_MDR_SHARED). Farmer-pig_carriage this dataset compares the gene carriage of a farmer at time T and thier pig at time T+1 in the same household. METADATA dataset has 476 rows and 14 columns This data set is named PHENOTYPE DATA it contains 8 columns and 2830 rows This data is output from analysis of bacteria culture from farmers and their pigs in the one-year longitudinal study. We collected these samples 6 times growing three bacteria E.coli, Klebsiella, and Salmonella Pig and Human ID SAMPLE ID E.G KLAMAK011P The first three letters District, Second three letter Sub-county The two number digits is for the household next number is for the visit number the last number is for the host (Pig or Human) Controls KLANANCTR021 CRT means control 02 = Negative control 01= Positive control The last number is for the visit number For analysis use column 3. SAMPLE_ID2 We often generate variables out of the ID as a data integrity validation process usually in a data set as ID3 SETTING Means District (Urban =Kampala(Intensive & Semi intensive pig), Rural=Mubende(free range or semi-free range)) Sub-county is an administrative division in the district SAMPLING.... is the visit time (1-6) Species mean the Host (Human or Pig) Isolate means Is a tracking number for the laboratory Bacteria is the Bacteria isolated Antibiotics, these will have three states(R, I, S) resistant, intermediate and Susceptible.