Dynamics of colistin resistance in chicken farms of the Mekong delta, Vietnam

Data

AMU is expressed either qualitative as presence (TRUE) / absence (FALSE) variables (here), or as g / kg of chicken (here). These CSV files are are generated by this code. The first data set can be downloaded as so:

# install.packages("readr")
viparc_qualitative <- readr::read_csv("https://raw.githubusercontent.com/viparc/colistin_resistance/master/data/viparc_qualitative.csv",
                                      col_types = paste(c("cii", rep("l", 52), "il"), collapse = ""))

It contains 5391 weeks of observation (rows) and 57 variables (columns). The variables are

• farm: farm ID;
• flock: flock ID (in a given farm);
• week: week number (in a given flock of a given farm);
• respiratory, …, sudden_death: presence (TRUE) / absence (FALSE) of 6 clinical signs in the flock;
• amoxicillin_g, …, unknown_g: use (TRUE) or not (FALSE) of the 44 antimicriobial used in the flock;
• completed: boolean informing whether the flock is done (TRUE) or still ongoing (FALSE);
• nb_chicken: total number of chicken in the farm;
• sampling: boolean informing whether there is feces sampling during the week (TRUE) or not (FALSE).

The second data set can be downloaded as so:

# install.packages("readr")
viparc_quantitative <- readr::read_csv("https://raw.githubusercontent.com/viparc/colistin_resistance/master/data/viparc_quantitative.csv",
                                       col_types = paste(c("cii", rep("l", 6), rep("d", 45), "lildd"), collapse = ""))

It contains 5391 weeks of observation (rows) and 59 variables (columns). The variables are

• farm: farm ID;
• flock: flock ID (in a given farm);
• week: week number (in a given flock of a given farm);
• respiratory, …, sudden_death: presence (TRUE) / absence (FALSE) of 6 clinical signs in the flock;
• amoxicillin_g, …, unknown_g: mass, in g / kg of chicken, of the 44 antimicriobial used in the flock;
• completed: boolean informing whether the flock is done (TRUE) or still ongoing (FALSE);
• nb_chicken: total number of chicken in the farm;
• sampling: boolean informing whether there is feces sampling during the week (TRUE) or not (FALSE);
• individual_weight_kg: average weight in kg of a chicken;
• farm_weight_kg: expected weight in kg of whole the chicken of the farm.