heat_map: Heatmap of disease and antimicrobial usage from surveillance...
In choisy/viparc: Utilitary functions for the ViParc project

Description Usage Arguments Author(s) Examples

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heat_map(df, dec = FALSE, xlab = "time", ylab = "space",
  col_na = "lightgrey", col_surv_no_dis = "blue",
  col_surv_dis = "red", ...)

`df`	data frame with 4 variable named "time", "space", "disease" and "drug". "time" and "space" are considered as integer and character respectively and "disease" and "drug" are both considered as logical.
`xlab`	label of the x axis. Default to "time".
`ylab`	label of the y axis. Default to "space".
`col_na`	color used for non surveyed time/space.
`col_surv_no_dis`	color used for surveyed time/space with no disease.
`col_surv_dis`	color used for surveyed time/space with disease
`...`	additional parameters passed to the "points" function that add the "drug" information.

Marc Choisy

library(dplyr)
chcknfarms %>%
  filter(CYCLE == 1) %>%
  transmute(space   = FARMCODE,
            time    = WEEK,
            disease = SRespiratory,
            drug    = AntibioticUse) %>%
  heat_map(xlab = "week", ylab = "farm")