Calculate Distribution of Complexities by Sample — calculate

Calculate the distribution of susceptibilities by sample id.

Usage

calculate_complexities(x, cutoff, control, sample, gene, perc_susc)

Arguments

x: a data.frame containing the data.
cutoff: value for percent susceptible cutoff. Numeric.
control: value used to denote the susceptible control in the gene column. Character.
sample: column providing the unique identification for each sample being tested. Character.
gene: column providing the gene(s) being tested. Character.
perc_susc: column providing the percent susceptible reactions. Character.

Value

An object of class hagis.complexities.

An object of class hagis.complexities is a list containing the following components

grouped_complexities: a data.table::data.table() object of grouped complexities
individual_complexities: a data.table::data.table() object of individual complexities

Examples

if (FALSE) { # interactive()

# Using the built-in data set, `P_sojae_survey`
data(P_sojae_survey)

P_sojae_survey

# calculate susceptibilities with a 60 % cutoff value
complexities <- calculate_complexities(x = P_sojae_survey,
                                       cutoff = 60,
                                       control = "susceptible",
                                       sample = "Isolate",
                                       gene = "Rps",
                                       perc_susc = "perc.susc")
complexities

summary(complexities)
}