Custom Print for hagis Diversities Tables

Print the frequency table of diversities from a hagis.diversities object The resulting object is a pander table (a text object for Markdown) for ease of use in reporting and viewing in the console.

Usage

diversities_table(x, ...)

Arguments

x

a hagis.diversities object generated by calculate_diversities()

...

other arguments passed to pander::panderOptions()

Value

A pander object of diversities

See also

calculate_diversities(), individual_pathotypes()

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
diversities <- calculate_diversities(x = P_sojae_survey,
                                     cutoff = 60,
                                     control = "susceptible",
                                     sample = "Isolate",
                                     gene = "Rps",
                                     perc_susc = "perc.susc")

# print the diversities table
diversities_table(diversities)
}