beans | R Documentation |
This is a subset of data from trials of bean varieties (Phaseolus vulgaris L.) in Nicaragua over five growing seasons. Farmers were asked to try three varieties of bean from a total of ten varieties and to rank them in order of preference. In addition, for each variety the farmers were asked to compare each trial variety to the local variety and state whether they considered it to be better or worse.
beans
A data frame with 842 records and 14 variables:
variety_a
The name of variety A in the comparison.
variety_b
The name of variety B in the comparison.
variety_c
The name of variety C in the comparison.
best
The variety the farmer ranked in first place ("A", "B" or "C").
worst
The variety the farmer ranked in last place ("A", "B" or "C").
var_a
How the farmer ranked variety A compared to the local variety ("Worse" or "Better").
var_b
How the farmer ranked variety B compared to the local variety ("Worse" or "Better").
var_c
How the farmer ranked variety C compared to the local variety ("Worse" or "Better").
season
A factor specifying the growing season ("Po - 15", "Ap - 15", "Pr - 16", "Po - 16", "Ap - 16".
year
The year of planting.
maxTN
The maximum temperature at night during the vegetative cycle (degrees Celsius).
lon
The geographic coordinate longitude (X axis) for where the plot was established.
lat
The geographic coordinate latitude (Y axis) for where the plot was established.
planting_date
A Date, specifying the start date of planting the trial.
There are three crop seasons in Central America:
May - August.
September - October.
November - January.
Beans can be planted near the beginning of each season, though are most commonly planted in the Postrera or Apante seasons.
van Etten, J. et al. (2019) PNAS, 116 (10), 4194–4199, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1073/pnas.1813720116")}.
# Consider the best and worst rankings. These give the variety the
# farmer thought was best or worst, coded as A, B or C for the
# first, second or third variety assigned to the farmer
# respectively.
data(beans)
head(beans[c("best", "worst")], 2)
# Fill in the missing item
beans$middle <- complete(beans[c("best", "worst")],
items = c("A", "B", "C"))
head(beans[c("best", "middle", "worst")], 2)
# This gives an ordering of the three varieties the farmer was
# given. The names of these varieties are stored in separate
# columns
varieties <- beans[c("variety_a", "variety_b", "variety_c")]
head(varieties, 2)
# Use these names to decode the orderings of order 3
order3 <- decode(beans[c("best", "middle", "worst")],
items = beans[c("variety_a", "variety_b", "variety_c")],
code = c("A", "B", "C"))
# Now consider the paired comparisons agains the local variety
head(beans[c("var_a", "var_b", "var_c")], 2)
# Convert these results to a vector and get the corresponding trial variety
outcome <- unlist(beans[c("var_a", "var_b", "var_c")])
trial_variety <- unlist(beans[c("variety_a", "variety_b", "variety_c")])
# Create a data frame of the implied orderings of order 2
order2 <- data.frame(Winner = ifelse(outcome == "Worse",
"Local", trial_variety),
Loser = ifelse(outcome == "Worse",
trial_variety, "Local"),
stringsAsFactors = FALSE, row.names = NULL)
head(order2, 2)
# Finally combine the rankings of order 2 and order 3
R <- rbind(as.rankings(order3, input = "orderings"),
as.rankings(order2, input = "orderings"))
head(R)
tail(R)
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