library("gosset")
library("PlackettLuce")
library("climatrends")
library("nasapower")
library("ggplot2")
library("chirps")
data("nicabean", package = "gosset")
dat <- nicabean$trial
covar <- nicabean$covar
traits <- unique(dat$trait)
R <- vector(mode = "list", length = length(traits))
for (i in seq_along(traits)) {
dat_i <- subset(dat, dat$trait == traits[i])
R[[i]] <- rank_numeric(data = dat_i,
items = "item",
input = "rank",
id = "id",
ascending = TRUE)
}
baseline <- which(grepl("OverallAppreciation", traits))
kendall <- lapply(R[-baseline], function(X){
kendallTau(x = X, y = R[[baseline]])
})
kendall <- do.call("rbind", kendall)
kendall$trait <- traits[-baseline]
mod <- lapply(R, PlackettLuce)
worth_map(mod[-baseline],
labels = traits[-baseline],
ref = "Amadeus 77") +
labs(x = "Variety",
y = "Trait")
dates <- c(min(covar[, "planting_date"]),
max(covar[, "planting_date"]) + 70)
# chirps <- get_chirps(covar[, c("longitude","latitude")],
# dates = as.character(dates),
# as.matrix = TRUE,
# server = "ClimateSERV")
load("inst/paper/nicabean_chirps.rda")
# rename the matrix
newnames <- dimnames(chirps)[[2]]
newnames <- gsub("chirps-v2.0.", "", newnames)
newnames <- gsub("[.]", "-", newnames)
dimnames(chirps)[[2]] <- newnames
rain <- rainfall(chirps, day.one = covar$planting_date, span = 45)
yield <- which(grepl("Yield", traits))
G <- group(R[[yield]], index = 1:length(R[[yield]]))
pldG <- cbind(G, rain)
pldG$Rtotal <- round(pldG$Rtotal, 2)
tree <- pltree(G ~ Rtotal, data = pldG, alpha = 0.1)
plot(tree, ref = "Amadeus 77", ci.level = 0.9)
node_labels(tree)
node_rules(tree)
top_items(tree, top = 3)
ggsave("inst/paper/pltree_01.png",
last_plot(),
width = 25,
height = 20,
dpi = 300,
units = "cm")
reliability(tree, ref = "Amadeus 77")
rel <- reliability(tree, ref = "Amadeus 77")
rel <- rel[rel$reliability >= 0.5, ]
rel <- rel[c(1:5)]
rel[c(3:5)] <- lapply(rel[c(3:5)], function(x){round(x, 3)})
rel
regret(tree)
Overall <- PlackettLuce(R[[baseline]])
Yield <- PlackettLuce(R[[yield]])
compare(Overall, Yield) +
labs(x = "Average log(worth)",
y = "Difference (Overall Appreciation - Yield)")
comp <- compare(Overall, Yield) +
labs(x = "Average log(worth)",
y = "Difference (Overall Appreciation - Yield)")
ggsave("inst/paper/compare_02.png",
comp,
width = 15,
height = 15,
dpi = 300,
units = "cm")
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