## ----lossdata, message=FALSE--------------------------------------------------
d <- agrodata::data_ibli("marsabit_losses")
d[1:5, c(1:6, 9:10)]


## ----lossvariables, echo=FALSE------------------------------------------------
vars <- c("hhid", "sublocation", "year", "month", "animal", "cause", "cause_other", "where", "totalloss", "adultloss", "unique household ID", "sublocation name", "year of loss event", "month of loss event", "animal species", "cause of loss", "other causes not on list", "at base or satellite camp?", "number of animals lost?", "number of adult animals lost (>= 3 years for cattle/camel, >= 6 months for sheep/goat)")
vars <- matrix(vars, ncol=2)
colnames(vars) <- c("name", "description")
knitr::kable(vars, caption="Livestock los variables")


## ----animals------------------------------------------------------------------
table(d$animal)
x <- tapply(d$totalloss, d$animal, sum, na.rm=TRUE)
barplot(x, col=rainbow(3), las=1)


## ----animals2-----------------------------------------------------------------
x
tlu <- c(camel=1.4, cattle=1, shoat=0.1)
xtlu <- x * tlu
barplot(xtlu, col=rainbow(3), las=1)


## ----tlu----------------------------------------------------------------------
animals <- match(trimws(d$animal), c("Goat/Sheep", "Camel", "Cattle"))
anitlu <- tlu[animals]
youngloss <- d$totalloss - d$adultloss
d$tluloss <- (d$adultloss + youngloss/2) * anitlu



## ----tluloss------------------------------------------------------------------
a <- aggregate(d[, "tluloss", drop=FALSE], d[, c("year", "month")], sum, na.rm=TRUE)
a <- a[order(a$year, a$month), ]
time <- as.Date(paste(a$year, a$month, 15, sep="-"))
plot(time, a$tluloss, ylab="Loss (TLU)")


## ----tab----------------------------------------------------------------------
xtabs(tluloss ~ month+year, d)


## ----barplot1-----------------------------------------------------------------
cause <- tapply(d$tluloss, d$cause, sum, na.rm=TRUE)
x <- sort(round(cause))
par(mai=c(1,2,1,1))
barplot(x, horiz=T, las=1)


## ----barplot2-----------------------------------------------------------------
i <- d$cause %in% c("Starvation/Drought", "Disease")
d$cause2 <- "Other"
d$cause2[i] <- d$cause[i]
d$cause2[d$cause2 == "Starvation/Drought"] <- "Starvation"


## ----mort40-------------------------------------------------------------------
yc <- aggregate(d[, "tluloss", drop=FALSE], d[, c("cause2", "year")], sum, na.rm=TRUE)
head(yc)


## ----mort50-------------------------------------------------------------------
r <- reshape(yc, direction="wide", idvar="cause2", timevar="year")
colnames(r) <- gsub("tluloss.", "", colnames(r))
r <- as.matrix(r)
rownames(r) <- r[,1]
barplot(r[,-1], legend =  rownames(r), las=2, args.leg=list(cex=1))