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set_up_data.R
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set_up = function(percentile, outlier_val){
nccpi = as.data.frame(fread("nccpi_collection.csv", check.names = TRUE))
CRD = as.data.frame(fread("FIPS_CRD.csv", check.names = TRUE))
names(CRD) = c("FIPS.formula", "CRD")
nccpi = join(nccpi, CRD, by = "FIPS.formula")
# Remove outliers.
# Do for all nccpis because some counties might be really good and have almost no pixels
# in low nccpi buckets
nccpi = remove_outliers(nccpi, percentile, outlier_val)
wnccpi = ddply(nccpi, .(FIPS.formula, CRD, year, prcp_cc_mean, prcp_cs_mean, prcp_sc_mean, prcp_ss_mean, # If you want weather nccpis, add 'em here
tmax_cc_mean, tmax_cs_mean, tmax_sc_mean, tmax_ss_mean,
tmin_cc_mean, tmin_cs_mean, tmin_sc_mean, tmin_ss_mean,
vp_cc_mean, vp_cs_mean, vp_sc_mean, vp_ss_mean),
function(x) data.frame(wyield_cc_mean = weighted.mean(x$yield_cc_mean, x$yield_cc_count),
wyield_sc_mean = weighted.mean(x$yield_sc_mean, x$yield_sc_count),
wyield_cs_mean = weighted.mean(x$yield_cs_mean, x$yield_cs_count),
wyield_ss_mean = weighted.mean(x$yield_ss_mean, x$yield_ss_count),
corn_count = x$yield_sc_count + x$yield_cc_count,
soy_count = x$yield_cs_count + x$yield_ss_count,
corn_diff_count = x$yield_sc_count - x$yield_cc_count,
soy_diff_count = x$yield_cs_count - x$yield_ss_count,
wyield_cc_nccpi1_mean = weighted.mean(x$yield_cc_nccpi1_mean, x$yield_cc_nccpi1_count),
wyield_cc_nccpi2_mean = weighted.mean(x$yield_cc_nccpi2_mean, x$yield_cc_nccpi2_count),
wyield_cc_nccpi3_mean = weighted.mean(x$yield_cc_nccpi3_mean, x$yield_cc_nccpi3_count),
wyield_cc_nccpi4_mean = weighted.mean(x$yield_cc_nccpi4_mean, x$yield_cc_nccpi4_count),
wyield_cc_nccpi5_mean = weighted.mean(x$yield_cc_nccpi5_mean, x$yield_cc_nccpi5_count),
wyield_sc_nccpi1_mean = weighted.mean(x$yield_sc_nccpi1_mean, x$yield_sc_nccpi1_count),
wyield_sc_nccpi2_mean = weighted.mean(x$yield_sc_nccpi2_mean, x$yield_sc_nccpi2_count),
wyield_sc_nccpi3_mean = weighted.mean(x$yield_sc_nccpi3_mean, x$yield_sc_nccpi3_count),
wyield_sc_nccpi4_mean = weighted.mean(x$yield_sc_nccpi4_mean, x$yield_sc_nccpi4_count),
wyield_sc_nccpi5_mean = weighted.mean(x$yield_sc_nccpi5_mean, x$yield_sc_nccpi5_count),
wyield_cs_nccpi1_mean = weighted.mean(x$yield_cs_nccpi1_mean, x$yield_cs_nccpi1_count),
wyield_cs_nccpi2_mean = weighted.mean(x$yield_cs_nccpi2_mean, x$yield_cs_nccpi2_count),
wyield_cs_nccpi3_mean = weighted.mean(x$yield_cs_nccpi3_mean, x$yield_cs_nccpi3_count),
wyield_cs_nccpi4_mean = weighted.mean(x$yield_cs_nccpi4_mean, x$yield_cs_nccpi4_count),
wyield_cs_nccpi5_mean = weighted.mean(x$yield_cs_nccpi5_mean, x$yield_cs_nccpi5_count),
wyield_ss_nccpi1_mean = weighted.mean(x$yield_ss_nccpi1_mean, x$yield_ss_nccpi1_count),
wyield_ss_nccpi2_mean = weighted.mean(x$yield_ss_nccpi2_mean, x$yield_ss_nccpi2_count),
wyield_ss_nccpi3_mean = weighted.mean(x$yield_ss_nccpi3_mean, x$yield_ss_nccpi3_count),
wyield_ss_nccpi4_mean = weighted.mean(x$yield_ss_nccpi4_mean, x$yield_ss_nccpi4_count),
wyield_ss_nccpi5_mean = weighted.mean(x$yield_ss_nccpi5_mean, x$yield_ss_nccpi5_count)
))
wnccpi$corn_diff = wnccpi$wyield_sc_mean - wnccpi$wyield_cc_mean
wnccpi$soy_diff = wnccpi$wyield_cs_mean - wnccpi$wyield_ss_mean
wnccpi$corn_diff_nccpi1 = wnccpi$wyield_sc_nccpi1_mean - wnccpi$wyield_cc_nccpi1_mean
wnccpi$soy_diff_nccpi1 = wnccpi$wyield_cs_nccpi1_mean - wnccpi$wyield_ss_nccpi1_mean
wnccpi$corn_diff_nccpi2 = wnccpi$wyield_sc_nccpi2_mean - wnccpi$wyield_cc_nccpi2_mean
wnccpi$soy_diff_nccpi2 = wnccpi$wyield_cs_nccpi2_mean - wnccpi$wyield_ss_nccpi2_mean
wnccpi$corn_diff_nccpi3 = wnccpi$wyield_sc_nccpi3_mean - wnccpi$wyield_cc_nccpi3_mean
wnccpi$soy_diff_nccpi3 = wnccpi$wyield_cs_nccpi3_mean - wnccpi$wyield_ss_nccpi3_mean
wnccpi$corn_diff_nccpi4 = wnccpi$wyield_sc_nccpi4_mean - wnccpi$wyield_cc_nccpi4_mean
wnccpi$soy_diff_nccpi4 = wnccpi$wyield_cs_nccpi4_mean - wnccpi$wyield_ss_nccpi4_mean
wnccpi$corn_diff_nccpi5 = wnccpi$wyield_sc_nccpi5_mean - wnccpi$wyield_cc_nccpi5_mean
wnccpi$soy_diff_nccpi5 = wnccpi$wyield_cs_nccpi5_mean - wnccpi$wyield_ss_nccpi5_mean
wnccpi$corn_pbenefit = ((wnccpi$wyield_sc_mean/wnccpi$wyield_cc_mean) - 1)*100
wnccpi$soy_pbenefit = ((wnccpi$wyield_cs_mean/wnccpi$wyield_ss_mean) - 1)*100
wnccpi$corn_pbenefit_nccpi1 = ((wnccpi$wyield_sc_nccpi1_mean/wnccpi$wyield_cc_nccpi1_mean) - 1)*100
wnccpi$soy_pbenefit_nccpi1 = ((wnccpi$wyield_cs_nccpi1_mean/wnccpi$wyield_ss_nccpi1_mean) - 1)*100
wnccpi$corn_pbenefit_nccpi2 = ((wnccpi$wyield_sc_nccpi2_mean/wnccpi$wyield_cc_nccpi2_mean) - 1)*100
wnccpi$soy_pbenefit_nccpi2 = ((wnccpi$wyield_cs_nccpi2_mean/wnccpi$wyield_ss_nccpi2_mean) - 1)*100
wnccpi$corn_pbenefit_nccpi3 = ((wnccpi$wyield_sc_nccpi3_mean/wnccpi$wyield_cc_nccpi3_mean) - 1)*100
wnccpi$soy_pbenefit_nccpi3 = ((wnccpi$wyield_cs_nccpi3_mean/wnccpi$wyield_ss_nccpi3_mean) - 1)*100
wnccpi$corn_pbenefit_nccpi4 = ((wnccpi$wyield_sc_nccpi4_mean/wnccpi$wyield_cc_nccpi4_mean) - 1)*100
wnccpi$soy_pbenefit_nccpi4 = ((wnccpi$wyield_cs_nccpi4_mean/wnccpi$wyield_ss_nccpi4_mean) - 1)*100
wnccpi$corn_pbenefit_nccpi5 = ((wnccpi$wyield_sc_nccpi5_mean/wnccpi$wyield_cc_nccpi5_mean) - 1)*100
wnccpi$soy_pbenefit_nccpi5 = ((wnccpi$wyield_cs_nccpi5_mean/wnccpi$wyield_ss_nccpi5_mean) - 1)*100
return(wnccpi)
}
outlierReplace = function(dataframe, cols, rows, newValue = NA) {
if (any(rows)) {
set(dataframe, rows, cols, newValue)
}
}
# If percentile is TRUE, then go by smallest percentile given by value. If FALSE, go by
# number of acres given by value (0.2 acres = 1 pixel).
remove_outliers = function(nccpi, percentile, value) {
if(percentile) {
pixels = quantile(nccpi$yield_cc_count, c(value), na.rm=T)
} else {
pixels = value/0.2
}
factors = c("yield_cc_count", "yield_sc_count", "yield_cc_count", "yield_ss_count",
"yield_cc_nccpi1_count", "yield_cc_nccpi2_count", "yield_cc_nccpi3_count", "yield_cc_nccpi4_count", "yield_cc_nccpi5_count",
"yield_cs_nccpi1_count", "yield_cs_nccpi2_count", "yield_cs_nccpi3_count", "yield_cs_nccpi4_count", "yield_cs_nccpi5_count",
"yield_sc_nccpi1_count", "yield_sc_nccpi2_count", "yield_sc_nccpi3_count", "yield_sc_nccpi4_count", "yield_sc_nccpi5_count",
"yield_ss_nccpi1_count", "yield_ss_nccpi2_count", "yield_ss_nccpi3_count", "yield_ss_nccpi4_count", "yield_ss_nccpi5_count")
for (f in factors) {
mean_name = paste0(substr(toString(f), 1, nchar(f) - 5), "mean")
outlierReplace(nccpi, mean_name, which(nccpi[,f] < pixels), NA)
}
return(nccpi)
}
get_cnccpi = function(wnccpi) {
cnccpi = wnccpi %>%
group_by(CRD, year) %>%
dplyr::summarize(wyield_cc_nccpi1_mean = mean(wyield_cc_nccpi1_mean, na.rm=T),
wyield_cc_nccpi2_mean = mean(wyield_cc_nccpi2_mean, na.rm=T),
wyield_cc_nccpi3_mean = mean(wyield_cc_nccpi3_mean, na.rm=T),
wyield_cc_nccpi4_mean = mean(wyield_cc_nccpi4_mean, na.rm=T),
wyield_cc_nccpi5_mean = mean(wyield_cc_nccpi5_mean, na.rm=T),
wyield_cs_nccpi1_mean = mean(wyield_cs_nccpi1_mean, na.rm=T),
wyield_cs_nccpi2_mean = mean(wyield_cs_nccpi2_mean, na.rm=T),
wyield_cs_nccpi3_mean = mean(wyield_cs_nccpi3_mean, na.rm=T),
wyield_cs_nccpi4_mean = mean(wyield_cs_nccpi4_mean, na.rm=T),
wyield_cs_nccpi5_mean = mean(wyield_cs_nccpi5_mean, na.rm=T),
wyield_ss_nccpi1_mean = mean(wyield_ss_nccpi1_mean, na.rm=T),
wyield_ss_nccpi2_mean = mean(wyield_ss_nccpi2_mean, na.rm=T),
wyield_ss_nccpi3_mean = mean(wyield_ss_nccpi3_mean, na.rm=T),
wyield_ss_nccpi4_mean = mean(wyield_ss_nccpi4_mean, na.rm=T),
wyield_ss_nccpi5_mean = mean(wyield_ss_nccpi5_mean, na.rm=T),
wyield_sc_nccpi1_mean = mean(wyield_sc_nccpi1_mean, na.rm=T),
wyield_sc_nccpi2_mean = mean(wyield_sc_nccpi2_mean, na.rm=T),
wyield_sc_nccpi3_mean = mean(wyield_sc_nccpi3_mean, na.rm=T),
wyield_sc_nccpi4_mean = mean(wyield_sc_nccpi4_mean, na.rm=T),
wyield_sc_nccpi5_mean = mean(wyield_sc_nccpi5_mean, na.rm=T),
prcp_sc_mean = mean(prcp_sc_mean, na.rm=T),
prcp_cs_mean = mean(prcp_cs_mean, na.rm=T),
prcp_cc_mean = mean(prcp_cc_mean, na.rm=T),
prcp_ss_mean = mean(prcp_ss_mean, na.rm=T),
tmax_sc_mean = mean(tmax_sc_mean, na.rm=T),
tmax_cs_mean = mean(tmax_cs_mean, na.rm=T),
tmax_cc_mean = mean(tmax_cc_mean, na.rm=T),
tmax_ss_mean = mean(tmax_ss_mean, na.rm=T),
tmin_sc_mean = mean(tmin_sc_mean, na.rm=T),
tmin_cs_mean = mean(tmin_cs_mean, na.rm=T),
tmin_cc_mean = mean(tmin_cc_mean, na.rm=T),
tmin_ss_mean = mean(tmin_ss_mean, na.rm=T),
vp_sc_mean = mean(vp_sc_mean, na.rm=T),
vp_cs_mean = mean(vp_cs_mean, na.rm=T),
vp_cc_mean = mean(vp_cc_mean, na.rm=T),
vp_ss_mean = mean(vp_ss_mean, na.rm=T),
wyield_cc_mean = mean(wyield_cc_mean, na.rm=T),
wyield_cs_mean = mean(wyield_cs_mean, na.rm=T),
wyield_sc_mean = mean(wyield_sc_mean, na.rm=T),
wyield_ss_mean = mean(wyield_ss_mean, na.rm=T),
corn_count = mean(corn_count, na.rm=T),
soy_count = mean(soy_count, na.rm=T),
soy_diff = mean(soy_diff, na.rm=T),
soy_diff_nccpi1 = mean(soy_diff_nccpi1, na.rm=T),
soy_diff_nccpi2 = mean(soy_diff_nccpi2, na.rm=T),
soy_diff_nccpi3 = mean(soy_diff_nccpi3, na.rm=T),
soy_diff_nccpi4 = mean(soy_diff_nccpi4, na.rm=T),
soy_diff_nccpi5 = mean(soy_diff_nccpi5, na.rm=T),
corn_diff = mean(corn_diff, na.rm=T),
corn_diff_nccpi1 = mean(corn_diff_nccpi1, na.rm=T),
corn_diff_nccpi2 = mean(corn_diff_nccpi2, na.rm=T),
corn_diff_nccpi3 = mean(corn_diff_nccpi3, na.rm=T),
corn_diff_nccpi4 = mean(corn_diff_nccpi4, na.rm=T),
corn_diff_nccpi5 = mean(corn_diff_nccpi5, na.rm=T),
soy_pbenefit = mean(soy_pbenefit, na.rm=T),
soy_pbenefit_nccpi1 = mean(soy_pbenefit_nccpi1, na.rm=T),
soy_pbenefit_nccpi2 = mean(soy_pbenefit_nccpi2, na.rm=T),
soy_pbenefit_nccpi3 = mean(soy_pbenefit_nccpi3, na.rm=T),
soy_pbenefit_nccpi4 = mean(soy_pbenefit_nccpi4, na.rm=T),
soy_pbenefit_nccpi5 = mean(soy_pbenefit_nccpi5, na.rm=T),
corn_pbenefit = mean(corn_pbenefit, na.rm=T),
corn_pbenefit_nccpi1 = mean(corn_pbenefit_nccpi1, na.rm=T),
corn_pbenefit_nccpi2 = mean(corn_pbenefit_nccpi2, na.rm=T),
corn_pbenefit_nccpi3 = mean(corn_pbenefit_nccpi3, na.rm=T),
corn_pbenefit_nccpi4 = mean(corn_pbenefit_nccpi4, na.rm=T),
corn_pbenefit_nccpi5 = mean(corn_pbenefit_nccpi5, na.rm=T)
)
return(cnccpi)
}