You want to set the color of a shaded region based on the y value.

Add a column that categorizes the y values, then map that column to fill. In this example, we'll first categorize the values as positive or negative:

library(gcookbook) # For the data set

cb <- subset(climate, Source=="Berkeley")

cb$valence[cb$Anomaly10y >= 0] <- "pos"
cb$valence[cb$Anomaly10y < 0]  <- "neg"

cb

   Source Year Anomaly1y Anomaly5y Anomaly10y Unc10y valence
 Berkeley 1800        NA        NA     -0.435  0.505     neg
 Berkeley 1801        NA        NA     -0.453  0.493     neg
 Berkeley 1802        NA        NA     -0.460  0.486     neg
 ...
 Berkeley 2002        NA        NA      0.856  0.028     pos
 Berkeley 2003        NA        NA      0.869  0.028     pos
 Berkeley 2004        NA        NA      0.884  0.029     pos