Error in nested loop using aggregate function

Question

I have a data.frame where I want to calculate min, mean and max and period (number of months with positive values) from annual data for each plot nested in each year and each site. I am trying to use nested loops and the aggregate function to do this but keep encountering errors.

This is what I have tried so far

DT5 <- NULL
for(i in levels(DT4$Site)) {
  for(j in levels(DT4$Year)) {
    tmp <- subset(subset(DT4, Site == i), Year== j)
    min <- aggregate(tmp[,5], list(tmp$Plot), min)
    mean <- aggregate(tmp[,5], list(tmp$Plot), mean)
    max <- aggregate(tmp[,5], list(tmp$Plot), max)
    per <- sum(tmp[,5] > 0)
    tmp <- cbind(rep(i, nrow(mean)), rep(j, nrow(mean)), tmp$Year, mean)
  }
  if(is.null(DT5)){DT5<-tmp} else {DT5<-rbind(DT5,tmp)} 
}

where DT4 is a data.frame with columns Site, Year, Month, Plot and WatLev

Ultimately, I want to achieve a data.frame with columns Site, Year, Plot, min, mean, max and per calculated for each plot, in each Site for each year.

Here is an example data set:

Site <- rep(rep(c("SiteA", "SiteB", "SiteC"), each=144),times=3)
Year <- rep(rep(2001:2003, each=48),times=3)
Month <- rep(rep(rep(c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"), each=4), times=3),3)
Plot <- rep(rep(c("A", "B", "C", "D"), times=36),3)
WatLev <- runif(1296, -50, 5)
DT4 <- cbind(Site, Year, Month, Plot, WatLev)

Hey Christopher, it looks like you can absolutely avoid this nested loops by using dplyr (eg with group_by() and summarise()). If you can provide some sample data of your DT4, we can give you some hands on solutions. — Stephan

Stephan Stephan · Accepted Answer · 2019-04-11T07:49:40

ok, try this:

library(dplyr)
DT4 %>% as_tibble() %>%
  mutate(WatLev = as.numeric(WatLev)) %>% 
  group_by(Site, Year) %>% 
  summarise(min = min(WatLev, na.rm = TRUE),
            mean = mean(WatLev, na.rm = TRUE),
            max = max(WatLev, na.rm = TRUE),
            per = sum(WatLev > 0))

output is:

# A tibble: 9 x 6
# Groups:   Site [3]
  Site  Year    min  mean   max   per
  <chr> <chr> <dbl> <dbl> <dbl> <int>
1 SiteA 2001  -49.8 -24.3  4.76    11
2 SiteA 2002  -50.0 -23.6  4.98     9
3 SiteA 2003  -49.2 -20.7  4.76    16
4 SiteB 2001  -49.3 -21.4  4.85    11
5 SiteB 2002  -49.7 -19.0  4.72    19
6 SiteB 2003  -50.0 -22.0  4.89    17
7 SiteC 2001  -49.2 -20.4  4.97    14
8 SiteC 2002  -49.6 -22.2  4.28    13
9 SiteC 2003  -49.0 -23.3  4.85    14

Error in nested loop using aggregate function

1 Answers