The lines that read in the files should be replaced as shown:
> A <- read.zoo("File1.csv", header = TRUE, tz = "", sep = ",")
> B <- read.zoo("File2.csv", header = TRUE, tz = "", sep = ",")
> merge(A, B)
A1 A2 B1 B2 B3
2013-08-01 12:10:21 NA NA 5 1 1
2013-08-05 00:00:00 2 1 NA NA NA
2013-08-05 00:01:00 2 1 NA NA NA
2013-08-05 00:02:00 1 1 5 1 1
2013-08-05 12:13:44 NA NA 14 1 2
Here it is in reproducible form:
Lines1 <- " Time, A1, A2
2013-08-05 00:00:00, 2, 1
2013-08-05 00:01:00, 2, 1
2013-08-05 00:02:00, 1, 1
"
Lines2 <- " Time, B1, B2, B3
2013-08-01 12:10:21, 5, 1, 1
2013-08-05 00:02:00, 5, 1, 1
2013-08-05 12:13:44, 14, 1, 2
"
library(zoo)
A <- read.zoo(text = Lines1, header = TRUE, tz = "", sep = ",")
B <- read.zoo(text = Lines2, header = TRUE, tz = "", sep = ",")
merge(A, B)