Nothing
## performance comparison
library(mefa)
library(mefa4)
data(abmibirds)
## NONE: no species was recorded (8)
## SNI: Species Not Identified (216)
## VNA: Variable Not Applicable (6)
## DNC: Did Not Collect (13)
## PNA: Protocol Not Available (0 in this case)
## S3 mefa processing
b3 <- abmibirds
b3 <- b3[!(b3$Scientific.Name %in% c("VNA", "DNC", "PNA")),]
levels(b3$Scientific.Name)[levels(b3$Scientific.Name) %in% c("NONE", "SNI")] <- "zero.pseudo"
b3$Counts <- ifelse(b3$Scientific.Name == "zero.pseudo", 0, 1)
b3$Label <- with(b3, paste(ABMI.Site, Year, Point.Count.Station, sep="_"))
x3 <- b3[!duplicated(b3$Label), c("Label", "ABMI.Site", "Year", "Field.Date", "Point.Count.Station",
"Wind.Conditions", "Precipitation")]
rownames(x3) <- x3$Label
z3 <- b3[!duplicated(b3$Scientific.Name), c("Common.Name",
"Scientific.Name", "Taxonomic.Resolution", "Unique.Taxonomic.Identification.Number")]
rownames(z3) <- z3$Scientific.Name
z3 <- z3[z3$Scientific.Name != "zero.pseudo",]
t31 <- system.time(s3 <- suppressWarnings(stcs(b3[,c("Label","Scientific.Name","Counts")])))
t32 <- system.time(m30 <- mefa(s3))
t33 <- system.time(m31 <- mefa(s3, x3, z3))
y30 <- m30$xtab
t34 <- system.time(m32 <- mefa(y30, x3, z3))
## S4 mefa4 processing
b4 <- abmibirds
b4$Label <- with(b4, paste(ABMI.Site, Year, Point.Count.Station, sep="_"))
x4 <- b4[!duplicated(b4$Label), c("Label", "ABMI.Site", "Year", "Field.Date", "Point.Count.Station",
"Wind.Conditions", "Precipitation")]
rownames(x4) <- x4$Label
z4 <- b4[!duplicated(b4$Scientific.Name), c("Common.Name",
"Scientific.Name", "Taxonomic.Resolution", "Unique.Taxonomic.Identification.Number")]
rownames(z4) <- z4$Scientific.Name
t41 <- system.time(s4 <- Xtab(~ Label + Scientific.Name, b4, cdrop = c("NONE", "SNI"),
subset = !(b4$Scientific.Name %in% c("VNA", "DNC", "PNA")), drop.unused.levels = TRUE))
t42 <- system.time(m40 <- Mefa(s4))
t43 <- system.time(m41 <- Mefa(s4, x4, z4))
y40 <- as.matrix(m40@xtab)
t44 <- system.time(m42 <- Mefa(y40, x4, z4))
res <- cbind("SIZE, *=3"=c("b*"=object.size(b3),
"s*"=object.size(s3),
"y*0"=object.size(y30),
"m*0"=object.size(m30),
"m*1"=object.size(m31),
"m*2"=object.size(m32)),
"SIZE, *=4"=c("b*"=object.size(b4),
"s*"=object.size(s4),
"y*0"=object.size(y40),
"m*0"=object.size(m40),
"m*1"=object.size(m41),
"m*2"=object.size(m42)),
"TIME, *=3"=c("b*"=NA,
"s*"=t31[3],
"y*0"=NA,
"m*0"=t32[3],
"m*1"=t33[3],
"m*2"=t34[3]),
"TIME, *=4"=c("b*"=NA,
"s*"=t41[3],
"y*0"=NA,
"m*0"=t42[3],
"m*1"=t43[3],
"m*2"=t44[3]))
(res <- cbind(res, "SIZE"=res[,2]/res[,1], "TIME"=res[,4]/res[,3]))
## debugging
dim(y30)
dim(y40)
setdiff(rownames(y30), rownames(y40))
setdiff(rownames(y40), rownames(y30))
setdiff(colnames(y30), colnames(y40))
setdiff(colnames(y40), colnames(y30))
system.time(xx3 <- aggregate(m31, "ABMI.Site"))
system.time(xx4 <- groupSums(m41, 1, m41@samp$ABMI.Site))
as.Mefa(xx3)
xx4
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.