R Under development (unstable) (2024-05-17 r86566 ucrt) -- "Unsuffered Consequences"
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> ## performance comparison
> library(mefa)
mefa 3.2-9 	 2024-05-19
> library(mefa4)
Loading required package: Matrix
mefa4 0.3-11 	 2024-05-20

Attaching package: 'mefa4'

The following objects are masked from 'package:mefa':

    samp, taxa, xtab

> 
> 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]))
    SIZE, *=3 SIZE, *=4 TIME, *=3 TIME, *=4      SIZE       TIME
b*    6522600   5813728        NA        NA 0.8913206         NA
s*    1458872    704384      0.37      0.03 0.4828278 0.08108108
y*0   6323296   6323008        NA        NA 0.9999545         NA
m*0   6324888    705560      1.60      0.00 0.1115530 0.00000000
m*1   7005368   1385648      1.05      0.00 0.1977980 0.00000000
m*2   7005368   1385648      0.01      0.01 0.1977980 1.00000000
> 
> ## debugging
> 
> dim(y30)
[1] 3534  214
> dim(y40)
[1] 3534  214
> 
> setdiff(rownames(y30), rownames(y40))
character(0)
> setdiff(rownames(y40), rownames(y30))
character(0)
> 
> setdiff(colnames(y30), colnames(y40))
character(0)
> setdiff(colnames(y40), colnames(y30))
character(0)
> 
> system.time(xx3 <- aggregate(m31, "ABMI.Site"))
   user  system elapsed 
   0.15    0.01    0.18 
> system.time(xx4 <- groupSums(m41, 1, m41@samp$ABMI.Site))
   user  system elapsed 
   0.01    0.00    0.01 
> as.Mefa(xx3)
Object of class "Mefa"
  ..@ xtab: 330 x 214 sparse Matrix
  ..@ samp: NULL
  ..@ taxa: data frame with 4 variables
  ..@ join: left 
> xx4
Object of class "Mefa"
  ..@ xtab: 330 x 214 sparse Matrix
  ..@ samp: NULL
  ..@ taxa: data frame with 4 variables
  ..@ join: left 
> 
> 
> proc.time()
   user  system elapsed 
   5.26    0.35    5.60