R Under development (unstable) (2023-08-20 r84995 ucrt) -- "Unsuffered Consequences"
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> library(Rarity)
> data(spid.occ)
> 
> # Preparation of rarity weights
> rarity.weights <- rWeights(spid.occ, extended = TRUE)
Rarity cut-off points:
 occurMA 0.0357142857142857 / 2
 occurWP 0.339285714285714 / 19 
> 
> # Generation of an assemblage matrix
> assemblages.matrix <- cbind(assemblage.1 = sample(c(0, 1), 50, replace = TRUE),
+                             assemblage.2 = sample(c(0, 1), 50, replace = TRUE),
+                             assemblage.3 = sample(c(0, 1), 50, replace = TRUE),
+                             assemblage.4 = sample(c(0, 1), 50, replace = TRUE),
+                             assemblage.5 = sample(c(0, 1), 50, replace = TRUE))
> # Random attribution of names to the sampled species
> rownames(assemblages.matrix) <- sample(rownames(spid.occ), 50, replace = FALSE)
> 
> 
> # Test 1: A vector - W vector
> curW <- rarity.weights$W
> names(curW) <- rownames(rarity.weights)
> curA <- assemblages.matrix[, 1]
> 
> result <- Irr(W = curW, assemblages = curA)
> result
     Irr Richness 
 0.09164 25.00000 
> tot.res <- result[1]
> if(any(is.na(result)) | any(result[grep("Irr", names(result))] < 0))
+ {
+   stop("Error in the test")
+ }
> # Testing NAs
> curW[2] <- NA
> result <- Irr(W = curW, assemblages = curA)
W contains NA values, they will be removed
> result
     Irr Richness 
 0.09164 25.00000 
> if(any(is.na(result)) | any(result[grep("Irr", names(result))] < 0))
+ {
+   stop("Error in the test")
+ }
> 
> 
> # Test 2: A vector - W matrix
> curW <- as.matrix(rarity.weights)
> curA <- assemblages.matrix[, 1]
> 
> result <- Irr(W = curW, assemblages = curA)
> result
  Irr_W1   Irr_W2    Irr_W Richness 
 0.12612  0.05712  0.09164 25.00000 
> if(any(is.na(result)) | any(result[grep("Irr", names(result))] < 0))
+ {
+   stop("Error in the test")
+ }
> tot.res <- c(tot.res,
+              result["Irr_W"])
> 
> # Testing NAs
> curW[1, 2] <- NA
> curW[10, 2] <- NA
> curW[5, 3] <- NA
> result <- Irr(W = curW, assemblages = curA)
W contains NA values, they will be removed
> result
  Irr_W1   Irr_W2    Irr_W Richness 
 0.12612  0.05712  0.09164 25.00000 
> if(any(is.na(result)) | any(result[grep("Irr", names(result))] < 0))
+ {
+   stop("Error in the test")
+ }
> 
> 
> # Test 3: A matrix - W vector
> curW <- rarity.weights$W
> names(curW) <- rownames(rarity.weights)
> curA <- assemblages.matrix
> 
> result <- Irr(W = curW, assemblages = curA)
> result
                    Irr Richness
assemblage.1 0.09164000       25
assemblage.2 0.04967500       20
assemblage.3 0.07303846       26
assemblage.4 0.13650000       26
assemblage.5 0.11530556       18
> tot.res <- c(tot.res,
+              result[1, 1])
> if(any(is.na(result)) | any(result[grep("Irr", names(result))] < 0))
+ {
+   stop("Error in the test")
+ }
> 
> # Testing NAs
> curW[2] <- NA
> result <- Irr(W = curW, assemblages = curA)
W contains NA values, they will be removed
> result
                    Irr Richness
assemblage.1 0.09164000       25
assemblage.2 0.04967500       20
assemblage.3 0.07303846       26
assemblage.4 0.13650000       26
assemblage.5 0.11530556       18
> if(any(is.na(result)) | any(result[grep("Irr", names(result))] < 0))
+ {
+   stop("Error in the test")
+ }
> 
> # Test 4: A matrix - W matrix
> curW <- rarity.weights
> curA <- assemblages.matrix
> 
> result <- Irr(W = curW, assemblages = curA)
> result
                 Irr_W1     Irr_W2      Irr_W Richness
assemblage.1 0.12612000 0.05712000 0.09164000       25
assemblage.2 0.05510000 0.04420000 0.04967500       20
assemblage.3 0.08476923 0.06123077 0.07303846       26
assemblage.4 0.16169231 0.11119231 0.13650000       26
assemblage.5 0.17516667 0.05538889 0.11530556       18
> tot.res <- c(tot.res,
+              result[1, 3])
> if(any(is.na(result)) | any(result[grep("Irr", names(result))] < 0))
+ {
+   stop("Error in the test")
+ }
> 
> # Testing NAs
> curW[1, 2] <- NA
> curW[10, 2] <- NA
> curW[5, 3] <- NA
> result <- Irr(W = curW, assemblages = curA)
W contains NA values, they will be removed
> result
                 Irr_W1     Irr_W2      Irr_W Richness
assemblage.1 0.12612000 0.05712000 0.09164000       25
assemblage.2 0.05510000 0.04420000 0.04967500       20
assemblage.3 0.08476923 0.06123077 0.07303846       26
assemblage.4 0.16169231 0.11119231 0.13650000       26
assemblage.5 0.17516667 0.05538889 0.11530556       18
> if(any(is.na(result)) | any(result[grep("Irr", names(result))] < 0))
+ {
+   stop("Error in the test")
+ }
> 
> 
> if(any(diff(tot.res)) > 0)
+ {
+   stop("Different values found for the same indices")
+ }
Warning message:
In any(diff(tot.res)) : coercing argument of type 'double' to logical
> 
> proc.time()
   user  system elapsed 
   0.32    0.07    0.39