Merge branch 'one-species-accumulation': fixes issue #501

vegandevs · Mar 11, 2022 · 6a5f9b3 · 6a5f9b3
2 parents 4d8d153 + ee2e591
commit 6a5f9b3
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 11 deletions.
diff --git a/R/plot.specaccum.R b/R/plot.specaccum.R
@@ -26,9 +26,10 @@
     if (!add) {
         if (missing(ylim))
             if (random)
-                ylim <- c(1, max(x$perm, na.rm = TRUE))
+                ylim <- c(min(1, x$perm), max(x$perm, na.rm = TRUE))
             else
-                ylim <- c(1, max(x$richness, x$richness + ci*x$sd, na.rm = TRUE))
+                ylim <- c(min(1, x$richness),
+                          max(x$richness, x$richness + ci*x$sd, na.rm = TRUE))
         plot(xaxvar, x$richness, xlab=xlab, ylab=ylab, ylim=ylim,
              type="n", ...)
     }

diff --git a/R/specaccum.R b/R/specaccum.R
@@ -15,19 +15,14 @@
     x <- x[, colSums(x) > 0, drop=FALSE]
     n <- nrow(x)
     p <- ncol(x)
-    if (p == 1) {
-        x <- t(x)
-        n <- nrow(x)
-        p <- ncol(x)
-    }
     accumulator <- function(x, ind) {
-        rowSums(apply(x[ind, ], 2, cumsum) > 0)
+        rowSums(apply(x[ind, , drop=FALSE], 2, cumsum) > 0)
     }
     specaccum <- sdaccum <- sites <- perm <- NULL
     if (n == 1 && method != "rarefaction")
         message("no actual accumulation since only one site provided")
     switch(method, collector = {
-        sites <- 1:n
+        sites <- seq_len(n)
         xout <- weights <- cumsum(w)
         specaccum <- accumulator(x, sites)
         perm <- as.matrix(specaccum)
@@ -37,7 +32,7 @@
         perm <- apply(permat, 1, accumulator, x = x)
         if (!is.null(w))
             weights <- as.matrix(apply(permat, 1, function(i) cumsum(w[i])))
-        sites <- 1:n
+        sites <- seq_len(n)
         if (is.null(w)) {
             specaccum <- apply(perm, 1, mean)
             sdaccum <- apply(perm, 1, sd)
@@ -99,7 +94,7 @@
             result[i, ] <- (1 - i/n)^freq
         }
         result <- 1 - result
-        sites <- 1:n
+        sites <- seq_len(n)
         specaccum <- rowSums(result)
         sdaccum <- sqrt(rowSums(result * (1 - result)))
     })