As sent to Paul and Rob

appendixes.prj

@@ -40,7 +40,7 @@ TeX:RNW:UNIX
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 R.plotting.Rnw
 TeX:RNW:UNIX
-286371835 0 -1 232100 -1 232100 380 380 1366 1438 1 1 315 667 -1 -1 0 0 114715 -1 -1 114715 1 0 232100 -1  0 -1 0
+286371835 0 -1 232100 -1 232100 380 380 1366 1438 1 1 354 3886 -1 -1 0 0 114715 -1 -1 114715 1 0 232100 -1  0 -1 0
 references.bib
 BibTeX:UNIX
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appendixes.prj.bak

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+286371835 0 -1 232100 -1 232100 380 380 1366 1438 1 1 354 667 -1 -1 0 0 114715 -1 -1 114715 1 0 232100 -1  0 -1 0
 references.bib
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benchmark-row-sums.R

@@ -1,124 +1,3 @@
-<<<<<<< Updated upstream
-library(microbenchmark)
-library(ggplot2)
-library(patchwork)
-
-powers <- c(2, 4, 6, 8) # square matrices
-
-benchmarks <- list()
-
-for (i in powers) {
-  cat("Doing", i, "...")
-  gc()
-
-  num_rows <- 10^(i %/% 2)
-  A <- matrix(rnorm(10^i), nrow = num_rows)
-
-  benchmarks[[paste("dimension",
-                    paste(dim(A), collapse = "*"),
-                    sep = " ")]] <-
-    microbenchmark(
-      {
-        row.sum <- numeric()
-        for (i in 1:nrow(A)) {
-          row.sum[i] <- 0
-          for (j in 1:ncol(A))
-            row.sum[i] <- row.sum[i] + A[i, j]
-        }
-      },
-      {
-        row.sum <- numeric(nrow(A))
-        for (i in 1:nrow(A)) {
-          row.sum[i] <- 0
-          for (j in 1:ncol(A))
-            row.sum[i] <- row.sum[i] + A[i, j]
-        }
-      },
-      {
-        row.sum <- numeric()
-        for (i in 1:nrow(A)) {
-          row.sum[i] <- sum(A[i, ])
-        }
-      },
-      {
-        row.sum <- numeric(nrow(A))
-        for (i in 1:nrow(A)) {
-          row.sum[i] <- sum(A[i, ])
-        }
-      },
-      {
-        row.sum <- apply(A, MARGIN = 1, sum)
-      },
-      {
-        row.sum <- rowSums(A)
-      },
-      times = c(300L, 300L, 300L, 200L, 100L, 50L, 25L, 12L)[i]
-    )
-  cat(" done\n")
-}
-
-summaries <- data.frame()
-for (b in benchmarks) {
-  summaries <-
-    rbind(summaries,
-          summary(b, unit = "millisecond")[ , c("expr", "median", "cld")])
-}
-summaries
-summaries$size <- rep(10^powers, each = 6)
-summaries$loop <- summaries$expr
-levels(summaries$loop) <- c("nested for", "nested for alloc.",
-                            "for and sum", "for and sum alloc.",
-                            "apply and sum", "rowSums")
-
-colnames(summaries)
-
-fig.seconds <-
-  ggplot(summaries, aes(size, median*1e-3, color = loop)) +
-  geom_point() +
-  geom_line() +
-  scale_x_log10(name = "Vector length") +
-  scale_y_log10(name = "Time (s)") +
-  scale_color_discrete(name = "Iteration\napproach") +
-  theme_bw() # + theme(legend.position = "top")
-fig.seconds
-
-rel.summaries <- data.frame()
-for (b in benchmarks) {
-  rel.summaries <-
-    rbind(rel.summaries,
-          summary(b, unit = "relative")[ , c("expr", "median", "cld")])
-}
-rel.summaries
-rel.summaries$size <- rep(10^powers, each = 6)
-rel.summaries$loop <- rel.summaries$expr
-levels(rel.summaries$loop) <- c("nested for", "nested for alloc.",
-                                "for and sum", "for and sum alloc.",
-                                "apply and sum", "rowSums")
-
-colnames(rel.summaries)
-
-fig.rel <-
-  ggplot(rel.summaries, aes(size, median, color = loop)) +
-  geom_point() +
-  geom_line() +
-  scale_x_log10(name = "Vector length") +
-  scale_y_log10(name = "Time (relative to shortest)",
-                breaks = c(1, 2, 5, 10, 20, 50, 100, 200, 500, 1000)) +
-  scale_color_discrete(name = "Iteration\napproach") +
-  theme_bw() # + theme(legend.position = "none")
-fig.rel
-
-diff.benchmark.fig <-
-fig.seconds / fig.rel + plot_layout(guides = "collect")
-diff.benchmark.fig
-
-save(diff.benchmark.fig,
-     fig.seconds,
-     fig.rel,
-     summaries,
-     rel.summaries,
-     file = "benchmarks-rowSums-pantera.Rda")
-=======
 library(microbenchmark)
 library(ggplot2)
 library(patchwork)
@@ -232,10 +111,16 @@ diff.benchmark.fig <-
 fig.seconds / fig.rel + plot_layout(guides = "collect")
 diff.benchmark.fig
 
+# save(diff.benchmark.fig,
+#      fig.seconds,
+#      fig.rel,
+#      summaries,
+#      rel.summaries,
+#      file = "benchmarks-rowSums-pantera.Rda")
+
 save(diff.benchmark.fig,
      fig.seconds,
      fig.rel,
      summaries,
      rel.summaries,
-     file = "benchmarks-rowSums-pantera.Rda")
->>>>>>> Stashed changes
+     file = "benchmarks-rowSums-angus.Rda")

benchmark-vector-diff.R

@@ -130,4 +130,11 @@ save(diff.benchmark.fig,
      fig.rel,
      summaries,
      rel.summaries,
-     file = "benchmarks.carbonilla.Rda")
+     file = "benchmarks.angus.Rda")
+
+# save(diff.benchmark.fig,
+#      fig.seconds,
+#      fig.rel,
+#      summaries,
+#      rel.summaries,
+#      file = "benchmarks.carbonilla.Rda")