Add memory bench

Author: RiboRings

R/plot.R

@@ -32,21 +32,31 @@ methods <- c(
 
 # Import results
 df_list <- lapply(
-    list.files("./out/", full.names = TRUE, recursive = TRUE),
+    list.files("./out", full.names = TRUE, recursive = TRUE),
     read.table, sep = "\t", header = TRUE
 )
 
 df <- do.call(rbind, df_list)
 
+df <- reshape(
+    df,
+    idvar = setdiff(names(df), c("var", "value")),
+    timevar = "var",
+    v.names = "value",
+    direction = "wide"
+)
+
+names(df) <- sub("value.", "", names(df), fixed = TRUE)
+
 # Set sample size
 n_iter <- length(unique(df$state))
 
 # Summarise benchmarking results with mean time and standard deviation
 df <- df |>
     group_by(method, object, rows, cols) |>
     summarise(
-        Time = mean(value), #Memory = mean(memory / 1e6),
-        TimeSD = sd(value), TimeSE = TimeSD / sqrt(n_iter),
+        Time = mean(time), Memory = mean(memory / 1e6),
+        TimeSD = sd(time), TimeSE = TimeSD / sqrt(n_iter),
         .groups = "drop"
     ) |>
     mutate(

R/run_function.R

@@ -140,11 +140,15 @@ file_name <- paste(
     obj.type, obj.fun, row.size, col.size, sep = "_"
 )
 
-file_name <- paste(
-    bench.var, rand.state, file_name, sep = "/"
+dir_name <- paste(
+    "out", bench.var, rand.state, sep = "/"
 )
 
+if( !dir.exists(dir_name) ) dir.create(dir_name, recursive = TRUE)
+
 write.table(
-    df, file = paste0("out/", file_name, ".tsv"), sep = "\t", row.names = FALSE
+    df,
+    file = paste0(dir_name, "/", file_name, ".tsv"),
+    sep = "\t",
+    row.names = FALSE
 )
-

R/tasks.R

@@ -34,6 +34,7 @@ times <- paste("run_function.R", times, "time", rand.state)
 writeLines(times, "times.txt")
 
 mems <- gsub("_", " ", prior.out, fixed = TRUE)
+mems <- mems[!startsWith(mems, "qiime")]
 mems <- paste("run_function.R", mems, "memory", rand.state)
 
-writeLines(mems, "mems.txt")
+writeLines(mems, "mems.txt")