From 8762cc0986cf9a605149d6e82d8e22da7bbcf846 Mon Sep 17 00:00:00 2001
From: Toby Dylan Hocking <toby.dylan.hocking@usherbrooke.ca>
Date: Fri, 20 Sep 2024 13:16:48 -0400
Subject: [PATCH] update examples

---
 man/atime.Rd           | 42 +++++++++-----------------------------
 man/references_best.Rd | 46 +++++++++++++++++++++++++++++++++---------
 2 files changed, 47 insertions(+), 41 deletions(-)

diff --git a/man/atime.Rd b/man/atime.Rd
index f213cd0..a436891 100644
--- a/man/atime.Rd
+++ b/man/atime.Rd
@@ -36,47 +36,25 @@ result=FALSE, ...)}
 \examples{
 
 ## Example 1: polynomial and exponential time string functions.
-string.result <- atime::atime(
+atime_result_string <- atime::atime(
+  seconds.limit=0.001,
   N=unique(as.integer(10^seq(0,3.5,l=100))),
   setup={
     subject <- paste(rep("a", N), collapse="")
     pattern <- paste(rep(c("a?", "a"), each=N), collapse="")
+    linear_size_replacement <- paste(rep("REPLACEMENT", N), collapse="")
   },
-  seconds.limit=0.001,
   PCRE.match=regexpr(pattern, subject, perl=TRUE),
   TRE.match=regexpr(pattern, subject, perl=FALSE),
   constant.replacement=gsub("a","constant size replacement",subject),
-  linear.replacement=gsub("a",subject,subject))
-plot(string.result)
+  linear.replacement=gsub("a",linear_size_replacement,subject))
+plot(atime_result_string)
 
-## Example 2: split data table vs frame, constant factor difference.
-library(data.table)
-split.result <- atime::atime(
-  setup={
-    set.seed(1)
-    DT <- data.table(
-      x1 = rep(c("c","d"), l=N),
-      x2 = rep(c("x","y"), l=N),
-      x3 = rep(c("a","b"), l=N),
-      y = rnorm(N)
-    )[sample(.N)]
-    DF <- as.data.frame(DT)
-  },
+## Example 2: combine using rbind inside or outside for loop.
+atime_result_rbind <- atime::atime(
   seconds.limit=0.001,
-  frame=split(DF[names(DF) != "x1"], DF["x1"], drop = TRUE),
-  table=split(DT, by = "x1", keep.by = FALSE, drop = TRUE)
-)
-plot(split.result)
-
-## Example 3: combine inside or outside for loop.
-atime.list <- atime::atime(
-  N=as.integer(10^seq(0, 5), by=0.25),
   setup={
-    Nrow <- 1e3
-    DF <- data.frame(
-      x1 = rep(c("c","d"), l=Nrow),
-      x2 = rep(c("x","y"), l=Nrow),
-      x3 = rep(c("a","b"), l=Nrow))
+    DF <- data.frame(i=1:100)
   },
   inside={
     big.frame <- data.frame()
@@ -89,9 +67,9 @@ atime.list <- atime::atime(
     for(table.i in 1:N){
       big.frame.list[[table.i]] <- DF
     }
-    do.call(rbind, big.frame.list)
+    big.frame <- do.call(rbind, big.frame.list)
   }
 )
-plot(atime.list)
+plot(atime_result_rbind)
 
 }
diff --git a/man/references_best.Rd b/man/references_best.Rd
index cabf070..0ed3004 100644
--- a/man/references_best.Rd
+++ b/man/references_best.Rd
@@ -26,26 +26,54 @@ references_best(L, fun.list=NULL)
 \examples{
 
 ## Example 1: polynomial and exponential time string functions.
-string.result <- atime::atime(
+atime_result_string <- atime::atime(
+  seconds.limit=0.001,
   N=unique(as.integer(10^seq(0,4,l=100))),
   setup={
     subject <- paste(rep("a", N), collapse="")
     pattern <- paste(rep(c("a?", "a"), each=N), collapse="")
+    linear_size_replacement <- paste(rep("REPLACEMENT", N), collapse="")
   },
-  seconds.limit=0.001,
   PCRE.match=regexpr(pattern, subject, perl=TRUE),
   TRE.match=regexpr(pattern, subject, perl=FALSE),
   constant.replacement=gsub("a","constant size replacement",subject),
-  linear.replacement=gsub("a",subject,subject))
-(string.best <- atime::references_best(string.result))
+  linear.replacement=gsub("a",linear_size_replacement,subject))
+(refs_best_string <- atime::references_best(atime_result_string))
 ## plot method shows each expr and unit in a separate panel.
 ## default is to show closest larger and smaller references.
-plot(string.best)
+plot(refs_best_string)
 ## modifying plot.references changes violet references shown by plot.
-string.best$plot.references <- string.best$ref[c("N","N^2","N^3","2^N"),on="fun.name"]
-plot(string.best)
+refs_best_string$plot.references <- refs_best_string$ref[c("N","N^2","N^3","2^N"),on="fun.name"]
+plot(refs_best_string)
 ## predict method computes N for given units (default seconds limit).
-string.pred = predict(string.best)
-plot(string.pred)
+(pred_string <- predict(refs_best_string))
+plot(pred_string)
+
+## Example 2: combine using rbind inside or outside for loop.
+atime_result_rbind <- atime::atime(
+  seconds.limit=0.001,
+  setup={
+    DF <- data.frame(i=1:100)
+  },
+  inside={
+    big.frame <- data.frame()
+    for(table.i in 1:N){
+      big.frame <- rbind(big.frame, DF)
+    }
+  },
+  outside={
+    big.frame.list <- list()
+    for(table.i in 1:N){
+      big.frame.list[[table.i]] <- DF
+    }
+    big.frame <- do.call(rbind, big.frame.list)
+  }
+)
+(refs_best_rbind <- atime::references_best(atime_result_rbind))
+plot(refs_best_rbind)
+refs_best_rbind$plot.references <- refs_best_rbind$ref[c("N","N^2"),on="fun.name"]
+plot(refs_best_rbind)
+(pred_rbind <- predict(refs_best_rbind))
+plot(pred_rbind)
 
 }