New scripts

R/demo.r

@@ -0,0 +1,12 @@
+myNestedFunc <- function(x){
+  return (2 * x)
+}
+
+myFunc <- function(x){
+  y <- myNestedFunc(x + 5)
+  return(y)
+}
+
+myFunc(3)
+myFunc(4)
+myFunc(5.5)

R/getFunctions.R

@@ -0,0 +1,11 @@
+library("NCmisc")
+listresult <- list.functions.in.file("test.R")
+listresult <- unlist(unname(listresult))
+
+for(f in listresult){
+  print(f) 
+  print(formals(f))
+}
+
+#grab each of the functions, separated by package
+# trace arguments of the functions (for ex., for filenames)

R/micro.R

@@ -0,0 +1,37 @@
+
+x <- 1 
+capture.output(x)
+y <-3 
+capture.output(y)
+capture.output(10+0)
+capture.output(10)#doesn't work
+10 #monitor interpreter processing, capture.output(wrap an entire line)
+x #1
+x <-x+y 
+capture.output(x+y)#expression evaluation
+x
+y^3
+capture.output(y^3)
+
+#trace(write.csv, tracer = quote(cat(sprintf("Tracing file argument = %s\n", file))))
+trace(write.table, tracer = quote(cat(sprintf("Tracing csv(file = %s)\n", file))))
+write.csv(x,"~/test.test") #traceable
+untrace(write.table)
+
+trace(pdf, tracer = quote(cat(sprintf("Tracing pdf(file = %s)\n", file))))
+pdf("~/test.pdf")#see if can grab all arguments in an ordered list
+untrace(pdf)
+
+trace(plot, tracer = quote(cat(sprintf("Tracing plot(x = %s)\n", x))))
+plot(x)# x
+untrace(plot)
+
+#trace(.External, tracer = quote(cat(sprintf("Finished graphics device monitoring: (.NAME = %s)\n", .NAME))))
+trace(.External, tracer = quote(sprintf("Traced")))
+#trace(dev.cur, exit = quote(cat(sprintf("Finished graphics device monitoring"))), print=FALSE)
+
+dev.cur()
+dev.off()#
+
+#untrace(dev.cur)
+untrace(.External)

R/micro2.R

@@ -0,0 +1,42 @@
+x <- 1 
+y <-3 
+10 #monitor interpreter processing, capture.output(wrap an entire line)
+x #1
+x <-x+y 
+x
+capture.output(x)
+capture.output(y)
+
+y^3
+capture.output(y^3)
+
+trace(write.table, tracer = quote(cat(sprintf("Tracing csv(file = %s)\n", file))))
+trace(pdf, tracer = quote(cat(sprintf("Tracing pdf(file = %s)\n", file))))
+trace(plot, tracer = quote(cat(sprintf("Tracing pdf(x = %s)\n", x))))
+trace(.External, exit = quote(cat(sprintf("Finished graphics device monitoring\n"))), print=FALSE)
+
+write.csv(x,"~/test.test") #traceable
+pdf("~/test.pdf")#see if can grab all arguments in an ordered list
+plot(x)# x
+dev.off()#
+
+untrace(write.table)
+untrace(pdf)
+untrace(plot)
+untrace(.External)
+
+myNestedFunc <- function(x){
+  return (2 * x)
+}
+
+myFunc <- function(x){
+  y <- myNestedFunc(x + 5)
+  return(y)
+}
+
+myFunc(3)
+myFunc(4)
+myFunc(5.5)
+
+
+

R/prov.capture.R

@@ -1,15 +1,51 @@
-#' prov.capture --- Capture R language provencance.
-#' OUTPUT = Provenance from code stored in memory.
-#' 
-#' Captures and records provenance from a script provided by the user.
-#' 
-#' @param x A script who's provenance should be recorded.
-#' @return Stores provenance in memory in PROV-JSON format.
-#' @importFrom base trace
-#' @export prov.capture
-#' @author ELizabeth Hu and Matthew K. Lau
-
-prov.capture <- function(x = "script"){
-    #### Insert funcntion tracing activities here
-
-}
+#' prov.capture --- Capture R language provencance.
+#' OUTPUT = Provenance from code stored in memory.
+#' 
+#' Captures and records provenance from a script provided by the user.
+#' 
+#' @param script A script who's provenance should be recorded.
+#' @return Stores provenance in memory in PROV-JSON format.
+#' @importFrom base trace
+#' @export prov.capture
+#' @author ELizabeth Hu and Matthew K. Lau
+
+prov.capture <- function(script){
+    #### Insert function tracing activities here
+
+  fnames = list("myFunc")
+  print(fnames)
+  ### User defined functions
+
+  ddg.annotate <- function(fnames){
+    if (is.null(fnames)) {
+      return()
+    }
+
+    getCall <- function(){
+      i <- -1
+      while (as.character(sys.call(i)[1]) != ".doTrace")
+        i <- i - 1
+      call <- sys.call(i-1)
+      callName <- as.character(call[[1]])
+      print(cat(sprintf("Function called: %s\n", callName)))
+    }
+    #trace the call of myNestedFunc within myFunc
+    for(f in fnames){
+        f = quote(get(f))
+        trace(f, getCall, exit = quote(cat(sprintf("Return = %.5g\n", returnValue()))))
+    }
+    source("demo.r", print.eval = TRUE)
+    print("Ending script run")
+    for(f in fnames){
+      untrace(f)
+    }
+
+
+  }
+  #set to working directory with the script
+  ddg.annotate(fnames)
+
+}
+
+prov.capture("demo.r")
+

R/test.R

@@ -0,0 +1,41 @@
+
+x <- 1 
+y <-3 
+10 #monitor interpreter processing, capture.output(wrap an entire line)
+x #1
+x <-x+y 
+x
+y^3
+
+write.csv(x,"~/test.test") #traceable
+
+pdf("~/test.pdf")#see if can grab all arguments in an ordered list
+
+
+plot(x)# x
+
+dev.cur()
+dev.off()#
+
+
+write.csv(x,"~/test.test") #traceable
+pdf("~/test.pdf")#see if can grab all arguments in an ordered list
+plot(x)# x
+dev.off()#
+
+
+myNestedFunc <- function(x){
+  return (2 * x)
+}
+
+myFunc <- function(x){
+  y <- myNestedFunc(x + 5)
+  return(y)
+}
+
+myFunc(3)
+myFunc(4)
+myFunc(5.5)
+
+
+