CVE/notes.md

Build and install.

To build the package the devtools package is used. This also provides roxygen2 which is used for documentation and authomatic creaton of the NAMESPACE file.

setwd("./CVE_R")  # Set path to the package root.
library(devtools) # Load required `devtools` package.
document()        # Create `.Rd` files and write `NAMESPACE`.

Next the package needs to be build, therefore (if pure R package, aka. C/C++, Fortran, ... code) just do the following.

R CMD build CVE_R
R CMD INSTALL CVE_0.1.tar.gz

Then we are ready for using the package.

library(CVE)
help(package = "CVE")

Build and install from within R.

An alternative approach is the following.

setwd('./CVE_R')
getwd()

library(devtools)
document()
# No vignettes to build but "inst/doc/" is required!
(path <- build(vignettes = FALSE))
install.packages(path, repos = NULL, type = "source")

Note: I only recommend this approach during development.

Reading log files.

The runtime tests (upcomming further tests) are creating log files saved in tmp/. These log files are CSV files (actualy TSV) with a header storing the test results. Depending on the test the files may contain differnt data. As an example we use the runtime test logs which store in each line the dataset, the used method as well as the error (actual error of estimated B against real B) and the time. For reading and analysing the data see the following example.

# Load log as `data.frame`
test0 <- read.csv('tmp/test0.log', sep = '\t')
# Create a error boxplot grouped by dataset.
boxplot(error ~ dataset, test0)

Environments and variable lookup.

In the following a view simple examples of how R searches for variables. In addition we manipulate funciton closures to alter the search path in variable lookup and outer scope variable manipulation.

droids <- "These aren't the droids you're looking for."

search <- function() {
    print(droids)
}

trooper.seeks <- function() {
    droids <- c("R2-D2", "C-3PO")
    search()
}

jedi.seeks <- function() {
    droids <- c("R2-D2", "C-3PO")
    environment(search) <- environment()
    search()
}

trooper.seeks()
jedi.seeks()

The next example ilustrates how to write (without local copies) to variables outside the functions local environment.

counting <- function() {
    count <<- count + 1 # Note the `<<-` assignment.
}

(function() {
    environment(counting) <- environment()
    count <- 0

    for (i in 1:10) {
        counting()
    }

    return(count)
})()

(function () {
    closure <- new.env()
    environment(counting) <- closure
    assign("count", 0, envir = closure)

    for (i in 1:10) {
        counting()
    }

    return(closure$count)
})()

Another example for the usage of do.call where the evaluation of parameters is illustated (example taken (and altered) from ?do.call).

## examples of where objects will be found.
A <- "A.Global"
f <- function(x) print(paste("f.new", x))
env <- new.env()
assign("A", "A.new", envir = env)
assign("f", f, envir = env)
f <- function(x) print(paste("f.Global", x))
f(A)                                          # f.Global A.Global
do.call("f", list(A))                         # f.Global A.Global
do.call("f", list(A), envir = env)            # f.new A.Global
do.call(f,   list(A), envir = env)            # f.Global A.Global
do.call("f", list(quote(A)), envir = env)     # f.new A.new
do.call(f,   list(quote(A)), envir = env)     # f.Global A.new
do.call("f", list(as.name("A")), envir = env) # f.new A.new
do.call("f", list(as.name("A")), envir = env) # f.new A.new