The purpose of this package is to generate verification trees and evaluations of user supplied statements. Trees are made by parsing a statement into a data structure composed of lists. Safe statement evaluations are done by executing the verification trees.
Verification TreesAny statement can be represented by a tree data structure. Here is a quote from Wikipedia to explain the concept:
In computer science, a tree is a widely used abstract data type that represents a hierarchical tree structure with a set of connected nodes. Each node in the tree can be connected to many children (depending on the type of tree), but must be connected to exactly one parent, except for the root node, which has no parent. These constraints mean there are no cycles or âloopsâ (no node can be its own ancestor), and also that each child can be treated like the root node of its own subtree, making recursion a useful technique for tree traversal. In contrast to linear data structures, many trees cannot be represented by relationships between neighboring nodes in a single straight line.
â Wikipedia.org Tree (data structure)
By default the package will know how to parse a R statement into a tree. In theory, you could supply your own tokens and use the package to parse any language that follows similar grammar.
These verification trees have been used to port R statements into other languages. For example, one use case is to write out formulas in excel that replicate the calculations done in R.
Safe EvaluationWriting code that executes unverified code can be both powerful and dangerous. A common approach to doing this is with the following pattern:
eval(parse(text="unverified_code"))The power comes from the flexibility this pattern gives us. It usually comes with a significant performance cost, but CPU time is cheaper than our developers.
The danger comes from unknown unknowns. Your own input on your personal computer may not pose much of a risk. The same does not hold for input from nefarious/clever users on a server.
Execution of a verification tree generated on unverified code is a different story. The risk is limited to what is deemed acceptable based on the supplied tokens. It comes with a greater performance cost, but removes the danger from unverified code.
FunctionsThe focus of this package is limited to just creating and evaluating trees. The next sections cover the main functions.
create_treeThe create_tree function takes a string and generates a tree. For example, we can parse the simple expression 2+3:
x <- evalR::create_tree("2+3")
str(x)
#> List of 2
#> $ pval: list()
#> $ eval:List of 3
#> ..$ : chr "+"
#> ..$ :List of 2
#> .. ..$ : chr "atomic"
#> .. ..$ : chr "2"
#> ..$ :List of 2
#> .. ..$ : chr "atomic"
#> .. ..$ : chr "3"We can see the structure is a list of lists.
Under the hoodYou donât need to understand the structure of the tree to use it. Just like you can drive a car without knowing how an engine works. This section will help reveal how the trees are formed.
First lets confirm that we can replicate the tree structure:
tree <- list(
pval = list(),
eval = list("+", list("atomic", "2"), list("atomic", "3"))
)
testthat::expect_equal(x,tree)This test passes with zero error.
A full tree is made up of two main branches:
pval - stands for parenthesis valueseval - stands for verification valuesThe first thing the function does is find all parenthesis blocks and treats them as sub statements. Each of these sub statements becomes an element of the pval element. The eval tree will have references to these pval entries.
For example, lets tweak the 2+3 to (2)+(3):
x <- evalR::create_tree("(2)+(3)")
str(x)
#> List of 2
#> $ pval:List of 2
#> ..$ \0:List of 2
#> .. ..$ pval: list()
#> .. ..$ eval:List of 2
#> .. .. ..$ : chr "atomic"
#> .. .. ..$ : chr "2"
#> ..$ \1:List of 2
#> .. ..$ pval: list()
#> .. ..$ eval:List of 2
#> .. .. ..$ : chr "atomic"
#> .. .. ..$ : chr "3"
#> $ eval:List of 3
#> ..$ : chr "+"
#> ..$ :List of 2
#> .. ..$ : chr "atomic"
#> .. ..$ : chr "\\0"
#> ..$ :List of 2
#> .. ..$ : chr "atomic"
#> .. ..$ : chr "\\1"To replicate the structure:
pval_list <- list(
"\\0"=list(
pval = list(),
eval = list("atomic", "2")
),
"\\1"=list(
pval = list(),
eval = list("atomic", "3")
)
)
tree <- list(
pval = pval_list,
eval = list("+", list("atomic", "\\0"), list("atomic", "\\1"))
)
testthat::expect_equal(x,tree)This test passes with zero error.
Now the pval list is not empty. We have an entry for (2) and (3). Each entry in pval is a new tree unto itself and contains pval and eval branches.
The eval branch splits the statement by operators into âatomicâ elements.
For example, if we just parse 2:
x <- evalR::create_tree("2")
str(x)
#> List of 2
#> $ pval: list()
#> $ eval:List of 2
#> ..$ : chr "atomic"
#> ..$ : chr "2"The eval is one level deep and the first element is the string atomic. This signifies that this is an end node of the tree.
Lets expand this just a little bit:
x <- evalR::create_tree("-2")
str(x)
#> List of 2
#> $ pval: list()
#> $ eval:List of 2
#> ..$ : chr "-"
#> ..$ :List of 2
#> .. ..$ : chr "atomic"
#> .. ..$ : chr "2"Now eval is two levels deep. The first element states the operator - and the second element is another branch that looks exactly like the eval branch in the previous example.
If a parenthesis block is found, then the atomic element will be a reference to the which pval element:
x <- evalR::create_tree("-(2)")
str(x)
#> List of 2
#> $ pval:List of 1
#> ..$ \0:List of 2
#> .. ..$ pval: list()
#> .. ..$ eval:List of 2
#> .. .. ..$ : chr "atomic"
#> .. .. ..$ : chr "2"
#> $ eval:List of 2
#> ..$ : chr "-"
#> ..$ :List of 2
#> .. ..$ : chr "atomic"
#> .. ..$ : chr "\\0"In this example, the eval second level atomic element is \0. This is a reference to the \0 named element of the pval branch.
Given a tree, we can execute it with the function eval_tree. Here is a basic example:
x <- evalR::create_tree("2+3")
y <- evalR::eval_tree(x)
print(y)
#> [1] 5There is a convenience function that contains the tree creation stage. The eval_text takes text as an input:
y <- evalR::eval_text("2+3")
print(y)
#> [1] 5These three functions share the following parameters:
- token is an operator to negate a vector. NULL value will be replaced with c("-", "!").+ token is an operator that adds a left vector to a right vector. NULL value will be replaced with c(",","|", "&", "<=", "<", ">=", ">", "==", "!=", "+", "-", "*", "%/%", "/", "%%", "%in%", ":", "^"). The order determines the precedence of the operators.log token will evaluate the logarithm value of the first parameter. Note named parameters are not support. NULL value will be replaced with c("log","c", "any","all", "abs","ifelse").For example, if you want to be able to use the function rnorm, then you need to provide that as a item in the valid_functions parameter:
y <- evalR::eval_text("2+rnorm(1)", valid_functions="rnorm")
print(y)
#> [1] -0.1208164The eval_tree and eval_text share the following parameter:
This parameter limits the scope of the execution environment (not in a strictly technical sense). In other words, they limit what values can be reference.
Here is a basic concert example:
map_obj <- list("#" = data.frame(x = 1:5, y = 5:1))
y <- evalR::eval_text("log(#x#)", map=map_obj)
print(y)
#> [1] 0.0000000 0.6931472 1.0986123 1.3862944 1.6094379Here is a more complex example:
map_obj <- list("#" = data.frame(x = 1:5, y = 5:1),"$" = list(z = -(1:5)))
y <- evalR::eval_text("#x# + $z$", map=map_obj)
print(y)
#> [1] 0 0 0 0 0To get a sense of the performance. Lets compare different ways we can run log(1+2):
text <- "log(1+3)"
tree <- evalR::create_tree(text)
microbenchmark::microbenchmark(
{log(1+2)},
{eval(parse(text=text))},
{evalR::eval_tree(tree)},
{evalR::eval_text(text)},
{evalR::create_tree(text)}, n=1000)
#> Warning in microbenchmark::microbenchmark({: Could not measure a positive
#> execution time for 72 evaluations.
#> Unit: nanoseconds
#> expr min lq mean median uq max
#> { log(1 + 2) } 100 100 216 200 200 3100
#> { eval(parse(text = text)) } 4200 5200 6936 6600 7350 27100
#> { evalR::eval_tree(tree) } 19500 21200 25518 22700 24950 83600
#> { evalR::eval_text(text) } 161600 169400 188252 172150 191350 438600
#> { evalR::create_tree(text) } 138000 144000 162132 147450 165850 390100
#> n 0 0 1 0 0 100
#> neval
#> 100
#> 100
#> 100
#> 100
#> 100
#> 100The pure R evaluation is much faster than any of the other methods. This is no surprise.
The evalR::eval_tree block takes a couple times longer than the eval(parse(text)) execution. This is a trade off considering the reduced risk. The eval(parse(text)) execution is sometimes much slower when ran outside R Markdown.
We also see that evalR::eval_text takes much longer than evalR::eval_tree. The majority of the evalR::eval_text time comes from the internal call to evalR::create_tree. This is where the no free lunch principle comes into play. The cost of the reduced risk is spent in creating the tree.
If youâre lucky enough to have a set of user input that will be evaluated multiple times, then the design pattern of generating the tree once and using evalR::eval_tree will give similar performance to a straight eval call.
This package should be viewed as a building block and not as an end unto itself. You can consider using it anytime youâre tempted to write an eval(parse(text)) statement.
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