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> library(CodeDepends)
>  # Simple but with a code block that is stand-alone/unrelated.
> p <- readScript(system.file("samples", "dual.R", package = "CodeDepends"))
> ## need formulaInputs=TRUE because there is an lm(y~x) call in there ...
> 
> ethread = getExpressionThread("fit", p, formulaInputs = TRUE) 
> stopifnot(length(ethread) == 3)
> 
> dthread = getDependsThread("fit", getInputs(p, formulaInputs=TRUE))
> stopifnot(identical(dthread, c(1L, 2L, 4L)))
> # With redefintions of variables
> s <- readScript(system.file("samples", "sitepairs.R", package = "CodeDepends"))
> getExpressionThread("covs", s)
An object of class "Script"
[[1]]
mdata <- .readRDS("monitor-data/monitor-subset.rds")

[[2]]
mdata$LATITUDE <- NULL

[[3]]
mdata$LONGITUDE <- NULL

[[4]]
spmdata <- split(mdata, mdata$SITEPOC)

[[5]]
index.names <- names(spmdata)

[[6]]
all.dates <- seq(as.Date("2000-01-01"), as.Date("2006-12-31"), 
    "day")

[[7]]
dateDF <- data.frame(DATE = all.dates)

[[8]]
pollutants <- c("SULFATE", "NITRATE", "silicon", "Elemental_Carbon", 
    "OC_K14", "Sodium_Ion", "AMMONIUM")

[[9]]
ad <- lapply(spmdata, function(x) {
    m <- merge(dateDF, x, by = "DATE", all.x = TRUE)
    data.matrix(m[, pollutants])
})

[[10]]
adata <- array(dim = c(dim(ad[[1]]), length(ad)))

[[11]]
for (i in seq_along(ad)) {
    adata[, , i] <- ad[[i]]
}

[[12]]
dimnames(adata) <- list(as.character(all.dates), pollutants, 
    index.names)

[[13]]
sitedata <- .readRDS("monitor-data/sitedata.rds")

[[14]]
row.names(sitedata) <- sitedata$SITEPOC

[[15]]
sitepairs <- as.matrix(expand.grid(sitedata$SITEPOC, sitedata$SITEPOC))

[[16]]
colnames(sitepairs) <- c("site1", "site2")

[[17]]
repeats <- sitepairs[, 1] == sitepairs[, 2]

[[18]]
sitepairs <- sitepairs[!repeats, ]

[[19]]
key <- apply(sitepairs, 1, function(x) paste(sort(x), collapse = ""))

[[20]]
sitepairs <- sitepairs[!duplicated(key), ]

[[21]]
sitepairs <- as.data.frame(sitepairs, stringsAsFactors = FALSE)

[[22]]
dist <- apply(sitepairs, 1, function(x) {
    s1 <- sitedata[x["site1"], ]
    s2 <- sitedata[x["site2"], ]
    yd <- (s1$LATITUDE - s2$LATITUDE) * 69.2
    xd <- (s1$LONGITUDE - s2$LONGITUDE) * 69.2 * 0.78
    sqrt(xd^2 + yd^2)
})

[[23]]
sitepairs$distance <- dist

[[24]]
covs <- t(mapply(function(site1, site2) {
    cc <- cov(adata[, , site1], adata[, , site2], use = "pairwise")
    diag(cc)
}, sitepairs[, 1], sitepairs[, 2]))

[[25]]
colnames(covs) <- paste(colnames(covs), "c", sep = ".")

[[26]]
rownames(covs) <- NULL

Slot "location":
[1] "D:/RCompile/CRANincoming/R-devel/lib/CodeDepends/samples/sitepairs.R"

> getDependsThread("covs", as(s, "ScriptInfo"))
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 27 28
[26] 36
> 
> # With redefintions of variables
> p <- readScript(system.file("samples", "results-multi.R", package = "CodeDepends"))
> getExpressionThread("results", p)
An object of class "Script"
[[1]]
outcome <- commandArgs(trailingOnly = TRUE)[1]

[[2]]
specdata <- .readRDS("SpecData-combined.rds")

[[3]]
pollutants <- c("SULFATE", "NITRATE", "silicon", "Elemental_Carbon", 
    "OC_K14", "Sodium_Ion")

[[4]]
spec.terms <- list(lag0 = pollutants, lag1 = paste("Lag(", pollutants, 
    ", 1)"), lag2 = paste("Lag(", pollutants, ", 2)"))

[[5]]
fipsList <- readLines("speciation-fips.txt")

[[6]]
ranges <- dget("data-ranges.R")

[[7]]
results <- lapply(spec.terms, function(sterms) {
    sterms <- sapply(parse(text = sterms), deparse, width.cutoff = 100)
    cat(sterms, "\n")
    cycleCounties(fipsList, specdata, sterms, outcome, type = "multiple", 
        ranges = ranges)
})

[[8]]
pollutants <- spec.terms[[1]]

[[9]]
results <- lapply(results, function(lag) {
    colnames(lag$beta) <- pollutants
    lag
})

Slot "location":
[1] "D:/RCompile/CRANincoming/R-devel/lib/CodeDepends/samples/results-multi.R"

> getDependsThread("results", as(p, "ScriptInfo"))
[1]  1  3  7  8  9 10 12 13 14
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
   1.00    0.09    1.06