[R/network-structure.R:135:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-structure.R#L135) *style:* **Lines should not be more than 80 characters.**
```r
              i <- tmp[seq_len(length(tmp) - 1)] != tmp[seq_len(length(tmp))[-1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:248:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L248) *style:* **Lines should not be more than 80 characters.**
```r
                     inDays = as.integer(x@ingoingContacts@tEnd - x@ingoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:251:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L251) *style:* **Lines should not be more than 80 characters.**
```r
                     outDays = as.integer(x@outgoingContacts@tEnd - x@outgoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:254:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L254) *style:* **Lines should not be more than 80 characters.**
```r
                     ingoingContactChain = IngoingContactChain(x@ingoingContacts),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:255:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L255) *style:* **Lines should not be more than 80 characters.**
```r
                     outgoingContactChain = OutgoingContactChain(x@outgoingContacts))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:261:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L261) *style:* **functions should have cyclomatic complexity of less than 15, this has 38.**
```r
setMethod("NetworkSummary",
^
```
[R/network-summary.R:315:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L315) *style:* **Lines should not be more than 80 characters.**
```r
              ## so test that root is a integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:323:20:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L323) *style:* **Only use double-quotes.**
```r
              stop('invalid class of root')
                   ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:331:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L331) *style:* **Lines should not be more than 80 characters.**
```r
              if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:332:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L332) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:343:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L343) *style:* **Lines should not be more than 80 characters.**
```r
              ## Test that days is a nonnegative integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:345:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
              if (any(is.na(days) | (days < 0)) || max(abs(days - daysr)) > 1e-07) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:365:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L365) *style:* **Lines should not be more than 80 characters.**
```r
          } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:370:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L370) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:373:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L373) *style:* **Lines should not be more than 80 characters.**
```r
              stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:456:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L456) *style:* **Lines should not be more than 80 characters.**
```r
              stop("root, inBegin, inEnd, outBegin and outEnd must have equal length")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:468:24:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L468) *style:* **Put spaces around all infix operators.**
```r
          contact_chain<- .Call("networkSummary",
                      ~^
```
[R/network-summary.R:469:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L469) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:470:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L470) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:472:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L472) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(root, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:489:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L489) *style:* **Lines should not be more than 80 characters.**
```r
                            ingoingContactChain = contact_chain[["ingoingContactChain"]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:490:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/network-summary.R#L490) *style:* **Lines should not be more than 80 characters.**
```r
                            outgoingContactChain = contact_chain[["outgoingContactChain"]]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/out-degree.R:119:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/out-degree.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
##'     Get the OutDegree for a data.frame with movements, see details and examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:67:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/outgoing-contact-chain.R#L67) *style:* **Lines should not be more than 80 characters.**
```r
##'     The \code{\link{OutgoingContactChain}} of the root within the time-interval
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:77:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/outgoing-contact-chain.R#L77) *style:* **Lines should not be more than 80 characters.**
```r
##'     Get the OutgoingContactChain for a data.frame with movements, see examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:137:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/outgoing-contact-chain.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Unable to determine OutgoingContactChain for ingoing contacts")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:82:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/plot.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
              tree$ingoing$bg <- ifelse(tree$ingoing$level > 0, "white", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:95:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/plot.R#L95) *style:* **Lines should not be more than 80 characters.**
```r
              tree$outgoing$bg <- ifelse(tree$outgoing$level > 0, "gray", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:74:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/report.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
    as.character(unlist(by(contacts, sprintf("%s - %s", contacts$lhs, contacts$rhs), function(x) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:79:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/report.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
                   sprintf('<h3><a name="%s-%s-%s">%s %s %s</a></h3>', direction,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:82:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/report.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
                   "<tr><th>Date</th><th>Id</th><th>N</th><th>Category</th><th>Source</th><th>Destination</th></tr>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:142:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/report.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
        lines <- c(lines, "<p>No ingoing contacts during the search period.</p>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:276:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/report.R#L276) *style:* **Lines should not be more than 80 characters.**
```r
##' @param template the Sweave template file to use. If none is provided, the default
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:369:38:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/report.R#L369) *style:* **Put spaces around all infix operators.**
```r
              Sweave(template, syntax="SweaveSyntaxNoweb")
                                    ~^~
```
[R/shortest-paths.R:168:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L168) *style:* **functions should have cyclomatic complexity of less than 15, this has 41.**
```r
setMethod("ShortestPaths",
^
```
[R/shortest-paths.R:239:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
              if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:240:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L240) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:254:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L254) *style:* **Lines should not be more than 80 characters.**
```r
              if (any(is.na(days) | (days < 0)) || max(abs(days - daysr)) > 1e-07) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:274:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L274) *style:* **Lines should not be more than 80 characters.**
```r
          } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:279:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:282:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
              stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:365:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L365) *style:* **Lines should not be more than 80 characters.**
```r
              stop("root, inBegin, inEnd, outBegin and outEnd must have equal length")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:411:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/shortest-paths.R#L411) *style:* **Lines should not be more than 80 characters.**
```r
                                         destination = x$destination[sp$outRowid],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:76:7:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/show.R#L76) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/show.R:88:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/show.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
              cat(sprintf("%sgoing contact chain: %i\n\n", prefix, OutgoingContactChain(object)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:91:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/show.R#L91) *style:* **Lines should not be more than 80 characters.**
```r
              cat(sprintf("%sgoing contact chain: %i\n\n", prefix, IngoingContactChain(object)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:102:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/show.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
              ## Rename source and destination to lhs and rhs, with respect to direction
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:111:18:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/show.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              for(i in seq_len(nrow(ns))) {
                 ^
```
[R/show.R:113:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/show.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:113:91:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/show.R#L113) *style:* **Put spaces around all infix operators.**
```r
                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
                                                                                ~^~
```
[R/show.R:119:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/show.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
              cat(sprintf("No %sgoing contacts during the search period.\n", object@direction))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:167:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L167) *style:* **functions should have cyclomatic complexity of less than 15, this has 56.**
```r
Trace <- function(movements,
^
```
[R/trace.R:207:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L207) *style:* **Lines should not be more than 80 characters.**
```r
    if (any(is.factor(movements$destination), is.integer(movements$destination))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:252:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L252) *style:* **Lines should not be more than 80 characters.**
```r
        if (any(is.factor(movements$category), is.integer(movements$category))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:306:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L306) *style:* **Lines should not be more than 80 characters.**
```r
        if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:307:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L307) *style:* **Lines should not be more than 80 characters.**
```r
            stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:318:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L318) *style:* **Lines should not be more than 80 characters.**
```r
        ## Test that days is a nonnegative integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:335:31:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                             ~^~
```
[R/trace.R:335:38:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                    ~^~
```
[R/trace.R:335:57:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                                       ~^~
```
[R/trace.R:336:32:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L336) *style:* **Put spaces around all infix operators.**
```r
        inEnd <- rep(tEnd, each=n.days, length.out=n)
                              ~^~
```
[R/trace.R:336:51:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L336) *style:* **Put spaces around all infix operators.**
```r
        inEnd <- rep(tEnd, each=n.days, length.out=n)
                                                 ~^~
```
[R/trace.R:337:42:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                        ~^~
```
[R/trace.R:337:56:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                                      ~^~
```
[R/trace.R:340:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L340) *style:* **Lines should not be more than 80 characters.**
```r
    } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:345:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
            stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:348:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L348) *style:* **Lines should not be more than 80 characters.**
```r
        stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:458:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L458) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:459:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L459) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:471:16:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L471) *style:* **Put spaces around all infix operators.**
```r
        j <- (i-1) * 4
              ~^~
```
[R/trace.R:481:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L481) *style:* **Lines should not be more than 80 characters.**
```r
        ## Create an index to contacts, so that the result matrix can be reconstructed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:483:12:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L483) *style:* **Commented code should be removed.**
```r
        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:484:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L484) *style:* **Lines should not be more than 80 characters.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:484:76:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L484) *style:* **Put spaces around all infix operators.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~
```
[R/trace.R:485:72:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L485) *style:* **Put spaces around all infix operators.**
```r
                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~
```
[R/trace.R:509:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L509) *style:* **Lines should not be more than 80 characters.**
```r
        ## Create an index to contacts, so that the result matrix can be reconstructed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:511:12:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L511) *style:* **Commented code should be removed.**
```r
        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:512:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L512) *style:* **Lines should not be more than 80 characters.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:512:76:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L512) *style:* **Put spaces around all infix operators.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~
```
[R/trace.R:513:72:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L513) *style:* **Put spaces around all infix operators.**
```r
                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~
```
[R/trace.R:535:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L535) *style:* **Lines should not be more than 80 characters.**
```r
    ## Name each list item with ContactTrace objects to the name of the ContactTrace root.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:536:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/trace.R#L536) *style:* **Lines should not be more than 80 characters.**
```r
    names(result) <-  sapply(result, function(listItem) listItem@ingoingContacts@root)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree.R:38:27:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L38) *style:* **Put spaces around all infix operators.**
```r
    result <- list(ingoing=NULL, outgoing=NULL)
                         ~^~
```
[R/tree.R:38:42:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L38) *style:* **Put spaces around all infix operators.**
```r
    result <- list(ingoing=NULL, outgoing=NULL)
                                        ~^~
```
[R/tree.R:53:12:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L53) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(lev in rev(seq_len(max(tree.in$level)))) {
           ^
```
[R/tree.R:54:16:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            for(src in tree.in$node[tree.in$level == lev]) {
               ^
```
[R/tree.R:64:38:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L64) *style:* **Put spaces around all infix operators.**
```r
                stopifnot(length(dst)>0)
                                    ~^~
```
[R/tree.R:83:12:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L83) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(lev in rev(seq_len(max(tree.out$level)))) {
           ^
```
[R/tree.R:84:16:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L84) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            for(dst in tree.out$node[tree.out$level == lev]) {
               ^
```
[R/tree.R:94:38:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L94) *style:* **Put spaces around all infix operators.**
```r
                stopifnot(length(src)>0)
                                    ~^~
```
[R/tree.R:131:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
##'   \item John Q. Walker II, A node positioning algorithm for general tress.\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree.R:134:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L134) *style:* **functions should have cyclomatic complexity of less than 15, this has 48.**
```r
position_tree <- function(tree,
^
```
[R/tree.R:152:14:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        while(all(!is.null(left_most),
             ^
```
[R/tree.R:162:16:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L162) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            for(i in seq_len(compare_depth)) {
               ^
```
[R/tree.R:182:22:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L182) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                while(all(!is.null(temp_node),
                     ^
```
[R/tree.R:194:26:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L194) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                    while(!identical(temp_node, ancestor_neighbor)) {
                         ^
```
[R/tree.R:196:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
                        set_modifier(temp_node, modifier(temp_node) + move_distance)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree.R:226:29:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L226) *style:* **Put spaces around all infix operators.**
```r
        if (length(children)>0) {
                           ~^~
```
[R/tree.R:241:18:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L241) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            while(all(is.null(left_most),
                 ^
```
[R/tree.R:273:30:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L273) *style:* **Put spaces around all infix operators.**
```r
                return(n[i[1]-1])
                            ~^~
```
[R/tree.R:389:26:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L389) *style:* **Put spaces around all infix operators.**
```r
            return(s[i[1]-1])
                        ~^~
```
[R/tree.R:398:26:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L398) *style:* **Put spaces around all infix operators.**
```r
            return(s[i[1]+1])
                        ~^~
```
[R/tree.R:431:18:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/R/tree.R#L431) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            while(has_right_sibling(right_most)) {
                 ^
```
[tests/arguments.R:172:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L172) *style:* **Lines should not be more than 80 characters.**
```r
## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/arguments.R:224:1:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L224) *style:* **Lines should not be more than 80 characters.**
```r
tools::assertError(Trace(movements = data.frame(source = 1L, destination = 2L, t = 1),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/arguments.R:235:44:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L235) *style:* **Commas should always have a space after.**
```r
                             source = c(1L,NA),
                                           ^
```
[tests/arguments.R:236:49:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L236) *style:* **Commas should always have a space after.**
```r
                             destination = c(2L,3L),
                                                ^
```
[tests/arguments.R:248:44:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L248) *style:* **Commas should always have a space after.**
```r
                             source = c(1L,2L),
                                           ^
```
[tests/arguments.R:249:49:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L249) *style:* **Commas should always have a space after.**
```r
                             destination = c(2L,NA),
                                                ^
```
[tests/arguments.R:261:44:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L261) *style:* **Commas should always have a space after.**
```r
                             source = c(1L,2L),
                                           ^
```
[tests/arguments.R:262:49:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L262) *style:* **Commas should always have a space after.**
```r
                             destination = c(2L,3L),
                                                ^
```
[tests/arguments.R:274:44:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L274) *style:* **Commas should always have a space after.**
```r
                             source = c(1L,2L),
                                           ^
```
[tests/arguments.R:275:49:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L275) *style:* **Commas should always have a space after.**
```r
                             destination = c(2L,3L),
                                                ^
```
[tests/arguments.R:394:4:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L394) *style:* **Commented code should be removed.**
```r
## inEnd < inBegin
   ^~~~~~~~~~~~~~~
```
[tests/arguments.R:407:4:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/arguments.R#L407) *style:* **Commented code should be removed.**
```r
## outEnd < outBegin
   ^~~~~~~~~~~~~~~~~
```
[tests/contact-chain.R:76:48:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/contact-chain.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    individual = c(NA_character_, NA_character_ ),
                                               ^
```
[tests/contact-chain.R:105:26:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/contact-chain.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    row.names = c(NA, -7L ),
                         ^
```
[tests/contact-chain.R:125:48:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/contact-chain.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    individual = c(NA_character_, NA_character_ ),
                                               ^
```
[tests/contact-chain.R:179:37:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/contact-chain.R#L179) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                   ~^~
```
[tests/contact-chain.R:179:45:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/contact-chain.R#L179) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                           ~^~
```
[tests/contact-chain.R:179:64:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/contact-chain.R#L179) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                                              ~^~
```
[tests/misc.R:329:44:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/misc.R#L329) *style:* **Commas should always have a space after.**
```r
                         ct_1_df$category),]
                                           ^
```
[tests/misc.R:336:44:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/misc.R#L336) *style:* **Commas should always have a space after.**
```r
                         ct_2_df$category),]
                                           ^
```
[tests/network-summary.R:31:10:](https://github.com/stewid/EpiContactTrace/blob/b05e6b87cfca4daed034d22456e678016d2b2e8f/tests/network-summary.R#L31) *style:* **Put spaces around all infix operators.**
```r
load(file=system.file("extdata", "ns.rda", package = "EpiContactTrace"))
        ~^~
```


good job 💯


because the values were not clipped betwee 0 and 1


In pytorch1.2.0, `torch.FloatTensor(1).to(kernel.device)` generate `tensor([1.3452e-43], device='cuda:0')`. I think `torch.ones(1).to(kernel.device)` is what you want.


[R/network-structure.R:135:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-structure.R#L135) *style:* **Lines should not be more than 80 characters.**
```r
              i <- tmp[seq_len(length(tmp) - 1)] != tmp[seq_len(length(tmp))[-1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:248:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L248) *style:* **Lines should not be more than 80 characters.**
```r
                     inDays = as.integer(x@ingoingContacts@tEnd - x@ingoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:251:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L251) *style:* **Lines should not be more than 80 characters.**
```r
                     outDays = as.integer(x@outgoingContacts@tEnd - x@outgoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:254:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L254) *style:* **Lines should not be more than 80 characters.**
```r
                     ingoingContactChain = IngoingContactChain(x@ingoingContacts),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:255:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L255) *style:* **Lines should not be more than 80 characters.**
```r
                     outgoingContactChain = OutgoingContactChain(x@outgoingContacts))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:261:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L261) *style:* **functions should have cyclomatic complexity of less than 15, this has 38.**
```r
setMethod("NetworkSummary",
^
```
[R/network-summary.R:315:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L315) *style:* **Lines should not be more than 80 characters.**
```r
              ## so test that root is a integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:323:20:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L323) *style:* **Only use double-quotes.**
```r
              stop('invalid class of root')
                   ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:331:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L331) *style:* **Lines should not be more than 80 characters.**
```r
              if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:332:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L332) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:343:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L343) *style:* **Lines should not be more than 80 characters.**
```r
              ## Test that days is a nonnegative integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:345:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
              if (any(is.na(days) | (days < 0)) || max(abs(days - daysr)) > 1e-07) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:365:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L365) *style:* **Lines should not be more than 80 characters.**
```r
          } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:370:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L370) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:373:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L373) *style:* **Lines should not be more than 80 characters.**
```r
              stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:456:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L456) *style:* **Lines should not be more than 80 characters.**
```r
              stop("root, inBegin, inEnd, outBegin and outEnd must have equal length")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:468:24:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L468) *style:* **Put spaces around all infix operators.**
```r
          contact_chain<- .Call("networkSummary",
                      ~^
```
[R/network-summary.R:469:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L469) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:470:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L470) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:472:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L472) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(root, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:489:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L489) *style:* **Lines should not be more than 80 characters.**
```r
                            ingoingContactChain = contact_chain[["ingoingContactChain"]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:490:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/network-summary.R#L490) *style:* **Lines should not be more than 80 characters.**
```r
                            outgoingContactChain = contact_chain[["outgoingContactChain"]]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/out-degree.R:119:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/out-degree.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
##'     Get the OutDegree for a data.frame with movements, see details and examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:67:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/outgoing-contact-chain.R#L67) *style:* **Lines should not be more than 80 characters.**
```r
##'     The \code{\link{OutgoingContactChain}} of the root within the time-interval
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:77:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/outgoing-contact-chain.R#L77) *style:* **Lines should not be more than 80 characters.**
```r
##'     Get the OutgoingContactChain for a data.frame with movements, see examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:137:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/outgoing-contact-chain.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Unable to determine OutgoingContactChain for ingoing contacts")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:82:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/plot.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
              tree$ingoing$bg <- ifelse(tree$ingoing$level > 0, "white", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:95:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/plot.R#L95) *style:* **Lines should not be more than 80 characters.**
```r
              tree$outgoing$bg <- ifelse(tree$outgoing$level > 0, "gray", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:74:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/report.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
    as.character(unlist(by(contacts, sprintf("%s - %s", contacts$lhs, contacts$rhs), function(x) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:79:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/report.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
                   sprintf('<h3><a name="%s-%s-%s">%s %s %s</a></h3>', direction,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:82:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/report.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
                   "<tr><th>Date</th><th>Id</th><th>N</th><th>Category</th><th>Source</th><th>Destination</th></tr>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:142:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/report.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
        lines <- c(lines, "<p>No ingoing contacts during the search period.</p>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:276:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/report.R#L276) *style:* **Lines should not be more than 80 characters.**
```r
##' @param template the Sweave template file to use. If none is provided, the default
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:369:38:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/report.R#L369) *style:* **Put spaces around all infix operators.**
```r
              Sweave(template, syntax="SweaveSyntaxNoweb")
                                    ~^~
```
[R/shortest-paths.R:168:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L168) *style:* **functions should have cyclomatic complexity of less than 15, this has 41.**
```r
setMethod("ShortestPaths",
^
```
[R/shortest-paths.R:239:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
              if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:240:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L240) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:254:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L254) *style:* **Lines should not be more than 80 characters.**
```r
              if (any(is.na(days) | (days < 0)) || max(abs(days - daysr)) > 1e-07) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:274:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L274) *style:* **Lines should not be more than 80 characters.**
```r
          } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:279:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:282:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
              stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:365:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L365) *style:* **Lines should not be more than 80 characters.**
```r
              stop("root, inBegin, inEnd, outBegin and outEnd must have equal length")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:411:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/shortest-paths.R#L411) *style:* **Lines should not be more than 80 characters.**
```r
                                         destination = x$destination[sp$outRowid],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:167:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L167) *style:* **functions should have cyclomatic complexity of less than 15, this has 56.**
```r
Trace <- function(movements,
^
```
[R/trace.R:207:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L207) *style:* **Lines should not be more than 80 characters.**
```r
    if (any(is.factor(movements$destination), is.integer(movements$destination))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:252:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L252) *style:* **Lines should not be more than 80 characters.**
```r
        if (any(is.factor(movements$category), is.integer(movements$category))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:306:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L306) *style:* **Lines should not be more than 80 characters.**
```r
        if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:307:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L307) *style:* **Lines should not be more than 80 characters.**
```r
            stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:318:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L318) *style:* **Lines should not be more than 80 characters.**
```r
        ## Test that days is a nonnegative integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:335:31:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                             ~^~
```
[R/trace.R:335:38:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                    ~^~
```
[R/trace.R:335:57:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                                       ~^~
```
[R/trace.R:336:32:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L336) *style:* **Put spaces around all infix operators.**
```r
        inEnd <- rep(tEnd, each=n.days, length.out=n)
                              ~^~
```
[R/trace.R:336:51:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L336) *style:* **Put spaces around all infix operators.**
```r
        inEnd <- rep(tEnd, each=n.days, length.out=n)
                                                 ~^~
```
[R/trace.R:337:42:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                        ~^~
```
[R/trace.R:337:56:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                                      ~^~
```
[R/trace.R:340:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L340) *style:* **Lines should not be more than 80 characters.**
```r
    } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:345:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
            stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:348:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L348) *style:* **Lines should not be more than 80 characters.**
```r
        stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:458:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L458) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:459:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L459) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:471:16:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L471) *style:* **Put spaces around all infix operators.**
```r
        j <- (i-1) * 4
              ~^~
```
[R/trace.R:481:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L481) *style:* **Lines should not be more than 80 characters.**
```r
        ## Create an index to contacts, so that the result matrix can be reconstructed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:483:12:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L483) *style:* **Commented code should be removed.**
```r
        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:484:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L484) *style:* **Lines should not be more than 80 characters.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:484:76:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L484) *style:* **Put spaces around all infix operators.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~
```
[R/trace.R:485:72:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L485) *style:* **Put spaces around all infix operators.**
```r
                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~
```
[R/trace.R:509:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L509) *style:* **Lines should not be more than 80 characters.**
```r
        ## Create an index to contacts, so that the result matrix can be reconstructed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:511:12:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L511) *style:* **Commented code should be removed.**
```r
        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:512:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L512) *style:* **Lines should not be more than 80 characters.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:512:76:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L512) *style:* **Put spaces around all infix operators.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~
```
[R/trace.R:513:72:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L513) *style:* **Put spaces around all infix operators.**
```r
                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~
```
[R/trace.R:535:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L535) *style:* **Lines should not be more than 80 characters.**
```r
    ## Name each list item with ContactTrace objects to the name of the ContactTrace root.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:536:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/trace.R#L536) *style:* **Lines should not be more than 80 characters.**
```r
    names(result) <-  sapply(result, function(listItem) listItem@ingoingContacts@root)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree.R:38:27:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L38) *style:* **Put spaces around all infix operators.**
```r
    result <- list(ingoing=NULL, outgoing=NULL)
                         ~^~
```
[R/tree.R:38:42:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L38) *style:* **Put spaces around all infix operators.**
```r
    result <- list(ingoing=NULL, outgoing=NULL)
                                        ~^~
```
[R/tree.R:53:12:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L53) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(lev in rev(seq_len(max(tree.in$level)))) {
           ^
```
[R/tree.R:54:16:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            for(src in tree.in$node[tree.in$level == lev]) {
               ^
```
[R/tree.R:64:38:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L64) *style:* **Put spaces around all infix operators.**
```r
                stopifnot(length(dst)>0)
                                    ~^~
```
[R/tree.R:83:12:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L83) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(lev in rev(seq_len(max(tree.out$level)))) {
           ^
```
[R/tree.R:84:16:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L84) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            for(dst in tree.out$node[tree.out$level == lev]) {
               ^
```
[R/tree.R:94:38:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L94) *style:* **Put spaces around all infix operators.**
```r
                stopifnot(length(src)>0)
                                    ~^~
```
[R/tree.R:131:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
##'   \item John Q. Walker II, A node positioning algorithm for general tress.\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree.R:134:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L134) *style:* **functions should have cyclomatic complexity of less than 15, this has 48.**
```r
position_tree <- function(tree,
^
```
[R/tree.R:152:14:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        while(all(!is.null(left_most),
             ^
```
[R/tree.R:162:16:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L162) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            for(i in seq_len(compare_depth)) {
               ^
```
[R/tree.R:182:22:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L182) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                while(all(!is.null(temp_node),
                     ^
```
[R/tree.R:194:26:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L194) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                    while(!identical(temp_node, ancestor_neighbor)) {
                         ^
```
[R/tree.R:196:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
                        set_modifier(temp_node, modifier(temp_node) + move_distance)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree.R:226:29:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L226) *style:* **Put spaces around all infix operators.**
```r
        if (length(children)>0) {
                           ~^~
```
[R/tree.R:241:18:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L241) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            while(all(is.null(left_most),
                 ^
```
[R/tree.R:273:30:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L273) *style:* **Put spaces around all infix operators.**
```r
                return(n[i[1]-1])
                            ~^~
```
[R/tree.R:389:26:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L389) *style:* **Put spaces around all infix operators.**
```r
            return(s[i[1]-1])
                        ~^~
```
[R/tree.R:398:26:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L398) *style:* **Put spaces around all infix operators.**
```r
            return(s[i[1]+1])
                        ~^~
```
[R/tree.R:431:18:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/R/tree.R#L431) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            while(has_right_sibling(right_most)) {
                 ^
```
[tests/arguments.R:172:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L172) *style:* **Lines should not be more than 80 characters.**
```r
## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/arguments.R:224:1:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L224) *style:* **Lines should not be more than 80 characters.**
```r
tools::assertError(Trace(movements = data.frame(source = 1L, destination = 2L, t = 1),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/arguments.R:235:44:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L235) *style:* **Commas should always have a space after.**
```r
                             source = c(1L,NA),
                                           ^
```
[tests/arguments.R:236:49:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L236) *style:* **Commas should always have a space after.**
```r
                             destination = c(2L,3L),
                                                ^
```
[tests/arguments.R:248:44:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L248) *style:* **Commas should always have a space after.**
```r
                             source = c(1L,2L),
                                           ^
```
[tests/arguments.R:249:49:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L249) *style:* **Commas should always have a space after.**
```r
                             destination = c(2L,NA),
                                                ^
```
[tests/arguments.R:261:44:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L261) *style:* **Commas should always have a space after.**
```r
                             source = c(1L,2L),
                                           ^
```
[tests/arguments.R:262:49:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L262) *style:* **Commas should always have a space after.**
```r
                             destination = c(2L,3L),
                                                ^
```
[tests/arguments.R:274:44:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L274) *style:* **Commas should always have a space after.**
```r
                             source = c(1L,2L),
                                           ^
```
[tests/arguments.R:275:49:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L275) *style:* **Commas should always have a space after.**
```r
                             destination = c(2L,3L),
                                                ^
```
[tests/arguments.R:394:4:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L394) *style:* **Commented code should be removed.**
```r
## inEnd < inBegin
   ^~~~~~~~~~~~~~~
```
[tests/arguments.R:407:4:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/arguments.R#L407) *style:* **Commented code should be removed.**
```r
## outEnd < outBegin
   ^~~~~~~~~~~~~~~~~
```
[tests/contact-chain.R:76:48:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/contact-chain.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    individual = c(NA_character_, NA_character_ ),
                                               ^
```
[tests/contact-chain.R:105:26:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/contact-chain.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    row.names = c(NA, -7L ),
                         ^
```
[tests/contact-chain.R:125:48:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/contact-chain.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    individual = c(NA_character_, NA_character_ ),
                                               ^
```
[tests/contact-chain.R:179:37:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/contact-chain.R#L179) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                   ~^~
```
[tests/contact-chain.R:179:45:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/contact-chain.R#L179) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                           ~^~
```
[tests/contact-chain.R:179:64:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/contact-chain.R#L179) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                                              ~^~
```
[tests/misc.R:329:44:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/misc.R#L329) *style:* **Commas should always have a space after.**
```r
                         ct_1_df$category),]
                                           ^
```
[tests/misc.R:336:44:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/misc.R#L336) *style:* **Commas should always have a space after.**
```r
                         ct_2_df$category),]
                                           ^
```
[tests/network-summary.R:31:10:](https://github.com/stewid/EpiContactTrace/blob/2a952b713a6ad0afd91266ee246e8d0f94f36f7d/tests/network-summary.R#L31) *style:* **Put spaces around all infix operators.**
```r
load(file=system.file("extdata", "ns.rda", package = "EpiContactTrace"))
        ~^~
```


> As you can already guess from the code, we are just creating an instance of gRPC server, registering our greeter service handler and then just starting it.


* `%__texlive_bin` can be found by
  ```
  dirname `which kpsewhich`
  ```
* `%__texlive_base` can be found by
  ```
  dirname `kpsewhich --var-value=TEXMFMAIN`
  ```
* `%__texmf_local` is
  ```
  kpsewhich --var-value=TEXMFLOCAL
  ```


@elpiankova
понял, тогда
    b['id'] = update.json()['id']
    assert b == update.json()

или
    b['id'] = update.json()['id']
     for item in b:
        assert b[item] == update.json()[item]


Будь проще:
```
numbers = str.split
[numbers.min, numbers.max]
```


mysql数据文件


Once the build is finished, let's test our implementation by running the server. Run the command below to start the server

```shell
npm run start
```

If everything goes well, you should see the message `gRPC listening on 50051`


Называй аргументы итераторов осознанно. `i` – это слишком общее название переменной, которое больше используется в других языках. В руби принято называть более очевидно. У тебя в массиве хранятся слова, значит аргументом итератора будет являться слово `word`, а не `i`.


In order to test our server, I am going to use [BloomRPC](https://github.com/uw-labs/bloomrpc) which is a GUI client to test RPC services.

Follow the [installation guide](https://github.com/uw-labs/bloomrpc#installation), import the `greeter.proto` file, update the URL to be `127.0.0.1:50051` and click the PLAY icon and you will see the output similar to the one given below


Here is the call that needs to be changed to coroutine creation, preferably scheduling it through something like `system.once` in ROS.


And that wraps it up. You can find the source code from the article here. Feel free to leave your feedback or questions in the comments section below.


why remove styled-components? @twocucao


STATICSDIR " : null , //  ตรวจจับอัตโนมัติ


Successfully deployed to following URLs:

* https://jsconsole-bot-aadpvw69l.now.sh
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* https://jsconsole-bot-git-master.oleksiyrudenko.now.sh


Этот тест для класса Route, а не Train. Будь внимательнее и меньше копипасть


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{
	"version": 2,
<<<<<<>>>>>> 40bc047ffef309c58379ab43c70bfc610eb01192
		"env": {
			"GITHUB_TOKEN": "@github_token"
		}
	},
	"env": {
		"GITHUB_TOKEN": "@github_token"
	}
}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


Successfully deployed to following URLs:

* https://autoshift-bbttxy9yc.now.sh
* https://autoshift.kaito.now.sh
* https://autoshift-git-master.kaito.now.sh


Не очень хороший подход к написанию теста. Лучше их делать максимально изолированными. И если ты пишешь тест на добавление станции в маршрут, то именно в этом тесте добавляешь станцию и проверяешь ее в маршруте. А не просто добавляешь все станции в маршрут разом и потом проверяешь их.


`let(:s2) {Station.new("station2")}` – разделяй пробелами блоки


this method if from `UIView`, no need to declare it in the header


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* https://vbb-journey-proxy-git-master.sklinkusch.now.sh


谢谢，来晚了


Congrats too!


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* https://affordable-docs-i5yhkz19l.now.sh
* https://affordable.io
* https://affordable-docs.affordable.now.sh
* https://affordable-docs-git-master.affordable.now.sh


У тебя в классе Station целых 6 публичных методов включая методы класса. Почему ты написал тесты только на два из них?
В задании же говорится "написать тесты на инстанс-методы и методы класса"


should be `nonatomic, weak` I believe


В классе Train у тебя аж 12 методов, которые нужно покрыть тестами. Почему ты выборочно написал тесты только на 4 из них?


no newline!!!!!!!!!! xD