[R/network-structure.R:135:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/R/network-summary.R#L469) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:470:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/network-summary.R#L470) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:472:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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:30:8:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L30) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in seq_len(nrow(contacts))) {
       ^
```
[R/report.R:35:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
                   paste(rep("<td> </td>", 2L * (contacts$distance[i] - 1L)), collapse = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:44:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
                             2L * (max(contacts$distance - 1L) - (contacts$distance[i] - 1L))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:73:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
    as.character(unlist(by(contacts, sprintf("%s - %s", contacts$lhs, contacts$rhs), function(x) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:78:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L78) *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:81:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L81) *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:83:12:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L83) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(i in seq_len(nrow(x))) {
           ^
```
[R/report.R:112:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L112) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<h3 align='center'>Version: %s</h3>", packageVersion("EpiContactTrace")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:117:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>In begin date:</td><td>%s</td></tr>", x@ingoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:118:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L118) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>In end date:</td><td>%s</td></tr>", x@ingoingContacts@tEnd),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:119:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>In days:</td><td>%i</td></tr>", x@ingoingContacts@tEnd - x@ingoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:120:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L120) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>In degree:</td><td>%i</td></tr>", InDegree(x@ingoingContacts)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:121:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L121) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>Ingoing contact chain:</td><td>%i</td></tr>", IngoingContactChain(x@ingoingContacts)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:135:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L135) *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:143:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L143) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>Out begin date:</td><td>%s</td></tr>", x@outgoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:144:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L144) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>Out end date:</td><td>%s</td></tr>", x@outgoingContacts@tEnd),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:145:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L145) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>Out days:</td><td>%i</td></tr>", x@outgoingContacts@tEnd - x@outgoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:146:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>Out degree:</td><td>%i</td></tr>", OutDegree(x@outgoingContacts)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:147:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<tr><td>Outgoing contact chain:</td><td>%i</td></tr>", OutgoingContactChain(x@outgoingContacts)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:161:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L161) *style:* **Lines should not be more than 80 characters.**
```r
        lines <- c(lines, "<p>No outgoing contacts during the search period.</p>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:237:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L237) *style:* **Lines should not be more than 80 characters.**
```r
##' available. To generate pdf files a TeX installation must exist to compile the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:260:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L260) *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:345:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
              writeLines(html_report(object), con = sprintf("%s.html", object@root))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:348:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L348) *style:* **Lines should not be more than 80 characters.**
```r
                  template <- system.file("Sweave/speak-latex.rnw", package = "EpiContactTrace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:351:45:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L351) *style:* **Put spaces around all infix operators.**
```r
              utils::Sweave(template, syntax="SweaveSyntaxNoweb")
                                           ~^~
```
[R/report.R:352:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L352) *style:* **Lines should not be more than 80 characters.**
```r
              tools::texi2pdf(sub("rnw$", "tex", basename(template)), clean = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:353:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L353) *style:* **Lines should not be more than 80 characters.**
```r
              file.rename(sub("rnw$", "pdf", basename(template)), sprintf("%s.pdf", object@root))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:400:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/report.R#L400) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/shortest-paths.R:168:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/R/shortest-paths.R#L411) *style:* **Lines should not be more than 80 characters.**
```r
                                         destination = x$destination[sp$outRowid],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:76:7:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/show.R#L76) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/show.R:88:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/show.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
              cat(sprintf("%sgoing contact chain: %i\n\n", prefix, OutgoingContactChain(object)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:91:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/show.R#L91) *style:* **Lines should not be more than 80 characters.**
```r
              cat(sprintf("%sgoing contact chain: %i\n\n", prefix, IngoingContactChain(object)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:102:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/show.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
              ## Rename source and destination to lhs and rhs, with respect to direction
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:111:18:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/show.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              for(i in seq_len(nrow(ns))) {
                 ^
```
[R/show.R:113:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/show.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:113:91:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/show.R#L113) *style:* **Put spaces around all infix operators.**
```r
                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
                                                                                ~^~
```
[R/show.R:119:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/show.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
              cat(sprintf("No %sgoing contacts during the search period.\n", object@direction))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:167:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/trace.R#L167) *style:* **functions should have cyclomatic complexity of less than 15, this has 56.**
```r
Trace <- function(movements,
^
```
[R/trace.R:207:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/trace.R#L207) *style:* **Lines should not be more than 80 characters.**
```r
    if (any(is.factor(movements$destination), is.integer(movements$destination))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:252:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/trace.R#L252) *style:* **Lines should not be more than 80 characters.**
```r
        if (any(is.factor(movements$category), is.integer(movements$category))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:306:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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$level)))) {
           ^
```
[R/tree.R:84:16:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/R/tree.R#L84) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            for(dst in tree.out$node[tree.out$level == lev]) {
               ^
```
[R/tree.R:94:38:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/tests/arguments.R#L394) *style:* **Commented code should be removed.**
```r
## inEnd < inBegin
   ^~~~~~~~~~~~~~~
```
[tests/arguments.R:407:4:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/arguments.R#L407) *style:* **Commented code should be removed.**
```r
## outEnd < outBegin
   ^~~~~~~~~~~~~~~~~
```
[tests/contact-chain.R:51:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L51) *style:* **Put spaces around all infix operators.**
```r
= "Date"), individual = c(NA_character_, NA_character_, NA_character_,
^
```
[tests/contact-chain.R:71:31:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L71) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
c(NA_character_, NA_character_ ), n = c(NA_integer_, NA_integer_)),
                              ^
```
[tests/contact-chain.R:73:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L73) *style:* **Put spaces around all infix operators.**
```r
= c(NA, -2L), class = "data.frame")
^
```
[tests/contact-chain.R:91:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L91) *style:* **Put spaces around all infix operators.**
```r
= c(NA_character_, NA_character_, NA_character_, NA_character_,
^
```
[tests/contact-chain.R:95:28:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L95) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
"n"), row.names = c(NA, -7L ), class = "data.frame")
                           ^
```
[tests/contact-chain.R:112:31:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L112) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
c(NA_character_, NA_character_ ), n = c(NA_integer_, NA_integer_)),
                              ^
```
[tests/contact-chain.R:114:1:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L114) *style:* **Put spaces around all infix operators.**
```r
= c(NA, -2L), class = "data.frame")
^
```
[tests/contact-chain.R:156:37:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L156) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                   ~^~
```
[tests/contact-chain.R:156:45:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L156) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                           ~^~
```
[tests/contact-chain.R:156:64:](https://github.com/stewid/EpiContactTrace/blob/78387ba666eedfd230550aa3bae53345efdadd46/tests/contact-chain.R#L156) *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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/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/78387ba666eedfd230550aa3bae53345efdadd46/tests/network-summary.R#L31) *style:* **Put spaces around all infix operators.**
```r
load(file=system.file("extdata", "ns.rda", package = "EpiContactTrace"))
        ~^~
```


2019.1.12 | 3a543c233aa42c6a5c786118747d73140745427b
2019.1.12-mbe | 44db3f8dfda1d22cdd03e9b72c507f9dc555b059
2019.1.13 | 3a543c233aa42c6a5c786118747d73140745427b
2019.1.13-mbe | 44db3f8dfda1d22cdd03e9b72c507f9dc555b059
2019.2.0-mbe | f93c5973976e4bec5e769a31a73f00003f0a32dc


fndndjdkdmxmxmxmx


[R/bbt_run_from_model.R:30:3:](https://github.com/ropensci/babette/blob/a4683b8c178f5354ca096c92f99541b050326968/R/bbt_run_from_model.R#L30) *warning:* **no visible global function definition for ‘prepare_file_creation’**
```r
  prepare_file_creation(inference_model, beast2_options)
  ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-bbt_process_pkg_output.R:17:19:](https://github.com/ropensci/babette/blob/a4683b8c178f5354ca096c92f99541b050326968/tests/testthat/test-bbt_process_pkg_output.R#L17) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = beautier::create_test_inference_model(
                  ^
```
[tests/testthat/test-bbt_run.R:112:16:](https://github.com/ropensci/babette/blob/a4683b8c178f5354ca096c92f99541b050326968/tests/testthat/test-bbt_run.R#L112) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  out_1$output[  out_1$output != out_2$output ]
               ^
```
[tests/testthat/test-bbt_run.R:112:46:](https://github.com/ropensci/babette/blob/a4683b8c178f5354ca096c92f99541b050326968/tests/testthat/test-bbt_run.R#L112) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  out_1$output[  out_1$output != out_2$output ]
                                             ^
```


Successfully deployed to following URLs:

* https://blogapi2ucn-a3vjs9uz3.now.sh
* https://ap.api2u.cn
* https://blogapi2ucn.youngje.now.sh
* https://blogapi2ucn-git-master.youngje.now.sh


Successfully deployed to following URLs:

* https://ne-ploho-moscow-first-dates-h7owf7lav.now.sh
* https://moscow-first-dates.now.sh
* https://new.map.ne-ploho.com
* https://ne-ploho-moscow-first-dates.alexkuz.now.sh
* https://ne-ploho-moscow-first-dates-git-master.alexkuz.now.sh


Successfully deployed to following URLs:

* https://shop-q87njj81j.now.sh
* https://shop.cacheup.now.sh
* https://shop-git-master.cacheup.now.sh


Successfully deployed to following URLs:

* https://shop-cz24ellpz.now.sh
* https://shop.cacheup.now.sh
* https://shop-git-master.cacheup.now.sh


> Implementing gRPC with NodeJs is simple. But there's an issue of no autocomplete, type hinting and also you have to do a-lot of work to just create client and server.

These are the benefits of typescript and it's usage with an IDE, nothing to do with gRPC. Remove this paragraph and directly explain how to generate typescript definitions from `proto` files e.g.

You can use gRPC without TypeScript but these benefits become tenfold when using TypeScript e.g. your RPC definitions become statically typed, you get type hinting, your IDE gives you autocomplete, etc. You can either write the Type definitions for your `proto` files by hand or use a certain set of plugins to automate the process. In this article, I am going to explain how you can generate service definitions against your proto files and create your clients and servers.


print("hello world")


Now go inside the directory and create the directory structure similar to the one given below


Explain the purpose of each dependency


I confirmed the sha256sum is correct


You must indicate which branch to use. Don't rely on a default set by the portgroup, because if that default were to change, you would have to revbump this port anyway, and without an explicit branch in the portfile you wouldn't remember to do that.


[R/network-structure.R:135:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/network-summary.R#L469) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:470:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/network-summary.R#L470) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:472:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/show.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:113:91:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/show.R#L113) *style:* **Put spaces around all infix operators.**
```r
                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
                                                                                ~^~
```
[R/show.R:119:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/trace.R#L458) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:459:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/trace.R#L459) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:471:16:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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$level)))) {
           ^
```
[R/tree.R:54:16:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/tree.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            for(src in tree.in$node[tree.in$level == lev]) {
               ^
```
[R/tree.R:64:38:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/tree.R#L64) *style:* **Put spaces around all infix operators.**
```r
                stopifnot(length(dst)>0)
                                    ~^~
```
[R/tree.R:83:12:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/R/tree.R#L83) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(lev in rev(seq_len(max(tree.out$level)))) {
           ^
```
[R/tree.R:84:16:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/arguments.R#L394) *style:* **Commented code should be removed.**
```r
## inEnd < inBegin
   ^~~~~~~~~~~~~~~
```
[tests/arguments.R:407:4:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/arguments.R#L407) *style:* **Commented code should be removed.**
```r
## outEnd < outBegin
   ^~~~~~~~~~~~~~~~~
```
[tests/contact-chain.R:51:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L51) *style:* **Put spaces around all infix operators.**
```r
= "Date"), individual = c(NA_character_, NA_character_, NA_character_,
^
```
[tests/contact-chain.R:71:31:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L71) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
c(NA_character_, NA_character_ ), n = c(NA_integer_, NA_integer_)),
                              ^
```
[tests/contact-chain.R:73:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L73) *style:* **Put spaces around all infix operators.**
```r
= c(NA, -2L), class = "data.frame")
^
```
[tests/contact-chain.R:91:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L91) *style:* **Put spaces around all infix operators.**
```r
= c(NA_character_, NA_character_, NA_character_, NA_character_,
^
```
[tests/contact-chain.R:95:28:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L95) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
"n"), row.names = c(NA, -7L ), class = "data.frame")
                           ^
```
[tests/contact-chain.R:112:31:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L112) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
c(NA_character_, NA_character_ ), n = c(NA_integer_, NA_integer_)),
                              ^
```
[tests/contact-chain.R:114:1:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L114) *style:* **Put spaces around all infix operators.**
```r
= c(NA, -2L), class = "data.frame")
^
```
[tests/contact-chain.R:156:37:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L156) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                   ~^~
```
[tests/contact-chain.R:156:45:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L156) *style:* **Put spaces around all infix operators.**
```r
ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                           ~^~
```
[tests/contact-chain.R:156:64:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/contact-chain.R#L156) *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/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/misc.R#L329) *style:* **Commas should always have a space after.**
```r
                         ct_1_df$category),]
                                           ^
```
[tests/misc.R:336:44:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/misc.R#L336) *style:* **Commas should always have a space after.**
```r
                         ct_2_df$category),]
                                           ^
```
[tests/network-summary.R:31:10:](https://github.com/stewid/EpiContactTrace/blob/8000eaf5ebffa1cc3c0ea1e52f9c22698a479903/tests/network-summary.R#L31) *style:* **Put spaces around all infix operators.**
```r
load(file=system.file("extdata", "ns.rda", package = "EpiContactTrace"))
        ~^~
```


Now could not deploy this pull request since it contains the following references to invalid secrets in the `env` sections of the `now.json` file:

* `the-secret-name` (in env: `FB_TOKEN)`

Add those secrets or remove them from the `env` maps in the `now.json` file.


Successfully deployed to following URLs:

* https://shop-6pj7pvg3c.now.sh
* https://shop.cacheup.now.sh
* https://shop-git-master.cacheup.now.sh


removeAirTermSDUncontrolled (mjwitte) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (674 of 674 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.49%25-green.png)


You do not need here flex-wrap property.


Improper capitalization on both input statements


use integer division `//` instead of this.


OK. I found the bug. At line 740 in the copy constructor, copy of real_starts/real_ends are missing, making Supervision::Write() wrote nothing for real_starts/real_ends


@JuliaRegistrator register


Registration pull request updated: [JuliaRegistries/General/4859](https://github.com/JuliaRegistries/General/pull/4859)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.0 -m "<description of version>" 1100d9fe210c3d7abe6639708c395164a816a859
git push origin v0.1.0
```


I went through and fixed all of the issues mentioned in these comments and have resubmitted the pull request.


Successfully deployed to following URLs:

* https://passive-alive-monitoring-7dso8fey3.now.sh
* https://pam.azma.work
* https://passive-alive-monitoring.segararai.now.sh
* https://passive-alive-monitoring-git-master.segararai.now.sh


I removed my .env and using the common dev.env under the config directory. However, it can not read the values from dev.env file and thus, can not connect to the DB.


link per la pagina di test del database: http://172.55.0.3/test/database.html;
per vedere il database http://172.55.0.10:8080/
Nel form di adminer:
host: 172.55.0.4:3306
i rimanenti campi tutti: testdrive