[R/ingoing-contact-chain.R:189:46:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/ingoing-contact-chain.R#L189) *style:* **Commas should always have a space after.**
```r
              return(length(setdiff(x@source,x@root)))
                                             ^
```
[R/network-structure.R:135:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/network-summary.R#L469) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:470:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/network-summary.R#L470) *style:* **Lines should not be more than 80 characters.**
```r
                                as.integer(factor(x$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:472:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/out-degree.R:208:7:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/out-degree.R#L208) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/outgoing-contact-chain.R:67:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/outgoing-contact-chain.R:140:51:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/outgoing-contact-chain.R#L140) *style:* **Commas should always have a space after.**
```r
              return(length(setdiff(x@destination,x@root)))
                                                  ^
```
[R/outgoing-contact-chain.R:167:7:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/outgoing-contact-chain.R#L167) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/plot.R:73:7:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/plot.R#L73) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/plot.R:83:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/plot.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
              tree$ingoing$bg <- ifelse(tree$ingoing$level > 0, "white", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:96:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/plot.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
              tree$outgoing$bg <- ifelse(tree$outgoing$level > 0, "gray", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:108:64:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/plot.R#L108) *style:* **Commas should always have a space after.**
```r
                  vertices <- rbind(vertices, tree$outgoing[-1,])
                                                               ^
```
[R/report.R:30:8:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L30) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in seq_len(nrow(contacts))) {
       ^
```
[R/report.R:35:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
                   paste(rep("<td> </td>", 2L * (contacts$distance[i] - 1L)), collapse = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:44:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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:62:77:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L62) *style:* **Commas should always have a space after.**
```r
    contacts <- contacts[order(contacts$t, contacts$id, decreasing = FALSE),]
                                                                            ^
```
[R/report.R:73:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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:104:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L104) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/report.R:113:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
               sprintf("<h3 align='center'>Version: %s</h3>", packageVersion("EpiContactTrace")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:118:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L118) *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:119:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L119) *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:120:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L120) *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:121:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L121) *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:122:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L122) *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:136:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L136) *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:144:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L144) *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:145:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L145) *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:146:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L146) *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:147:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L147) *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:148:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L148) *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:162:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L162) *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:177:69:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L177) *style:* **Commas should always have a space after.**
```r
                   html_detailed_table(df[df$destination == df$root,], "in"))
                                                                    ^
```
[R/report.R:179:44:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L179) *style:* **Commas should always have a space after.**
```r
        df <- df[df$destination != df$root,]
                                           ^
```
[R/report.R:199:53:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L199) *style:* **Commas should always have a space after.**
```r
        html_detailed_table(df[df$source == df$root,], "out")
                                                    ^
```
[R/report.R:201:39:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L201) *style:* **Commas should always have a space after.**
```r
        df <- df[df$source != df$root,]
                                      ^
```
[R/report.R:238:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L238) *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:261:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L261) *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:333:7:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L333) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/report.R:347:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L347) *style:* **Lines should not be more than 80 characters.**
```r
              writeLines(html_report(object), con = sprintf("%s.html", object@root))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:350:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L350) *style:* **Lines should not be more than 80 characters.**
```r
                  template <- system.file("Sweave/speak-latex.rnw", package = "EpiContactTrace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:353:45:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L353) *style:* **Put spaces around all infix operators.**
```r
              utils::Sweave(template, syntax="SweaveSyntaxNoweb")
                                           ~^~
```
[R/report.R:354:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L354) *style:* **Lines should not be more than 80 characters.**
```r
              tools::texi2pdf(sub("rnw$", "tex", basename(template)), clean = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:355:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L355) *style:* **Lines should not be more than 80 characters.**
```r
              file.rename(sub("rnw$", "pdf", basename(template)), sprintf("%s.pdf", object@root))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:368:7:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L368) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/report.R:403:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/report.R#L403) *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:137:7:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L137) *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:139:44:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L139) *style:* **Commas should always have a space after.**
```r
          ns.in <- ns[ns$direction == "in",]
                                           ^
```
[R/shortest-paths.R:140:46:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L140) *style:* **Commas should always have a space after.**
```r
          ns.out <- ns[ns$direction == "out",]
                                             ^
```
[R/shortest-paths.R:144:66:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L144) *style:* **Commas should always have a space after.**
```r
              ns.in <- ns.in[order(ns.in$distance, ns.in$source),]
                                                                 ^
```
[R/shortest-paths.R:145:56:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L145) *style:* **Commas should always have a space after.**
```r
              ns.in <- ns.in[!duplicated(ns.in$source),]
                                                       ^
```
[R/shortest-paths.R:151:75:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L151) *style:* **Commas should always have a space after.**
```r
              ns.out <- ns.out[order(ns.out$distance, ns.out$destination),]
                                                                          ^
```
[R/shortest-paths.R:152:64:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L152) *style:* **Commas should always have a space after.**
```r
              ns.out <- ns.out[!duplicated(ns.out$destination),]
                                                               ^
```
[R/shortest-paths.R:169:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L169) *style:* **functions should have cyclomatic complexity of less than 15, this has 41.**
```r
setMethod("ShortestPaths",
^
```
[R/shortest-paths.R:179:7:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L179) *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:241:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L241) *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:242:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L242) *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:256:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L256) *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:276:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L276) *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:281:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L281) *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:284:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L284) *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:367:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L367) *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:413:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/shortest-paths.R#L413) *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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/show.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show.R:113:91:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/show.R#L113) *style:* **Put spaces around all infix operators.**
```r
                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
                                                                                ~^~
```
[R/show.R:119:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/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:29:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L29) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/trace.R:168:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L168) *style:* **functions should have cyclomatic complexity of less than 15, this has 56.**
```r
Trace <- function(movements,
^
```
[R/trace.R:177:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L177) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/trace.R:182:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L182) *style:* **Only use double-quotes.**
```r
        stop('Missing parameters in call to Trace')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:186:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L186) *style:* **Only use double-quotes.**
```r
        stop('movements must be a data.frame')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:189:16:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L189) *style:* **Only use double-quotes.**
```r
    if (!all(c('source', 'destination', 't') %in% names(movements))) {
               ^~~~~~~~
```
[R/trace.R:189:26:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L189) *style:* **Only use double-quotes.**
```r
    if (!all(c('source', 'destination', 't') %in% names(movements))) {
                         ^~~~~~~~~~~~~
```
[R/trace.R:189:41:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L189) *style:* **Only use double-quotes.**
```r
    if (!all(c('source', 'destination', 't') %in% names(movements))) {
                                        ^~~
```
[R/trace.R:190:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L190) *style:* **Only use double-quotes.**
```r
        stop('movements must contain the columns source, destination and t.')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:199:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L199) *style:* **Only use double-quotes.**
```r
        stop('invalid class of column source in movements')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:203:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L203) *style:* **Only use double-quotes.**
```r
        stop('source in movements contains NA')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:209:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L209) *style:* **Lines should not be more than 80 characters.**
```r
    if (any(is.factor(movements$destination), is.integer(movements$destination))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:212:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L212) *style:* **Only use double-quotes.**
```r
        stop('invalid class of column destination in movements')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:216:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L216) *style:* **Only use double-quotes.**
```r
        stop('destination in movements contains NA')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:225:40:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L225) *style:* **Only use double-quotes.**
```r
    if (!identical(class(movements$t), 'Date')) {
                                       ^~~~~~
```
[R/trace.R:226:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L226) *style:* **Only use double-quotes.**
```r
        stop('invalid class of column t in movements')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:230:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L230) *style:* **Only use double-quotes.**
```r
        stop('t in movements contains NA')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:233:9:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L233) *style:* **Only use double-quotes.**
```r
    if ('n' %in% names(movements)) {
        ^~~
```
[R/trace.R:237:18:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L237) *style:* **Only use double-quotes.**
```r
            stop('invalid class of column n in movements')
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:243:9:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L243) *style:* **Only use double-quotes.**
```r
    if ('id' %in% names(movements)) {
        ^~~~
```
[R/trace.R:247:18:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L247) *style:* **Only use double-quotes.**
```r
            stop('invalid class of column id in movements')
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:253:9:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L253) *style:* **Only use double-quotes.**
```r
    if ('category' %in% names(movements)) {
        ^~~~~~~~~~
```
[R/trace.R:254:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L254) *style:* **Lines should not be more than 80 characters.**
```r
        if (any(is.factor(movements$category), is.integer(movements$category))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:257:18:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L257) *style:* **Only use double-quotes.**
```r
            stop('invalid class of column category in movements')
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:264:40:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L264) *style:* **Only use double-quotes.**
```r
    if (!identical(names(movements), c('source',
                                       ^~~~~~~~
```
[R/trace.R:265:39:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L265) *style:* **Only use double-quotes.**
```r
                                      'destination',
                                      ^~~~~~~~~~~~~
```
[R/trace.R:266:39:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L266) *style:* **Only use double-quotes.**
```r
                                      't',
                                      ^~~
```
[R/trace.R:267:39:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L267) *style:* **Only use double-quotes.**
```r
                                      'id',
                                      ^~~~
```
[R/trace.R:268:39:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L268) *style:* **Only use double-quotes.**
```r
                                      'n',
                                      ^~~
```
[R/trace.R:269:39:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L269) *style:* **Only use double-quotes.**
```r
                                      'category'))) {
                                      ^~~~~~~~~~
```
[R/trace.R:270:36:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L270) *style:* **Only use double-quotes.**
```r
        movements <- movements[, c('source',
                                   ^~~~~~~~
```
[R/trace.R:271:36:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L271) *style:* **Only use double-quotes.**
```r
                                   'destination',
                                   ^~~~~~~~~~~~~
```
[R/trace.R:272:36:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L272) *style:* **Only use double-quotes.**
```r
                                   't',
                                   ^~~
```
[R/trace.R:273:36:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L273) *style:* **Only use double-quotes.**
```r
                                   'id',
                                   ^~~~
```
[R/trace.R:274:36:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L274) *style:* **Only use double-quotes.**
```r
                                   'n',
                                   ^~~
```
[R/trace.R:275:36:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L275) *style:* **Only use double-quotes.**
```r
                                   'category')]
                                   ^~~~~~~~~~
```
[R/trace.R:296:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L296) *style:* **Only use double-quotes.**
```r
        stop('invalid class of root')
             ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:300:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L300) *style:* **Only use double-quotes.**
```r
        stop('root contains NA')
             ^~~~~~~~~~~~~~~~~~
```
[R/trace.R:308:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L308) *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:309:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L309) *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:309:18:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L309) *style:* **Only use double-quotes.**
```r
            stop('Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace')
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:316:37:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L316) *style:* **Only use double-quotes.**
```r
        if (!identical(class(tEnd), 'Date')) {
                                    ^~~~~~
```
[R/trace.R:320:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L320) *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:337:31:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                             ~^~
```
[R/trace.R:337:38:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                    ~^~
```
[R/trace.R:337:57:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                                       ~^~
```
[R/trace.R:338:32:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L338) *style:* **Put spaces around all infix operators.**
```r
        inEnd <- rep(tEnd, each=n.days, length.out=n)
                              ~^~
```
[R/trace.R:338:51:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L338) *style:* **Put spaces around all infix operators.**
```r
        inEnd <- rep(tEnd, each=n.days, length.out=n)
                                                 ~^~
```
[R/trace.R:339:42:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L339) *style:* **Put spaces around all infix operators.**
```r
        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                        ~^~
```
[R/trace.R:339:56:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L339) *style:* **Put spaces around all infix operators.**
```r
        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                                      ~^~
```
[R/trace.R:342:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L342) *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:347:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L347) *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:347:18:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L347) *style:* **Only use double-quotes.**
```r
            stop('Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace')
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:350:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L350) *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:350:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L350) *style:* **Only use double-quotes.**
```r
        stop('Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:360:36:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L360) *style:* **Only use double-quotes.**
```r
    if (!identical(class(inBegin), 'Date')) {
                                   ^~~~~~
```
[R/trace.R:365:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L365) *style:* **Only use double-quotes.**
```r
        stop('inBegin contains NA')
             ^~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:375:34:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L375) *style:* **Only use double-quotes.**
```r
    if (!identical(class(inEnd), 'Date')) {
                                 ^~~~~~
```
[R/trace.R:380:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L380) *style:* **Only use double-quotes.**
```r
        stop('inEnd contains NA')
             ^~~~~~~~~~~~~~~~~~~
```
[R/trace.R:390:37:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L390) *style:* **Only use double-quotes.**
```r
    if (!identical(class(outBegin), 'Date')) {
                                    ^~~~~~
```
[R/trace.R:395:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L395) *style:* **Only use double-quotes.**
```r
        stop('outBegin contains NA')
             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:405:35:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L405) *style:* **Only use double-quotes.**
```r
    if (!identical(class(outEnd), 'Date')) {
                                  ^~~~~~
```
[R/trace.R:410:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L410) *style:* **Only use double-quotes.**
```r
        stop('outEnd contains NA')
             ^~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:417:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L417) *style:* **Only use double-quotes.**
```r
        stop('inEnd < inBegin')
             ^~~~~~~~~~~~~~~~~
```
[R/trace.R:421:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L421) *style:* **Only use double-quotes.**
```r
        stop('outEnd < outBegin')
             ^~~~~~~~~~~~~~~~~~~
```
[R/trace.R:433:14:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L433) *style:* **Only use double-quotes.**
```r
        stop('root, inBegin, inEnd, outBegin and outEnd must have equal length')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:460:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L460) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$source, levels=levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:460:71:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L460) *style:* **Put spaces around all infix operators.**
```r
                            as.integer(factor(movements$source, levels=levels(nodes))),
                                                                     ~^~
```
[R/trace.R:461:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L461) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$destination, levels=levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:461:76:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L461) *style:* **Put spaces around all infix operators.**
```r
                            as.integer(factor(movements$destination, levels=levels(nodes))),
                                                                          ~^~
```
[R/trace.R:463:59:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L463) *style:* **Put spaces around all infix operators.**
```r
                            as.integer(factor(root, levels=levels(nodes))),
                                                         ~^~
```
[R/trace.R:473:16:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L473) *style:* **Put spaces around all infix operators.**
```r
        j <- (i-1) * 4
              ~^~
```
[R/trace.R:483:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L483) *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:485:12:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L485) *style:* **Commented code should be removed.**
```r
        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:486:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L486) *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:486:76:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L486) *style:* **Put spaces around all infix operators.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~
```
[R/trace.R:487:72:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L487) *style:* **Put spaces around all infix operators.**
```r
                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~
```
[R/trace.R:489:32:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L489) *style:* **Only use double-quotes.**
```r
        ingoingContacts <- new('Contacts',
                               ^~~~~~~~~~
```
[R/trace.R:493:51:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L493) *style:* **Commas should always have a space after.**
```r
                               source = contacts[,1],
                                                  ^
```
[R/trace.R:494:56:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L494) *style:* **Commas should always have a space after.**
```r
                               destination = contacts[,2],
                                                       ^
```
[R/trace.R:495:46:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L495) *style:* **Commas should always have a space after.**
```r
                               t = contacts[,3],
                                             ^
```
[R/trace.R:496:47:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L496) *style:* **Commas should always have a space after.**
```r
                               id = contacts[,4],
                                              ^
```
[R/trace.R:497:46:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L497) *style:* **Commas should always have a space after.**
```r
                               n = contacts[,5],
                                             ^
```
[R/trace.R:498:53:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L498) *style:* **Commas should always have a space after.**
```r
                               category = contacts[,6],
                                                    ^
```
[R/trace.R:501:44:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L501) *style:* **Only use double-quotes.**
```r
                               direction = 'in')
                                           ^~~~
```
[R/trace.R:511:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L511) *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:513:12:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L513) *style:* **Commented code should be removed.**
```r
        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:514:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L514) *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:514:76:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L514) *style:* **Put spaces around all infix operators.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~
```
[R/trace.R:515:72:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L515) *style:* **Put spaces around all infix operators.**
```r
                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~
```
[R/trace.R:517:33:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L517) *style:* **Only use double-quotes.**
```r
        outgoingContacts <- new('Contacts',
                                ^~~~~~~~~~
```
[R/trace.R:521:52:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L521) *style:* **Commas should always have a space after.**
```r
                                source = contacts[,1],
                                                   ^
```
[R/trace.R:522:57:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L522) *style:* **Commas should always have a space after.**
```r
                                destination = contacts[,2],
                                                        ^
```
[R/trace.R:523:47:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L523) *style:* **Commas should always have a space after.**
```r
                                t = contacts[,3],
                                              ^
```
[R/trace.R:524:48:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L524) *style:* **Commas should always have a space after.**
```r
                                id = contacts[,4],
                                               ^
```
[R/trace.R:525:47:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L525) *style:* **Commas should always have a space after.**
```r
                                n = contacts[,5],
                                              ^
```
[R/trace.R:526:54:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L526) *style:* **Commas should always have a space after.**
```r
                                category = contacts[,6],
                                                     ^
```
[R/trace.R:529:45:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L529) *style:* **Only use double-quotes.**
```r
                                direction = 'out')
                                            ^~~~~
```
[R/trace.R:531:20:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L531) *style:* **Only use double-quotes.**
```r
        return(new('ContactTrace',
                   ^~~~~~~~~~~~~~
```
[R/trace.R:537:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L537) *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:538:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/trace.R#L538) *style:* **Lines should not be more than 80 characters.**
```r
    names(result) <-  sapply(result, function(listItem) listItem@ingoingContacts@root)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree.R:31:1:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/tree.R#L31) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/tree.R:36:70:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/tree.R#L36) *style:* **Commas should always have a space after.**
```r
    tree.in <- network_structure[network_structure$direction == "in",]
                                                                     ^
```
[R/tree.R:37:72:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/tree.R#L37) *style:* **Commas should always have a space after.**
```r
    tree.out <- network_structure[network_structure$direction == "out",]
                                                                       ^
```
[R/tree.R:39:27:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/tree.R#L39) *style:* **Put spaces around all infix operators.**
```r
    result <- list(ingoing=NULL, outgoing=NULL)
                         ~^~
```
[R/tree.R:39:42:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/tree.R#L39) *style:* **Put spaces around all infix operators.**
```r
    result <- list(ingoing=NULL, outgoing=NULL)
                                        ~^~
```
[R/tree.R:48:33:](https://github.com/stewid/EpiContactTrace/blob/52be0ce8bd69a1cdc8f630570fab94ca0e5ab699/R/tree.R#L48) *style:* **Only use double-quotes.**
```r
        tree.in <- tree.in[i, c('source', 'distance')]
                                ^~~~~~~~
```


Первое задание выполнено.


Successfully deployed to following URLs:

* https://blogapi2ucn-le9apteow.now.sh
* https://ap.api2u.cn
* https://blogapi2ucn.youngje.now.sh
* https://blogapi2ucn-git-master.youngje.now.sh


# Giving Title

I just thought I should give my site a title


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


您是否打算将全部内容翻译成中文？


Successfully deployed to following URLs:

* https://pansy-2aj3vvmho.now.sh
* https://pansy-practical-prawn.now.sh
* https://pansy.now.sh
* https://pansy.walrus-plus.now.sh
* https://pansy-git-master.walrus-plus.now.sh


@Bvanderlecq s/the rest of the information is informed/the rest of the team is informed


Successfully deployed to following URLs:

* https://blogapi2ucn-pm5eudh9t.now.sh
* https://ap.api2u.cn
* https://blogapi2ucn.youngje.now.sh
* https://blogapi2ucn-git-master.youngje.now.sh


Ahhh so that's where the bug came from. Original is buggy as well.

Is there a better fix?


@JuliaRegistrator register

Release notes:

Add more keyword parameters to AtariEnv.


Registration pull request created: [JuliaRegistries/General/4977](https://github.com/JuliaRegistries/General/pull/4977)

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 v0.1.3 -m "<description of version>" 9d0ae3600bb8caa577dec2eb285c23bea3d419f4
git push origin v0.1.3
```


Successfully deployed to following URLs:

* https://pansy-1kiaxkhxq.now.sh
* https://pansy-practical-prawn.now.sh
* https://pansy.now.sh
* https://pansy.walrus-plus.now.sh
* https://pansy-git-master.walrus-plus.now.sh


я немного не понял вот это :) вроде бы у тебя в функцию out подается путь к файлу, который будешь открывать и читать, но вот конкретно тут захардкожен файл, поправь, пожалуйста


Successfully deployed to following URLs:

* https://cbitoscgithubio-ptmx2z5dx.now.sh
* https://cbitoscgithubio.cbitosc.now.sh
* https://cbitoscgithubio-git-master.cbitosc.now.sh


Successfully deployed to following URLs:

* https://pansy-ri5f9ir0o.now.sh
* https://pansy-practical-prawn.now.sh
* https://pansy.now.sh
* https://pansy.walrus-plus.now.sh
* https://pansy-git-master.walrus-plus.now.sh


This is not a proper dataset transform function signature. It should be `def __call(self, *args)`


Третье задание выполнено.


thank you


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
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Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Try to think for better names for your ids


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

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

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

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


Successfully deployed to following URLs:

* https://social-network-8n5fnmstg.now.sh
* https://social-network.marchenkoulya26.now.sh
* https://social-network-git-master.marchenkoulya26.now.sh


@Igor7086 👍


Successfully deployed to following URLs:

* https://golangtest-fqhofk1v5.now.sh
* https://golangtest.ruslanzhelezo.now.sh
* https://golangtest-git-master.ruslanzhelezo.now.sh


You can add placeholders for inputs.
` <input type="text" name="lastname" placeholder="Last name">`