[R/Contacts.r:31:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L31) *style:* **Lines should not be more than 80 characters.**
```r
##' dataset during contact tracing. The \code{index} slot is an index to the extracted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Contacts.r:53:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L53) *style:* **Lines should not be more than 80 characters.**
```r
##'     A \code{character} vector with the identifier of the destination holdings
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Contacts.r:72:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L72) *style:* **Lines should not be more than 80 characters.**
```r
##'     A \code{integer} vector with the distance from root for the contact[index]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Contacts.r:75:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L75) *style:* **Lines should not be more than 80 characters.**
```r
##'     A \code{character} vector of length one equal to the direction 'in' or 'out'
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Contacts.r:103:10:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L103) *style:* **Only use double-quotes.**
```r
setClass('Contacts',
         ^~~~~~~~~~
```
[R/Contacts.r:104:27:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L104) *style:* **Only use double-quotes.**
```r
         slots = c(root = 'character',
                          ^~~~~~~~~~~
```
[R/Contacts.r:105:29:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L105) *style:* **Only use double-quotes.**
```r
                   tBegin = 'Date',
                            ^~~~~~
```
[R/Contacts.r:106:27:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L106) *style:* **Only use double-quotes.**
```r
                   tEnd = 'Date',
                          ^~~~~~
```
[R/Contacts.r:107:29:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L107) *style:* **Only use double-quotes.**
```r
                   source = 'character',
                            ^~~~~~~~~~~
```
[R/Contacts.r:108:34:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L108) *style:* **Only use double-quotes.**
```r
                   destination = 'character',
                                 ^~~~~~~~~~~
```
[R/Contacts.r:109:24:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L109) *style:* **Only use double-quotes.**
```r
                   t = 'Date',
                       ^~~~~~
```
[R/Contacts.r:110:25:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L110) *style:* **Only use double-quotes.**
```r
                   id = 'character',
                        ^~~~~~~~~~~
```
[R/Contacts.r:111:24:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L111) *style:* **Only use double-quotes.**
```r
                   n = 'numeric',
                       ^~~~~~~~~
```
[R/Contacts.r:112:31:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L112) *style:* **Only use double-quotes.**
```r
                   category = 'character',
                              ^~~~~~~~~~~
```
[R/Contacts.r:113:28:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L113) *style:* **Only use double-quotes.**
```r
                   index = 'integer',
                           ^~~~~~~~~
```
[R/Contacts.r:114:31:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L114) *style:* **Only use double-quotes.**
```r
                   distance = 'integer',
                              ^~~~~~~~~
```
[R/Contacts.r:115:32:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L115) *style:* **Only use double-quotes.**
```r
                   direction = 'character'),
                               ^~~~~~~~~~~
```
[R/Contacts.r:125:16:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L125) *style:* **Place a space before left parenthesis, except in a function call.**
```r
             if(!identical(length(l), 1L)) {
               ^
```
[R/Contacts.r:126:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L126) *style:* **Lines should not be more than 80 characters.**
```r
                 retval <- 'Lengths of source, destination, t, id, n and category should have equal length'
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Contacts.r:126:28:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L126) *style:* **Only use double-quotes.**
```r
                 retval <- 'Lengths of source, destination, t, id, n and category should have equal length'
                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Contacts.r:129:16:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L129) *style:* **Place a space before left parenthesis, except in a function call.**
```r
             if(is.null(retval)) {
               ^
```
[R/Contacts.r:137:11:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L137) *style:* **Put spaces around all infix operators.**
```r
setAs(from='Contacts',
         ~^~
```
[R/Contacts.r:137:12:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L137) *style:* **Only use double-quotes.**
```r
setAs(from='Contacts',
           ^~~~~~~~~~
```
[R/Contacts.r:138:9:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L138) *style:* **Put spaces around all infix operators.**
```r
      to='data.frame',
       ~^~
```
[R/Contacts.r:138:10:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L138) *style:* **Only use double-quotes.**
```r
      to='data.frame',
         ^~~~~~~~~~~~
```
[R/Contacts.r:139:10:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L139) *style:* **Put spaces around all infix operators.**
```r
      def=function(from)
        ~^~
```
[R/Contacts.r:140:3:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L140) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/Contacts.r:141:9:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L141) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(length(from@source) > 0L) {
        ^
```
[R/Contacts.r:142:35:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L142) *style:* **Put spaces around all infix operators.**
```r
          df1 <- data.frame(source=from@source,
                                 ~^~
```
[R/Contacts.r:143:40:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L143) *style:* **Put spaces around all infix operators.**
```r
                            destination=from@destination,
                                      ~^~
```
[R/Contacts.r:144:30:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L144) *style:* **Put spaces around all infix operators.**
```r
                            t=from@t,
                            ~^~
```
[R/Contacts.r:145:31:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L145) *style:* **Put spaces around all infix operators.**
```r
                            id=from@id,
                             ~^~
```
[R/Contacts.r:146:30:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L146) *style:* **Put spaces around all infix operators.**
```r
                            n=from@n,
                            ~^~
```
[R/Contacts.r:147:37:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L147) *style:* **Put spaces around all infix operators.**
```r
                            category=from@category,
                                   ~^~
```
[R/Contacts.r:148:45:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L148) *style:* **Put spaces around all infix operators.**
```r
                            stringsAsFactors=FALSE)
                                           ~^~
```
[R/Contacts.r:150:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L150) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(identical(from@direction, 'in')) {
            ^
```
[R/Contacts.r:150:40:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L150) *style:* **Only use double-quotes.**
```r
          if(identical(from@direction, 'in')) {
                                       ^~~~
```
[R/Contacts.r:151:37:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L151) *style:* **Put spaces around all infix operators.**
```r
              df2 <- data.frame(root=from@root,
                                   ~^~
```
[R/Contacts.r:152:40:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L152) *style:* **Put spaces around all infix operators.**
```r
                                inBegin=from@tBegin,
                                      ~^~
```
[R/Contacts.r:153:38:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L153) *style:* **Put spaces around all infix operators.**
```r
                                inEnd=from@tEnd,
                                    ~^~
```
[R/Contacts.r:154:41:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L154) *style:* **Put spaces around all infix operators.**
```r
                                outBegin=as.Date(as.character(NA)),
                                       ~^~
```
[R/Contacts.r:155:39:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L155) *style:* **Put spaces around all infix operators.**
```r
                                outEnd=as.Date(as.character(NA)),
                                     ~^~
```
[R/Contacts.r:156:42:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L156) *style:* **Put spaces around all infix operators.**
```r
                                direction='in',
                                        ~^~
```
[R/Contacts.r:156:43:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L156) *style:* **Only use double-quotes.**
```r
                                direction='in',
                                          ^~~~
```
[R/Contacts.r:157:49:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L157) *style:* **Put spaces around all infix operators.**
```r
                                stringsAsFactors=FALSE)
                                               ~^~
```
[R/Contacts.r:159:37:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L159) *style:* **Put spaces around all infix operators.**
```r
              df2 <- data.frame(root=from@root,
                                   ~^~
```
[R/Contacts.r:160:40:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L160) *style:* **Put spaces around all infix operators.**
```r
                                inBegin=as.Date(as.character(NA)),
                                      ~^~
```
[R/Contacts.r:161:38:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L161) *style:* **Put spaces around all infix operators.**
```r
                                inEnd=as.Date(as.character(NA)),
                                    ~^~
```
[R/Contacts.r:162:41:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L162) *style:* **Put spaces around all infix operators.**
```r
                                outBegin=from@tBegin,
                                       ~^~
```
[R/Contacts.r:163:39:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L163) *style:* **Put spaces around all infix operators.**
```r
                                outEnd=from@tEnd,
                                     ~^~
```
[R/Contacts.r:164:42:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L164) *style:* **Put spaces around all infix operators.**
```r
                                direction='out',
                                        ~^~
```
[R/Contacts.r:164:43:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L164) *style:* **Only use double-quotes.**
```r
                                direction='out',
                                          ^~~~~
```
[R/Contacts.r:165:49:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L165) *style:* **Put spaces around all infix operators.**
```r
                                stringsAsFactors=FALSE)
                                               ~^~
```
[R/Contacts.r:171:33:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L171) *style:* **Put spaces around all infix operators.**
```r
          return(data.frame(root=character(0),
                               ~^~
```
[R/Contacts.r:172:36:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L172) *style:* **Put spaces around all infix operators.**
```r
                            inBegin=as.Date(character(0)),
                                  ~^~
```
[R/Contacts.r:173:34:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L173) *style:* **Put spaces around all infix operators.**
```r
                            inEnd=as.Date(character(0)),
                                ~^~
```
[R/Contacts.r:174:37:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L174) *style:* **Put spaces around all infix operators.**
```r
                            outBegin=as.Date(character(0)),
                                   ~^~
```
[R/Contacts.r:175:35:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L175) *style:* **Put spaces around all infix operators.**
```r
                            outEnd=as.Date(character(0)),
                                 ~^~
```
[R/Contacts.r:176:38:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L176) *style:* **Put spaces around all infix operators.**
```r
                            direction=character(0),
                                    ~^~
```
[R/Contacts.r:177:35:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L177) *style:* **Put spaces around all infix operators.**
```r
                            source=character(0),
                                 ~^~
```
[R/Contacts.r:178:40:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L178) *style:* **Put spaces around all infix operators.**
```r
                            destination=character(0),
                                      ~^~
```
[R/Contacts.r:179:30:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L179) *style:* **Put spaces around all infix operators.**
```r
                            t=as.Date(character(0)),
                            ~^~
```
[R/Contacts.r:180:31:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L180) *style:* **Put spaces around all infix operators.**
```r
                            id=character(0),
                             ~^~
```
[R/Contacts.r:181:30:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L181) *style:* **Put spaces around all infix operators.**
```r
                            n=numeric(0),
                            ~^~
```
[R/Contacts.r:182:37:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L182) *style:* **Put spaces around all infix operators.**
```r
                            category=character(0),
                                   ~^~
```
[R/Contacts.r:183:45:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/Contacts.r#L183) *style:* **Put spaces around all infix operators.**
```r
                            stringsAsFactors=FALSE))
                                           ~^~
```
[R/ContactTrace.r:35:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ContactTrace.r#L35) *style:* **Lines should not be more than 80 characters.**
```r
##'     A \code{Contacts} object with the contacts for the ingoing contact chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ContactTrace.r:38:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ContactTrace.r#L38) *style:* **Lines should not be more than 80 characters.**
```r
##'     A \code{Contacts} object with the contacts for the outgoing contact chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ContactTrace.r:69:3:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ContactTrace.r#L69) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/in-degree.r:82:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L82) *style:* **Lines should not be more than 80 characters.**
```r
##'     Get the InDegree for a data.frame with movements, see details and examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/in-degree.r:177:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L177) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/in-degree.r:178:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L178) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(!identical(x@direction, "in")) {
            ^
```
[R/in-degree.r:182:54:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L182) *style:* **Put spaces around all infix operators.**
```r
          return(length(unique(x@source[x@destination==x@root])))
                                                    ~^~~
```
[R/in-degree.r:190:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L190) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
          function (x)
                   ^
```
[R/in-degree.r:191:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L191) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/in-degree.r:210:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L210) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/in-degree.r:211:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(missing(root)) {
            ^
```
[R/in-degree.r:215:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/in-degree.r#L215) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(all(is.null(tEnd), is.null(days))) {
            ^
```
[R/ingoing-contact-chain.r:111:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L111) *style:* **Lines should not be more than 80 characters.**
```r
##'     The \code{\link{IngoingContactChain}} of the root within the time-interval
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ingoing-contact-chain.r:180:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L180) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
          function (x)
                   ^
```
[R/ingoing-contact-chain.r:181:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L181) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/ingoing-contact-chain.r:182:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L182) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(!identical(x@direction, "in")) {
            ^
```
[R/ingoing-contact-chain.r:183:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L183) *style:* **Lines should not be more than 80 characters.**
```r
              stop("Unable to determine IngoingContactChain for outgoing contacts")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ingoing-contact-chain.r:186:42:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L186) *style:* **Commas should always have a space after.**
```r
          return(length(setdiff(x@source,x@root)))
                                         ^
```
[R/ingoing-contact-chain.r:194:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L194) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
          function (x)
                   ^
```
[R/ingoing-contact-chain.r:195:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L195) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/ingoing-contact-chain.r:214:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L214) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/ingoing-contact-chain.r:215:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L215) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(missing(root)) {
            ^
```
[R/ingoing-contact-chain.r:219:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/ingoing-contact-chain.r#L219) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(all(is.null(tEnd), is.null(days))) {
            ^
```
[R/network-structure.r:119:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L119) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/network-structure.r:120:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L120) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(length(object@source) > 0L) {
            ^
```
[R/network-structure.r:125:39:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L125) *style:* **Put spaces around all infix operators.**
```r
                         deparse.level=0)
                                     ~^~
```
[R/network-structure.r:128:63:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L128) *style:* **Put spaces around all infix operators.**
```r
              tmp <- apply(m, 1, function(x) paste(x, collapse="\r"))
                                                             ~^~
```
[R/network-structure.r:132:43:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L132) *style:* **Put spaces around all infix operators.**
```r
              i <- tmp[seq_len(length(tmp)-1)] != tmp[seq_len(length(tmp))[-1]]
                                         ~^~
```
[R/network-structure.r:135:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L135) *style:* **Lines should not be more than 80 characters.**
```r
              m <- as.data.frame(m[c(TRUE, i), , drop=FALSE], stringsAsFactors=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-structure.r:135:54:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L135) *style:* **Put spaces around all infix operators.**
```r
              m <- as.data.frame(m[c(TRUE, i), , drop=FALSE], stringsAsFactors=FALSE)
                                                    ~^~
```
[R/network-structure.r:135:79:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L135) *style:* **Put spaces around all infix operators.**
```r
              m <- as.data.frame(m[c(TRUE, i), , drop=FALSE], stringsAsFactors=FALSE)
                                                                             ~^~
```
[R/network-structure.r:141:17:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L141) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(identical(object@direction, "in")) {
                ^
```
[R/network-structure.r:142:44:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L142) *style:* **Put spaces around all infix operators.**
```r
                  result <- data.frame(root=object@root,
                                          ~^~
```
[R/network-structure.r:143:47:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L143) *style:* **Put spaces around all infix operators.**
```r
                                       inBegin=object@tBegin,
                                             ~^~
```
[R/network-structure.r:144:45:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L144) *style:* **Put spaces around all infix operators.**
```r
                                       inEnd=object@tEnd,
                                           ~^~
```
[R/network-structure.r:145:48:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L145) *style:* **Put spaces around all infix operators.**
```r
                                       outBegin=as.Date(as.character(NA)),
                                              ~^~
```
[R/network-structure.r:146:46:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L146) *style:* **Put spaces around all infix operators.**
```r
                                       outEnd=as.Date(as.character(NA)),
                                            ~^~
```
[R/network-structure.r:147:49:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L147) *style:* **Put spaces around all infix operators.**
```r
                                       direction="in",
                                               ~^~
```
[R/network-structure.r:148:56:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L148) *style:* **Put spaces around all infix operators.**
```r
                                       stringsAsFactors=FALSE)
                                                      ~^~
```
[R/network-structure.r:150:44:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L150) *style:* **Put spaces around all infix operators.**
```r
                  result <- data.frame(root=object@root,
                                          ~^~
```
[R/network-structure.r:151:47:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L151) *style:* **Put spaces around all infix operators.**
```r
                                       inBegin=as.Date(as.character(NA)),
                                             ~^~
```
[R/network-structure.r:152:45:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L152) *style:* **Put spaces around all infix operators.**
```r
                                       inEnd=as.Date(as.character(NA)),
                                           ~^~
```
[R/network-structure.r:153:48:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L153) *style:* **Put spaces around all infix operators.**
```r
                                       outBegin=object@tBegin,
                                              ~^~
```
[R/network-structure.r:154:46:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L154) *style:* **Put spaces around all infix operators.**
```r
                                       outEnd=object@tEnd,
                                            ~^~
```
[R/network-structure.r:155:49:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L155) *style:* **Put spaces around all infix operators.**
```r
                                       direction="out",
                                               ~^~
```
[R/network-structure.r:156:56:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L156) *style:* **Put spaces around all infix operators.**
```r
                                       stringsAsFactors=FALSE)
                                                      ~^~
```
[R/network-structure.r:162:37:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L162) *style:* **Put spaces around all infix operators.**
```r
              return(data.frame(root=character(0),
                                   ~^~
```
[R/network-structure.r:163:40:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L163) *style:* **Put spaces around all infix operators.**
```r
                                inBegin=as.Date(character(0)),
                                      ~^~
```
[R/network-structure.r:164:38:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L164) *style:* **Put spaces around all infix operators.**
```r
                                inEnd=as.Date(character(0)),
                                    ~^~
```
[R/network-structure.r:165:41:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L165) *style:* **Put spaces around all infix operators.**
```r
                                outBegin=as.Date(character(0)),
                                       ~^~
```
[R/network-structure.r:166:39:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L166) *style:* **Put spaces around all infix operators.**
```r
                                outEnd=as.Date(character(0)),
                                     ~^~
```
[R/network-structure.r:167:42:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L167) *style:* **Put spaces around all infix operators.**
```r
                                direction=character(0),
                                        ~^~
```
[R/network-structure.r:168:39:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L168) *style:* **Put spaces around all infix operators.**
```r
                                source=character(0),
                                     ~^~
```
[R/network-structure.r:169:44:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L169) *style:* **Put spaces around all infix operators.**
```r
                                destination=character(0),
                                          ~^~
```
[R/network-structure.r:170:41:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L170) *style:* **Put spaces around all infix operators.**
```r
                                distance=integer(0),
                                       ~^~
```
[R/network-structure.r:171:49:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L171) *style:* **Put spaces around all infix operators.**
```r
                                stringsAsFactors=FALSE))
                                               ~^~
```
[R/network-structure.r:179:27:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L179) *style:* **Put spaces around all infix operators.**
```r
          signature(object="ContactTrace"),
                         ~^~
```
[R/network-structure.r:181:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-structure.r#L181) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/network-summary.r:236:12:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L236) *style:* **Only use double-quotes.**
```r
setGeneric('NetworkSummary',
           ^~~~~~~~~~~~~~~~
```
[R/network-summary.r:237:24:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L237) *style:* **Only use double-quotes.**
```r
           signature = 'x',
                       ^~~
```
[R/network-summary.r:238:45:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L238) *style:* **Only use double-quotes.**
```r
           function(x, ...) standardGeneric('NetworkSummary'))
                                            ^~~~~~~~~~~~~~~~
```
[R/network-summary.r:242:11:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L242) *style:* **Only use double-quotes.**
```r
setMethod('NetworkSummary',
          ^~~~~~~~~~~~~~~~
```
[R/network-summary.r:243:25:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L243) *style:* **Only use double-quotes.**
```r
          signature(x = 'ContactTrace'),
                        ^~~~~~~~~~~~~~
```
[R/network-summary.r:245:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L245) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/network-summary.r:246:26:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L246) *style:* **Put spaces around all infix operators.**
```r
          data.frame(root=x@root,
                        ~^~
```
[R/network-summary.r:247:29:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L247) *style:* **Put spaces around all infix operators.**
```r
                     inBegin=x@ingoingContacts@tBegin,
                           ~^~
```
[R/network-summary.r:248:27:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L248) *style:* **Put spaces around all infix operators.**
```r
                     inEnd=x@ingoingContacts@tEnd,
                         ~^~
```
[R/network-summary.r:249:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L249) *style:* **Lines should not be more than 80 characters.**
```r
                     inDays=as.integer(x@ingoingContacts@tEnd - x@ingoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:249:28:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L249) *style:* **Put spaces around all infix operators.**
```r
                     inDays=as.integer(x@ingoingContacts@tEnd - x@ingoingContacts@tBegin),
                          ~^~
```
[R/network-summary.r:250:30:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L250) *style:* **Put spaces around all infix operators.**
```r
                     outBegin=x@outgoingContacts@tBegin,
                            ~^~
```
[R/network-summary.r:251:28:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L251) *style:* **Put spaces around all infix operators.**
```r
                     outEnd=x@outgoingContacts@tEnd,
                          ~^~
```
[R/network-summary.r:252:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L252) *style:* **Lines should not be more than 80 characters.**
```r
                     outDays=as.integer(x@outgoingContacts@tEnd - x@outgoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:252:29:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L252) *style:* **Put spaces around all infix operators.**
```r
                     outDays=as.integer(x@outgoingContacts@tEnd - x@outgoingContacts@tBegin),
                           ~^~
```
[R/network-summary.r:253:30:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L253) *style:* **Put spaces around all infix operators.**
```r
                     inDegree=InDegree(x@ingoingContacts),
                            ~^~
```
[R/network-summary.r:254:31:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L254) *style:* **Put spaces around all infix operators.**
```r
                     outDegree=OutDegree(x@outgoingContacts),
                             ~^~
```
[R/network-summary.r:255:41:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L255) *style:* **Put spaces around all infix operators.**
```r
                     ingoingContactChain=IngoingContactChain(x@ingoingContacts),
                                       ~^~
```
[R/network-summary.r:256:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L256) *style:* **Lines should not be more than 80 characters.**
```r
                     outgoingContactChain=OutgoingContactChain(x@outgoingContacts))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:256:42:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L256) *style:* **Put spaces around all infix operators.**
```r
                     outgoingContactChain=OutgoingContactChain(x@outgoingContacts))
                                        ~^~
```
[R/network-summary.r:262:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L262) *style:* **functions should have cyclomatic complexity of less than 15, this has 38.**
```r
setMethod('NetworkSummary',
^
```
[R/network-summary.r:262:11:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L262) *style:* **Only use double-quotes.**
```r
setMethod('NetworkSummary',
          ^~~~~~~~~~~~~~~~
```
[R/network-summary.r:263:25:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L263) *style:* **Only use double-quotes.**
```r
          signature(x = 'data.frame'),
                        ^~~~~~~~~~~~
```
[R/network-summary.r:272:7:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L272) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/network-summary.r:276:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L276) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(!all(c('source', 'destination', 't') %in% names(x))) {
            ^
```
[R/network-summary.r:276:21:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L276) *style:* **Only use double-quotes.**
```r
          if(!all(c('source', 'destination', 't') %in% names(x))) {
                    ^~~~~~~~
```
[R/network-summary.r:276:31:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L276) *style:* **Only use double-quotes.**
```r
          if(!all(c('source', 'destination', 't') %in% names(x))) {
                              ^~~~~~~~~~~~~
```
[R/network-summary.r:276:46:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L276) *style:* **Only use double-quotes.**
```r
          if(!all(c('source', 'destination', 't') %in% names(x))) {
                                             ^~~
```
[R/network-summary.r:277:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L277) *style:* **Only use double-quotes.**
```r
              stop('x must contain the columns source, destination and t.')
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:280:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L280) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.factor(x$source), is.integer(x$source))) {
            ^
```
[R/network-summary.r:282:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L282) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          } else if(!is.character(x$source)) {
                   ^
```
[R/network-summary.r:283:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L283) *style:* **Only use double-quotes.**
```r
              stop('invalid class of column source in x')
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:286:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L286) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.factor(x$destination), is.integer(x$destination))) {
            ^
```
[R/network-summary.r:288:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L288) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          } else if(!is.character(x$destination)) {
                   ^
```
[R/network-summary.r:289:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L289) *style:* **Only use double-quotes.**
```r
              stop('invalid class of column destination in x')
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:292:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L292) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.character(x$t), is.factor(x$t))) {
            ^
```
[R/network-summary.r:296:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L296) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(!identical(class(x$t), 'Date')) {
            ^
```
[R/network-summary.r:296:37:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L296) *style:* **Only use double-quotes.**
```r
          if(!identical(class(x$t), 'Date')) {
                                    ^~~~~~
```
[R/network-summary.r:297:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L297) *style:* **Only use double-quotes.**
```r
              stop('invalid class of column t in x')
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:300:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L300) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.na(x$t))) {
            ^
```
[R/network-summary.r:306:29:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L306) *style:* **Only use double-quotes.**
```r
          x <- unique(x[, c('source', 'destination', 't')])
                            ^~~~~~~~
```
[R/network-summary.r:306:39:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L306) *style:* **Only use double-quotes.**
```r
          x <- unique(x[, c('source', 'destination', 't')])
                                      ^~~~~~~~~~~~~
```
[R/network-summary.r:306:54:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L306) *style:* **Only use double-quotes.**
```r
          x <- unique(x[, c('source', 'destination', 't')])
                                                     ^~~
```
[R/network-summary.r:309:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L309) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(missing(root)) {
            ^
```
[R/network-summary.r:310:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L310) *style:* **Only use double-quotes.**
```r
              stop('Missing root in call to NetworkSummary')
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:313:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L313) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.factor(root), is.integer(root))) {
            ^
```
[R/network-summary.r:315:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L315) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          } else if(is.numeric(root)) {
                   ^
```
[R/network-summary.r:317:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L317) *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:319:17:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L319) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(any(max(abs(root - rootr) > 1e-07))) {
                ^
```
[R/network-summary.r:324:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L324) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          } else if(!is.character(root)) {
                   ^
```
[R/network-summary.r:325:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L325) *style:* **Only use double-quotes.**
```r
              stop('invalid class of root')
                   ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:330:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L330) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(all(!is.null(tEnd), !is.null(days))) {
            ^
```
[R/network-summary.r:333:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L333) *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:333:17:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L333) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
                ^
```
[R/network-summary.r:334:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L334) *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:334:24:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L334) *style:* **Only use double-quotes.**
```r
                  stop('Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary')
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:337:17:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L337) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(any(is.character(tEnd), is.factor(tEnd))) {
                ^
```
[R/network-summary.r:341:17:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L341) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(!identical(class(tEnd), 'Date')) {
                ^
```
[R/network-summary.r:341:42:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L341) *style:* **Only use double-quotes.**
```r
              if(!identical(class(tEnd), 'Date')) {
                                         ^~~~~~
```
[R/network-summary.r:345:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L345) *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:347:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L347) *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:362:37:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L362) *style:* **Put spaces around all infix operators.**
```r
              root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                   ~^~
```
[R/network-summary.r:362:44:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L362) *style:* **Put spaces around all infix operators.**
```r
              root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                          ~^~
```
[R/network-summary.r:362:63:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L362) *style:* **Put spaces around all infix operators.**
```r
              root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                                             ~^~
```
[R/network-summary.r:363:38:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L363) *style:* **Put spaces around all infix operators.**
```r
              inEnd <- rep(tEnd, each=n.days, length.out=n)
                                    ~^~
```
[R/network-summary.r:363:57:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L363) *style:* **Put spaces around all infix operators.**
```r
              inEnd <- rep(tEnd, each=n.days, length.out=n)
                                                       ~^~
```
[R/network-summary.r:364:48:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L364) *style:* **Put spaces around all infix operators.**
```r
              inBegin <- inEnd - rep(days, each=1, length.out=n)
                                              ~^~
```
[R/network-summary.r:364:62:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L364) *style:* **Put spaces around all infix operators.**
```r
              inBegin <- inEnd - rep(days, each=1, length.out=n)
                                                            ~^~
```
[R/network-summary.r:367:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L367) *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:367:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L367) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          } else if(all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
                   ^
```
[R/network-summary.r:371:17:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L371) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(!all(is.null(tEnd), is.null(days))) {
                ^
```
[R/network-summary.r:372:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L372) *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:372:24:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L372) *style:* **Only use double-quotes.**
```r
                  stop('Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary')
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:375:1:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L375) *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:375:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L375) *style:* **Only use double-quotes.**
```r
              stop('Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary')
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:381:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L381) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.character(inBegin), is.factor(inBegin))) {
            ^
```
[R/network-summary.r:385:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L385) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(!identical(class(inBegin), 'Date')) {
            ^
```
[R/network-summary.r:385:41:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L385) *style:* **Only use double-quotes.**
```r
          if(!identical(class(inBegin), 'Date')) {
                                        ^~~~~~
```
[R/network-summary.r:389:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L389) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.na(inBegin))) {
            ^
```
[R/network-summary.r:390:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L390) *style:* **Only use double-quotes.**
```r
              stop('inBegin contains NA')
                   ^~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:396:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L396) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.character(inEnd), is.factor(inEnd))) {
            ^
```
[R/network-summary.r:400:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L400) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(!identical(class(inEnd), 'Date')) {
            ^
```
[R/network-summary.r:400:39:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L400) *style:* **Only use double-quotes.**
```r
          if(!identical(class(inEnd), 'Date')) {
                                      ^~~~~~
```
[R/network-summary.r:404:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L404) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.na(inEnd))) {
            ^
```
[R/network-summary.r:405:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L405) *style:* **Only use double-quotes.**
```r
              stop('inEnd contains NA')
                   ^~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:411:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L411) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.character(outBegin), is.factor(outBegin))) {
            ^
```
[R/network-summary.r:415:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L415) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(!identical(class(outBegin), 'Date')) {
            ^
```
[R/network-summary.r:415:42:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L415) *style:* **Only use double-quotes.**
```r
          if(!identical(class(outBegin), 'Date')) {
                                         ^~~~~~
```
[R/network-summary.r:419:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L419) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.na(outBegin))) {
            ^
```
[R/network-summary.r:420:20:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L420) *style:* **Only use double-quotes.**
```r
              stop('outBegin contains NA')
                   ^~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.r:426:13:](https://github.com/stewid/EpiContactTrace/blob/98686c40e7231f3a20dde8727766b223af5e9cd0/R/network-summary.r#L426) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(any(is.character(outEnd), is.factor(outEnd))) {
            ^
```


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


Successfully deployed to following URLs:

* https://demo-preview-mu50m25wz.now.sh
* https://demo-preview.617754841.now.sh
* https://demo-preview-git-master.617754841.now.sh


The point is we should never evaluate an identical position with reversed colors differently.


Successfully deployed to following URLs:

* https://41waller-g1rp032zu.now.sh
* https://41waller.com
* https://*.41waller.com
* https://41waller.ahrjarrett.now.sh
* https://41waller-git-master.ahrjarrett.now.sh


Successfully deployed to following URLs:

* https://pansy-q7vs3nkaf.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


[R/calc_sum_stats.R:69:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/calc_sum_stats.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
  output[10] <- phyloTop::ILnumber(focal_tree) # number of internal nodes with a single child
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_reference_table.R:35:8:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/create_reference_table.R#L35) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(focal_model in 1:3) {
       ^
```
[R/create_reference_table.R:48:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/create_reference_table.R#L48) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:49:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/create_reference_table.R#L49) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:50:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/create_reference_table.R#L50) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:51:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/create_reference_table.R#L51) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/generate_from_prior.R:14:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/generate_from_prior.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
generate_from_prior <- function(number_of_particles = 1000,
^
```
[R/generate_from_prior.R:24:5:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/generate_from_prior.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(emp_tree)) {
    ^
```
[R/generate_from_prior.R:27:5:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/generate_from_prior.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(crown_age)) {
    ^
```
[R/generate_naive.R:13:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/generate_naive.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
generate_naive <- function(number_of_particles = 1000,
^
```
[R/generate_naive.R:22:5:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/generate_naive.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(emp_tree)) {
    ^
```
[R/generate_naive.R:25:5:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/generate_naive.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(crown_age)) {
    ^
```
[R/infer_params.R:16:16:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/infer_params.R#L16) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
  emp_stats <- calc_sum_stats(emp_tree, emp_tree)
               ^~~~~~~~~~~~~~
```
[R/infer_params.R:19:44:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/infer_params.R#L19) *warning:* **no visible binding for global variable ‘param_from_prior’**
```r
  previous_par <- t(apply(param_matrix, 1, param_from_prior))
                                           ^~~~~~~~~~~~~~~~
```
[R/infer_params.R:74:44:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/infer_params.R#L74) *warning:* **no visible binding for global variable ‘calc_fit’**
```r
        local_fit <- apply(stat_matrix, 1, calc_fit, emp_stats)
                                           ^~~~~~~~
```
[R/infer_params.R:76:22:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/infer_params.R#L76) *warning:* **no visible global function definition for ‘calc_fit’**
```r
        local_fit <- calc_fit(stat_matrix, emp_stats)
                     ^~~~~~~~
```
[R/infer_params.R:102:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/infer_params.R#L102) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
get_next_par <- function(number_of_particles = 1000,
^
```
[R/is_within_prior.R:5:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/is_within_prior.R#L5) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
is_within_prior <- function(params) {
^
```
[R/read_reference_table.R:1:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/read_reference_table.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' collect reference table based on previously generated reference tables for each model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:8:6:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/read_reference_table.R#L8) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in 1:3) {
     ^
```
[R/read_reference_table.R:18:3:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/read_reference_table.R#L18) *warning:* **local variable ‘focal_models’ assigned but may not be used**
```r
  focal_models <- as.factor(reference_table$model)
  ^~~~~~~~~~~~
```
[R/read_reference_table.R:24:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/read_reference_table.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
  ref_table <- dplyr::select(reference_table, c("nltt", "gamma", "mbr", "num_lin",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:25:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/read_reference_table.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
                                         "beta", "colless", "sackin", "ladder", "cherries", "ILnumber",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:27:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/read_reference_table.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
                                         "spectr_eigen", "spectr_asymmetry", "spectr_peakedness"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:16:20:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/sim_envidiv_tree.R#L16) *warning:* **no visible global function definition for ‘generate_water’**
```r
  water_changes <- generate_water(params[6], crown_age)
                   ^~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:23:1:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/R/sim_envidiv_tree.R#L23) *style:* **functions should have cyclomatic complexity of less than 15, this has 32.**
```r
sim_envidiv_tree <- function(params,
^
```
[tests/testthat/test-generate_naive.R:9:5:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/tests/testthat/test-generate_naive.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(1 == 2) {
    ^
```
[tests/testthat/test-infer_params.R:37:6:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/tests/testthat/test-infer_params.R#L37) *style:* **Commented code should be removed.**
```r
  #  future::plan(future::multiprocess())
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:47:6:](https://github.com/thijsjanzen/enviDiv/blob/ca0319aa6ebecdcab7b8be8ff3a45cec3c4f5f0b/tests/testthat/test-infer_params.R#L47) *style:* **Commented code should be removed.**
```r
  #  testthat::expect_equal(mean(do_smc$sym_high), birth_rate, tolerance = 0.1)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://labulaka521githubio-ntucn361j.now.sh
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'DWT' was not declared in this scope...


Nice job :)


Thanks for this - I've bumped up the version to v6, we'll have to do another release.


Successfully deployed to following URLs:

* https://labulaka521githubio-p5zh8hg9w.now.sh
* https://labulaka521githubio.labulakalia.now.sh
* https://labulaka521githubio-git-master.labulakalia.now.sh


Smart work .Good information to the new comer and also for the old users.


это глава 1, №3


Successfully deployed to following URLs:

* https://labulaka521githubio-pvxyxnyd8.now.sh
* https://labulaka521githubio.labulakalia.now.sh
* https://labulaka521githubio-git-master.labulakalia.now.sh


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://labulaka521githubio-koasga78v.now.sh
* https://labulaka521githubio.labulakalia.now.sh
* https://labulaka521githubio-git-master.labulakalia.now.sh


[R/calc_sum_stats.R:69:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/calc_sum_stats.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
  output[10] <- phyloTop::ILnumber(focal_tree) # number of internal nodes with a single child
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_reference_table.R:35:8:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/create_reference_table.R#L35) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(focal_model in 1:3) {
       ^
```
[R/create_reference_table.R:48:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/create_reference_table.R#L48) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:49:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/create_reference_table.R#L49) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:50:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/create_reference_table.R#L50) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:51:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/create_reference_table.R#L51) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/generate_from_prior.R:14:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/generate_from_prior.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
generate_from_prior <- function(number_of_particles = 1000,
^
```
[R/generate_from_prior.R:24:5:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/generate_from_prior.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(emp_tree)) {
    ^
```
[R/generate_from_prior.R:27:5:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/generate_from_prior.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(crown_age)) {
    ^
```
[R/generate_naive.R:13:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/generate_naive.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
generate_naive <- function(number_of_particles = 1000,
^
```
[R/generate_naive.R:22:5:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/generate_naive.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(emp_tree)) {
    ^
```
[R/generate_naive.R:25:5:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/generate_naive.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(crown_age)) {
    ^
```
[R/infer_params.R:16:16:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/infer_params.R#L16) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
  emp_stats <- calc_sum_stats(emp_tree, emp_tree)
               ^~~~~~~~~~~~~~
```
[R/infer_params.R:19:44:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/infer_params.R#L19) *warning:* **no visible binding for global variable ‘param_from_prior’**
```r
  previous_par <- t(apply(param_matrix, 1, param_from_prior))
                                           ^~~~~~~~~~~~~~~~
```
[R/infer_params.R:74:44:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/infer_params.R#L74) *warning:* **no visible binding for global variable ‘calc_fit’**
```r
        local_fit <- apply(stat_matrix, 1, calc_fit, emp_stats)
                                           ^~~~~~~~
```
[R/infer_params.R:76:22:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/infer_params.R#L76) *warning:* **no visible global function definition for ‘calc_fit’**
```r
        local_fit <- calc_fit(stat_matrix, emp_stats)
                     ^~~~~~~~
```
[R/infer_params.R:102:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/infer_params.R#L102) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
get_next_par <- function(number_of_particles = 1000,
^
```
[R/is_within_prior.R:5:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/is_within_prior.R#L5) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
is_within_prior <- function(params) {
^
```
[R/read_reference_table.R:1:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/read_reference_table.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' collect reference table based on previously generated reference tables for each model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:8:6:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/read_reference_table.R#L8) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in 1:3) {
     ^
```
[R/read_reference_table.R:25:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/read_reference_table.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
  ref_table <- dplyr::select(reference_table, c("nltt", "gamma", "mbr", "num_lin",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:26:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/read_reference_table.R#L26) *style:* **Lines should not be more than 80 characters.**
```r
                                         "beta", "colless", "sackin", "ladder", "cherries", "ILnumber",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:28:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/read_reference_table.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
                                         "spectr_eigen", "spectr_asymmetry", "spectr_peakedness"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:16:20:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/sim_envidiv_tree.R#L16) *warning:* **no visible global function definition for ‘generate_water’**
```r
  water_changes <- generate_water(params[6], crown_age)
                   ^~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:23:1:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/R/sim_envidiv_tree.R#L23) *style:* **functions should have cyclomatic complexity of less than 15, this has 32.**
```r
sim_envidiv_tree <- function(params,
^
```
[tests/testthat/test-generate_naive.R:9:5:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/tests/testthat/test-generate_naive.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(1 == 2) {
    ^
```
[tests/testthat/test-infer_params.R:37:6:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/tests/testthat/test-infer_params.R#L37) *style:* **Commented code should be removed.**
```r
  #  future::plan(future::multiprocess())
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:47:6:](https://github.com/thijsjanzen/enviDiv/blob/3e1eb6679a3ec66ad8099a7ba9f72f4f9c38004a/tests/testthat/test-infer_params.R#L47) *style:* **Commented code should be removed.**
```r
  #  testthat::expect_equal(mean(do_smc$sym_high), birth_rate, tolerance = 0.1)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Лабораторная 1 зачтена.
Для справки: чтобы не писать такие длинные списки каждый раз, то можно обозначить список 1 раз какой-нибудь константой через defconstant, но сейчас это не критично.