[inst/examples/example_distanceFromEachPoint.R:37:2:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/inst/examples/example_distanceFromEachPoint.R#L37) *style:* **Commented code should be removed.**
```r
#beginCluster(3) # can do parallel
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/examples/example_distanceFromEachPoint.R:40:2:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/inst/examples/example_distanceFromEachPoint.R#L40) *style:* **Commented code should be removed.**
```r
#endCluster() # if beginCluster was run
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:192:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L192) *style:* **Variable or function name should be lowerCamelCase.**
```r
      results.df <- out %>%
      ^~~~~~~~~~
```
[R/downloadData.R:197:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L197) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        {
        ^
```
[R/downloadData.R:205:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L205) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        {
        ^
```
[R/downloadData.R:248:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L248) *style:* **Lines should not be more than 100 characters.**
```r
appendChecksumsTable <- function(checkSumFilePath, filesToChecksum, destinationPath, append = TRUE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:249:15:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L249) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (append) {# needChecksums == 2) { # a checksums file already existed, need to keep some of it
              ^
```
[R/downloadData.R:251:30:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L251) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (is(cs, "try-error")) { # meant that it was an empty CHECKSUMS.txt file -- rebuild it
                             ^
```
[R/downloadData.R:260:15:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L260) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (append) { # a checksums file already existed, need to keep some of it
              ^
```
[R/downloadData.R:388:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L388) *style:* **Lines should not be more than 100 characters.**
```r
  definition = function(module, path, quiet, quickCheck, overwrite, files, checked, urls, children) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:393:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L393) *style:* **Commented code should be removed.**
```r
    # urls <- inputs$sourceURL
      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:400:8:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L400) *style:* **Commented code should be removed.**
```r
      #urls <- moduleMetadata(module, path)$inputObjects$sourceURL
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:404:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L404) *style:* **Variable or function name should be lowerCamelCase.**
```r
    to.dl <- if (length(ids)) urls[-ids] else urls
    ^~~~~
```
[R/downloadData.R:412:46:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L412) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    dataDir <- file.path(path, module, "data" )
                                             ^
```
[R/downloadData.R:427:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L427) *style:* **Variable or function name should be lowerCamelCase.**
```r
      to.dl <- to.dl[fileMatching]
      ^~~~~
```
[R/downloadData.R:432:12:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L432) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if (! ( NROW(chksums) > 0 && all(compareNA(chksums$result, "OK")))) {
           ^
```
[R/downloadData.R:446:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L446) *style:* **Commented code should be removed.**
```r
        #   out <- readline(prompt = "Would you like to download it now anyway? (Y)es or (N)o: ")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:448:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L448) *style:* **Commented code should be removed.**
```r
        #   out = "No"
            ^~~~~~~~~~
```
[R/downloadData.R:450:49:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L450) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if (!isTRUE(any(pmatch("Y", toupper(out) )))) {
                                                ^
```
[R/downloadData.R:493:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L493) *style:* **Lines should not be more than 100 characters.**
```r
                                    paste(chksums$expectedFile[id], collapse = ",\n      "), sep = ""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:559:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L559) *style:* **Lines should not be more than 100 characters.**
```r
        #   readline("If download was successful, would you like to run a new checksums? (Y)es or (N)o: ")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:559:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L559) *style:* **Commented code should be removed.**
```r
        #   readline("If download was successful, would you like to run a new checksums? (Y)es or (N)o: ")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:561:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L561) *style:* **Commented code should be removed.**
```r
        #   out = "No"
            ^~~~~~~~~~
```
[R/downloadData.R:572:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L572) *style:* **Commented code should be removed.**
```r
          # files = file.path(destinationPath, filesToChecksum)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:573:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L573) *style:* **Commented code should be removed.**
```r
          # checksums(module = module, path = path, write = TRUE)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:589:37:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L589) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
             !(chksums$actualFile %>% is.na() )) %>%
                                  ~~^
```
[R/downloadData.R:589:46:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L589) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
             !(chksums$actualFile %>% is.na() )) %>%
                                             ^
```
[R/downloadData.R:593:46:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L593) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if (!is.na(chksums$expectedFile[id])  ) {
                                             ^
```
[R/downloadData.R:606:27:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L606) *style:* **Commas should always have a space after.**
```r
    chksums2 <- chksums[0,]
                          ^
```
[R/downloadData.R:607:6:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L607) *style:* **Commented code should be removed.**
```r
    #children <- moduleMetadata(module, path)$childModules
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/downloadData.R:610:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L610) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( all( nzchar(children) & !is.na(children) ) ) {
            ^
```
[R/downloadData.R:610:18:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L610) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( all( nzchar(children) & !is.na(children) ) ) {
                 ^
```
[R/downloadData.R:610:54:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L610) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( all( nzchar(children) & !is.na(children) ) ) {
                                                     ^
```
[R/downloadData.R:610:56:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/downloadData.R#L610) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( all( nzchar(children) & !is.na(children) ) ) {
                                                       ^
```
[R/gis.R:307:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/gis.R#L307) *style:* **Lines should not be more than 100 characters.**
```r
      # write the polygon object to disk as a shapefile -- can't handle NAs without showing a warning
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:82:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L82) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( method != "RMexp") {
        ^
```
[R/initialize.R:242:3:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L242) *style:* **Variable or function name should be lowerCamelCase.**
```r
  X <- c(jitter(sort(rbeta(nPoints, betaPar, betaPar) * (maxX - minX) + minX)),
  ^
```
[R/initialize.R:244:3:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L244) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Y <- c(jitter(sort(rbeta(nPoints / 2, betaPar, betaPar) * (maxY - meanY) + meanY)),
  ^
```
[R/initialize.R:248:3:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L248) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Sr1 <- Polygon(cbind(X + xAdd, Y + yAdd))
  ^~~
```
[R/initialize.R:249:3:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L249) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Srs1 <- Polygons(list(Sr1), "s1")
  ^~~~
```
[R/initialize.R:346:3:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L346) *style:* **Commented code should be removed.**
```r
# ### INCORPORATE RELEVANT PARTS OF THIS OLD INIT FUNCTION INTO INITCOORDS()
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:351:3:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L351) *style:* **Commented code should be removed.**
```r
# #'                      (currently only \code{RasterLayer} or
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:352:3:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L352) *style:* **Commented code should be removed.**
```r
# #'                      \code{SpatialPolygonsDataFrame}) accepted.
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:362:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L362) *style:* **Commented code should be removed.**
```r
#     ext <- extent(agentlocation)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:364:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L364) *style:* **Commented code should be removed.**
```r
#       #            nonNAs <- !is.na(getvalue(probinit))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:365:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L365) *style:* **Commented code should be removed.**
```r
#       nonNAs <- !is.na(getValues(probinit))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:366:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L366) *style:* **Commented code should be removed.**
```r
#       wh.nonNAs <- which(nonNAs)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:367:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L367) *style:* **Commented code should be removed.**
```r
#       #            ProbInit.v <- cumsum(getvalue(probinit)[nonNAs])
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:368:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L368) *style:* **Commented code should be removed.**
```r
#       ProbInit.v <- cumsum(getValues(probinit)[nonNAs])
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:370:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L370) *style:* **Commented code should be removed.**
```r
#         ran <- runif(numagents,0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:371:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L371) *style:* **Commented code should be removed.**
```r
#         fI <- findInterval(ran, ProbInit.v)+1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:372:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L372) *style:* **Commented code should be removed.**
```r
#         fI2 <- wh.nonNAs[fI]
          ^~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:373:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L373) *style:* **Commented code should be removed.**
```r
#         last.ran <- runif(numagents,0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:374:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L374) *style:* **Commented code should be removed.**
```r
#         last.fI <- findInterval(last.ran, ProbInit.v)+1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:375:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L375) *style:* **Commented code should be removed.**
```r
#         last.fI2 <- wh.nonNAs[last.fI]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:377:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L377) *style:* **Commented code should be removed.**
```r
#         #                va <- getvalue(probinit)[nonNAs]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:378:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L378) *style:* **Commented code should be removed.**
```r
#         va <- getValues(probinit)[nonNAs]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:379:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L379) *style:* **Commented code should be removed.**
```r
#         ran <- runif(length(va), 0, 1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:380:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L380) *style:* **Commented code should be removed.**
```r
#         fI2 <- wh.nonNAs[ran<va]
          ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:382:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L382) *style:* **Commented code should be removed.**
```r
#         last.ran <- runif(length(fI2), 0, 1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:383:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L383) *style:* **Commented code should be removed.**
```r
#         last.fI <- findInterval(last.ran, ProbInit.v) + 1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:384:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L384) *style:* **Commented code should be removed.**
```r
#         last.fI2 <- wh.nonNAs[last.fI]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:386:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L386) *style:* **Commented code should be removed.**
```r
#         #                last.ran <- runif(length(fI2),0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:387:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L387) *style:* **Commented code should be removed.**
```r
#         #                last.fI2 <- wh.nonNAs[last.ran<va]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:390:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L390) *style:* **Commented code should be removed.**
```r
#         position <- xyFromCell(agentlocation,fI2,spatial = TRUE)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:392:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L392) *style:* **Commented code should be removed.**
```r
#         position <- coordinates(agentlocation)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:394:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L394) *style:* **Commented code should be removed.**
```r
#         stop("need raster layer or Spatial Points object")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:396:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L396) *style:* **Commented code should be removed.**
```r
#       numagents <- length(position)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:404:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L404) *style:* **Commented code should be removed.**
```r
#           colnames(xy) = c("x", "y")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:405:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L405) *style:* **Commented code should be removed.**
```r
#           position <- SpatialPoints(xy)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:406:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L406) *style:* **Commented code should be removed.**
```r
#           position <- SpatialPoints(sampleRandom(agentlocation, numagents, xy = TRUE, sp = TRUE))
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:408:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L408) *style:* **Commented code should be removed.**
```r
#           sam <- sample(1:length(agentlocation),numagents)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:409:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L409) *style:* **Commented code should be removed.**
```r
#           position <- SpatialPoints(agentlocation[sam,])
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:411:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L411) *style:* **Commented code should be removed.**
```r
#           stop("need raster layer or Spatial Points object")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:418:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L418) *style:* **Commented code should be removed.**
```r
#           position <- SpatialPoints(agentlocation)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:420:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L420) *style:* **Commented code should be removed.**
```r
#           stop("need raster layer or Spatial Points object")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:422:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L422) *style:* **Commented code should be removed.**
```r
#         numagents <- length(position)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:430:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L430) *style:* **Commented code should be removed.**
```r
#         numagents <- length(position)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:434:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L434) *style:* **Commented code should be removed.**
```r
#     stop("Need to provide agentlocation, which can be a map layer")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:436:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L436) *style:* **Commented code should be removed.**
```r
#   heading1 <- runif(numagents, 0, 360)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:437:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L437) *style:* **Commented code should be removed.**
```r
#   distance <- runif(numagents, 0.1, 10)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:439:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L439) *style:* **Commented code should be removed.**
```r
#   .Object@ID <- as.character(1:numagents)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:440:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L440) *style:* **Commented code should be removed.**
```r
#   .Object@spatial <- position
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:441:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L441) *style:* **Commented code should be removed.**
```r
#   .Object@heading <- heading1
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:442:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L442) *style:* **Commented code should be removed.**
```r
#   .Object@distance <- distance
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialize.R:444:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/initialize.R#L444) *style:* **Commented code should be removed.**
```r
#   return(.Object)
    ^~~~~~~~~~~~~~~
```
[R/mapReduce.R:53:3:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/mapReduce.R#L53) *style:* **Variable or function name should be lowerCamelCase.**
```r
  BsumVec <- reduced[fullRasterVals] # join
  ^~~~~~~
```
[R/neighbourhood.R:112:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L112) *style:* **Variable or function name should be lowerCamelCase.**
```r
adj.raw <- function(x = NULL, cells, directions = 8, sort = FALSE, pairs = TRUE,
^~~~~~~
```
[R/neighbourhood.R:114:21:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L114) *style:* **Variable or function name should be lowerCamelCase.**
```r
                    match.adjacent = FALSE, cutoff.for.data.table = 2e3,
                    ^~~~~~~~~~~~~~
```
[R/neighbourhood.R:114:45:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L114) *style:* **Variable or function name should be lowerCamelCase.**
```r
                    match.adjacent = FALSE, cutoff.for.data.table = 2e3,
                                            ^~~~~~~~~~~~~~~~~~~~~
```
[R/neighbourhood.R:233:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L233) *style:* **Lines should not be more than 100 characters.**
```r
              ((adj[, "from"] %% numCol + adj[, "to"] %% numCol) == 1)) # | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/neighbourhood.R:238:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L238) *style:* **Lines should not be more than 100 characters.**
```r
              ((adj[, "from"] %% numCol + adj[, "to"] %% numCol) == 1)) # | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/neighbourhood.R:297:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L297) *style:* **Lines should not be more than 100 characters.**
```r
              ((from %% numCol + to %% numCol) == 1))# | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/neighbourhood.R:813:29:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L813) *style:* **Variable or function name should be lowerCamelCase.**
```r
setGeneric("wrap", function(X, bounds, withHeading) {
                            ^
```
[R/neighbourhood.R:822:25:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L822) *style:* **Variable or function name should be lowerCamelCase.**
```r
  definition = function(X, bounds) {
                        ^
```
[R/neighbourhood.R:839:25:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L839) *style:* **Variable or function name should be lowerCamelCase.**
```r
  definition = function(X, bounds) {
                        ^
```
[R/neighbourhood.R:849:25:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L849) *style:* **Variable or function name should be lowerCamelCase.**
```r
  definition = function(X, bounds) {
                        ^
```
[R/neighbourhood.R:850:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L850) *style:* **Variable or function name should be lowerCamelCase.**
```r
    X <- wrap(X, bounds = extent(bounds))
    ^
```
[R/neighbourhood.R:859:25:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L859) *style:* **Variable or function name should be lowerCamelCase.**
```r
  definition = function(X, bounds) {
                        ^
```
[R/neighbourhood.R:860:5:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L860) *style:* **Variable or function name should be lowerCamelCase.**
```r
    X <- wrap(X, bounds = extent(bounds))
    ^
```
[R/neighbourhood.R:869:25:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L869) *style:* **Variable or function name should be lowerCamelCase.**
```r
  definition = function(X, bounds) {
                        ^
```
[R/neighbourhood.R:872:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L872) *style:* **Variable or function name should be lowerCamelCase.**
```r
      X <- wrap(X, bounds = extent(bounds))
      ^
```
[R/neighbourhood.R:884:25:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L884) *style:* **Variable or function name should be lowerCamelCase.**
```r
  definition = function(X, bounds, withHeading) {
                        ^
```
[R/neighbourhood.R:909:25:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L909) *style:* **Variable or function name should be lowerCamelCase.**
```r
  definition = function(X, bounds, withHeading) {
                        ^
```
[R/neighbourhood.R:910:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L910) *style:* **Variable or function name should be lowerCamelCase.**
```r
      X <- wrap(X, bounds = extent(bounds), withHeading = withHeading)
      ^
```
[R/neighbourhood.R:919:25:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L919) *style:* **Variable or function name should be lowerCamelCase.**
```r
  definition = function(X, bounds, withHeading) {
                        ^
```
[R/neighbourhood.R:922:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L922) *style:* **Variable or function name should be lowerCamelCase.**
```r
      X <- wrap(X, bounds = extent(bounds), withHeading = withHeading)
      ^
```
[R/neighbourhood.R:1059:40:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/neighbourhood.R#L1059) *style:* **Commas should always have a space after.**
```r
  cc <- cbind(pureCircle2[, "x"] - xy[,"x"], pureCircle2[, "y"] - xy[, "y"])
                                       ^
```
[R/prepInputs.R:294:21:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L294) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (is.null(url)) { # the only way for this to be useful is if there is a SpaDES module
                    ^
```
[R/prepInputs.R:320:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L320) *style:* **Lines should not be more than 100 characters.**
```r
    checkSums <- try(checksums(path = destinationPath, write = FALSE)#, checksumFile = checkSumFilePath)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:332:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L332) *style:* **Lines should not be more than 100 characters.**
```r
                                     destinationPath, quick, checkSums, url, needChecksums = needChecksums,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:333:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L333) *style:* **Lines should not be more than 100 characters.**
```r
                                     overwrite = overwrite, moduleName = moduleName, modulePath = modulePath)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:345:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L345) *style:* **Commented code should be removed.**
```r
      #   cs <- try(read.table(checkSumFilePath, header = TRUE), silent = TRUE)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:347:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L347) *style:* **Commented code should be removed.**
```r
      #     needChecksums <- 1
            ^~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:350:15:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L350) *style:* **Commented code should be removed.**
```r
      #       filter(!file %in% filesToChecksum)
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:353:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L353) *style:* **Lines should not be more than 100 characters.**
```r
      # currentFiles <- checksums(path = destinationPath, write = TRUE, #checksumFile = checkSumFilePath,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:356:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L356) *style:* **Commented code should be removed.**
```r
      #   currentFiles <- rbind(nonCurrentFiles, currentFiles)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:357:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L357) *style:* **Commented code should be removed.**
```r
      #   writeChecksumsTable(currentFiles, checkSumFilePath, dots = list())
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:394:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L394) *style:* **Lines should not be more than 100 characters.**
```r
  # dots will contain too many things for some functions -- need to remove those that are known going
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:408:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L408) *style:* **Lines should not be more than 100 characters.**
```r
    # Don't cache the reading of a raster -- normal reading of raster on disk is fast b/c only reads metadata
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:448:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L448) *style:* **Variable or function name should be lowerCamelCase.**
```r
fixErrors.default <- function(x, objectName, attemptErrorFixes = TRUE,
^~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:461:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L461) *style:* **Variable or function name should be lowerCamelCase.**
```r
fixErrors.SpatialPolygons <- function(x, objectName = NULL,
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:465:41:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L465) *style:* **Use <-, not =, for assignment.**
```r
    if (is.null(objectName)) objectName = "SpatialPolygon"
                                        ^
```
[R/prepInputs.R:535:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L535) *style:* **Lines should not be more than 100 characters.**
```r
        filesInArchive <- filesInArchive[filesInArchive$Length != 0,]$Name # for zips, rm directories (length = 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:535:69:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L535) *style:* **Commas should always have a space after.**
```r
        filesInArchive <- filesInArchive[filesInArchive$Length != 0,]$Name # for zips, rm directories (length = 0)
                                                                    ^
```
[R/prepInputs.R:543:30:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L543) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          NROW(result) == 0) { # don't extract if we already have all files and they are fine
                             ^
```
[R/prepInputs.R:544:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L544) *style:* **Lines should not be more than 100 characters.**
```r
        if (needChecksums == 0) needChecksums <- 2 # use binary addition -- 1 is new file, 2 is append
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:548:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L548) *style:* **Lines should not be more than 100 characters.**
```r
                              .unzipOrUnTar(funWArgs$fun, funWArgs$args, files = basename(archive[2])))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:551:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L551) *style:* **Lines should not be more than 100 characters.**
```r
                                              neededFiles = neededFiles, extractedArchives = extractedArchives,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:552:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L552) *style:* **Lines should not be more than 100 characters.**
```r
                                              checkSums, needChecksums, filesExtracted = filesExtracted)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:554:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L554) *style:* **Lines should not be more than 100 characters.**
```r
          extractingTheseFiles <- paste(basename(filesInArchive[basename(filesInArchive) %in% neededFiles]),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:557:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L557) *style:* **Lines should not be more than 100 characters.**
```r
            extractingTheseFiles <- paste0("all files: ", paste(basename(filesInArchive), collapse = ", "))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:561:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L561) *style:* **Lines should not be more than 100 characters.**
```r
                                            files = filesInArchive[basename(filesInArchive) %in% neededFiles]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:579:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L579) *style:* **Lines should not be more than 100 characters.**
```r
                                     neededFiles = neededFiles, extractedArchives = extractedArchives,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:588:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L588) *style:* **Lines should not be more than 100 characters.**
```r
        filesExtracted <- checkSums[checkSums$expectedFile %in% basename(filesInArchive), ]$expectedFile
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:611:4:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L611) *style:* **Commented code should be removed.**
```r
  #filesExtracted <- dir(destinationPath)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:615:21:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L615) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (is.null(fun)) { #i.e., the default
                    ^
```
[R/prepInputs.R:616:9:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L616) *style:* **Put spaces around all infix operators.**
```r
    fun <-if (any(isShapefile)) {
        ^~~
```
[R/prepInputs.R:636:61:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L636) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    targetFilePath <- if (endsWith(suffix = "shapefile", fun )) {
                                                            ^
```
[R/prepInputs.R:679:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L679) *style:* **Variable or function name should be lowerCamelCase.**
```r
postProcess.default <- function(x, ...) {
^~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:777:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L777) *style:* **Variable or function name should be lowerCamelCase.**
```r
postProcess.spatialObjects <- function(x, inputFilePath = NULL,
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:830:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L830) *style:* **Lines should not be more than 100 characters.**
```r
      mess <- capture.output(type = "message", # no Cache at the method level because may be just passed through if raster
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:861:82:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L861) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      x <- writeOutputs(x = x, filename = newFilename, overwrite = overwrite, ... )
                                                                                ^
```
[R/prepInputs.R:900:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L900) *style:* **Variable or function name should be lowerCamelCase.**
```r
cropInputs.default <- function(x, studyArea, rasterToMatch, ...) {
^~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:913:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L913) *style:* **Variable or function name should be lowerCamelCase.**
```r
cropInputs.spatialObjects <- function(x, studyArea, rasterToMatch = NULL, extentToMatch = NULL,
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:978:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L978) *style:* **Variable or function name should be lowerCamelCase.**
```r
projectInputs.Raster <- function(x, targetCRS = NULL, rasterToMatch = NULL, ...) {
^~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1000:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1000) *style:* **Variable or function name should be lowerCamelCase.**
```r
projectInputs.sf <- function(x, targetCRS, ...) {
^~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1015:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1015) *style:* **Variable or function name should be lowerCamelCase.**
```r
projectInputs.Spatial <- function(x, targetCRS, ...) {
^~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1063:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1063) *style:* **Variable or function name should be lowerCamelCase.**
```r
maskInputs.Raster <- function(x, studyArea, rasterToMatch, maskWithRTM = FALSE, ...) {
^~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1082:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1082) *style:* **Variable or function name should be lowerCamelCase.**
```r
maskInputs.Spatial <- function(x, studyArea, ...) {
^~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1119:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1119) *style:* **Lines should not be more than 100 characters.**
```r
#' @param destinationPath Optional. If \code{postProcessedFilename} is a relative file path, then this
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1149:64:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1149) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  newFilename <- if (!identical(postProcessedFilename, FALSE)) { # allow TRUE or path
                                                               ^
```
[R/prepInputs.R:1150:38:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1150) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if (isTRUE(postProcessedFilename) ) {
                                     ^
```
[R/prepInputs.R:1193:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1193) *style:* **Variable or function name should be lowerCamelCase.**
```r
writeOutputs.Raster <- function(x, filename, overwrite = FALSE, ...) {
^~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1198:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1198) *style:* **Lines should not be more than 100 characters.**
```r
    # +proj=lcc +lat_1=49 +lat_2=77 +lat_0=0 +lon_0=-95 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1200:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1200) *style:* **Lines should not be more than 100 characters.**
```r
    # +proj=lcc +lat_1=49 +lat_2=77 +lat_0=0 +lon_0=-95 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1209:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1209) *style:* **Variable or function name should be lowerCamelCase.**
```r
writeOutputs.Spatial <- function(x, filename, overwrite = FALSE, ...) {
^~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1216:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1216) *style:* **Variable or function name should be lowerCamelCase.**
```r
writeOutputs.sf <- function(x, filename, overwrite = FALSE, ...) {
^~~~~~~~~~~~~~~
```
[R/prepInputs.R:1227:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1227) *style:* **Variable or function name should be lowerCamelCase.**
```r
writeOutputs.default <- function(x, filename, ...) {
^~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1278:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1278) *style:* **Use <-, not =, for assignment.**
```r
  archive = if (file_ext(filename) %in% c("zip", "tar")) {
          ^
```
[R/prepInputs.R:1300:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1300) *style:* **Lines should not be more than 100 characters.**
```r
                         checkSums, url, needChecksums, overwrite = TRUE, moduleName, modulePath, ...) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1303:43:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1303) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if ("shp" %in% file_ext(neededFiles)) { # if user wants .shp file, needs other anciliary files
                                          ^
```
[R/prepInputs.R:1323:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1323) *style:* **Lines should not be more than 100 characters.**
```r
  missingNeededFiles <- (!(all(compareNA(result, "OK")) && all(neededFiles %in% checkSums$expectedFile)) ||
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1344:31:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1344) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (!is.null(moduleName)) { # means it is inside a SpaDES module
                              ^
```
[R/prepInputs.R:1346:91:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1346) *style:* **Only use double-quotes.**
```r
        parsedModule <- parse(file = file.path(modulePath, moduleName, paste0(moduleName, '.R')))
                                                                                ^~~~
```
[R/prepInputs.R:1354:35:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1354) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if (!is.null(fileToDownload) ) {#|| is.null(targetFile)) {
                                  ^
```
[R/prepInputs.R:1354:38:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1354) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (!is.null(fileToDownload) ) {#|| is.null(targetFile)) {
                                     ^
```
[R/prepInputs.R:1374:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1374) *style:* **Lines should not be more than 100 characters.**
```r
            if (!isTRUE(checkSums[ checkSums$expectedFile ==  basename(destFile), ]$result == "OK")) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputs.R:1374:35:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/prepInputs.R#L1374) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            if (!isTRUE(checkSums[ checkSums$expectedFile ==  basename(destFile), ]$result == "OK")) {
                                  ^
```
[R/RcppExports.R:68:20:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/RcppExports.R#L68) *style:* **Variable or function name should be lowerCamelCase.**
```r
runifC <- function(N) {
                   ^
```
[R/RcppExports.R:71:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/RcppExports.R#L71) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/SELES.R:53:23:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/SELES.R#L53) *style:* **Variable or function name should be lowerCamelCase.**
```r
numAgents <- function(N, probInit) {
                      ^
```
[R/splitRaster.R:51:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/splitRaster.R#L51) *style:* **Lines should not be more than 100 characters.**
```r
  function(r, nx = 1, ny = 1, buffer = c(0, 0), path = file.path(getwd(), names(r)), cl, rType = "FLT4S") {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/splitRaster.R:111:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/splitRaster.R#L111) *style:* **Lines should not be more than 100 characters.**
```r
      clusterApplyLB(cl = cl, x = seq_along(extents), fun = croppy, e = extents, r = r, path = path, rType = rType)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread.R:538:8:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread.R#L538) *style:* **Commented code should be removed.**
```r
      #isNASpreadProb <- is.na(spreadProb[])
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread.R:540:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread.R#L540) *style:* **Commented code should be removed.**
```r
      #   isNASpreadProb <- is.na(spreadProb[])
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread.R:541:11:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread.R#L541) *style:* **Commented code should be removed.**
```r
      #   spreadProb[isNASpreadProb] <- 0L
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread.R:942:41:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread.R#L942) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              notDupsEvents <- notDups[-(1:(nrSpreads - nrPotentials))]
                                        ^
```
[R/spread2.R:5:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L5) *style:* **Lines should not be more than 100 characters.**
```r
                           "quantityAdj", "quantityAdj2", "state", "size", "tooBigByNCells", "V1", "proportion"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:674:12:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L674) *style:* **Commented code should be removed.**
```r
          #pureCircle <- unique(pureCircle)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:759:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L759) *style:* **Commented code should be removed.**
```r
          # colnamesDtPot <- colnames(dtPotential)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:760:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L760) *style:* **Commented code should be removed.**
```r
          # ll <-  lapply(colnamesDtPot, function(x) dtPotential[[x]][!spreadProbNA])
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:761:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L761) *style:* **Commented code should be removed.**
```r
          # names(ll) <- colnamesDtPot
            ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:762:13:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L762) *style:* **Commented code should be removed.**
```r
          # dtPotential <- as.data.table(ll)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:772:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L772) *style:* **Lines should not be more than 100 characters.**
```r
                                                                   .I[sample.int(length(numNeighs), size = numNeighs, prob = spreadProbRel)],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:787:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L787) *style:* **Variable or function name should be lowerCamelCase.**
```r
      NAaSP <- !is.na(actualSpreadProb)
      ^~~~~
```
[R/spread2.R:789:42:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L789) *style:* **Commas should always have a space after.**
```r
        dtPotential <- dtPotential[NAaSP,]
                                         ^
```
[R/spread2.R:830:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L830) *style:* **Lines should not be more than 100 characters.**
```r
        # this is to prevent overlap within an event... in some cases, overlap within event is desired, so skip this block
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:848:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L848) *style:* **Lines should not be more than 100 characters.**
```r
        #successCells <- na.omit(successCells[!dupsWithinDtPotential]) # remove the dupsWithinDtPotential
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/spread2.R:848:10:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/spread2.R#L848) *style:* **Commented code should be removed.**
```r
        #successCells <- na.omit(successCells[!dupsWithinDtPotential]) # remove the dupsWithinDtPotential
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/webDatabases.R:122:1:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/webDatabases.R#L122) *style:* **Lines should not be more than 100 characters.**
```r
    stop("You must provide a data.table that contain the link between url, datasetName and password.")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/webDatabases.R:127:4:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/webDatabases.R#L127) *style:* **Commented code should be removed.**
```r
  #if (missing(dfile)) dfile <- "all"
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/webDatabases.R:141:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/webDatabases.R#L141) *style:* **Variable or function name should be lowerCamelCase.**
```r
      file.list <- getURL(url2data, ftp.use.epsv = FALSE, dirlistonly = TRUE)
      ^~~~~~~~~
```
[R/webDatabases.R:142:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/webDatabases.R#L142) *style:* **Variable or function name should be lowerCamelCase.**
```r
      file.list <- strsplit(file.list, "\r*\n")[[1]]
      ^~~~~~~~~
```
[R/webDatabases.R:143:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/webDatabases.R#L143) *style:* **Variable or function name should be lowerCamelCase.**
```r
      file.list <- file.list[!file.list %in% c(".", "..")]
      ^~~~~~~~~
```
[R/webDatabases.R:144:7:](https://github.com/PredictiveEcology/SpaDES.tools/blob/42a88f6d890fb94c015a170362dd966357311b4a/R/webDatabases.R#L144) *style:* **Variable or function name should be lowerCamelCase.**
```r
      file.list <- paste(url2data, file.list, sep = "")
      ^~~~~~~~~
```


@erezh51 The two branches are now synced. Your changes are merged onto the ```master``` branch now.


OK, let me check.


I wonder if this adds to the size of the bytecode. If not, then its fine


erer


Sure I'll take a look


Don't worry about this atm though. We could optimize later


remove autoFocus from Select InputGroup to fix scroll jumping

Preview: documentation | landing | table


New-Feature---Account-for-fan-heat-is-zone-cooling-coils (rraustad) - i386-Windows-7-VisualStudio-14: OK (2927 of 2927 tests passed, 0 test warnings)

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


### These comments are addressing your code changes for the pair programming lab - you still need to address the comments above as well

**app.js**
* `abductionGame ()`  Is it a game or a question?  Your function name is slightly misleading...  :)
* does the alert on line 7 belong in your first function?  It will only show up if you call that function but it doesn't really have anything to do with that question specifically.
* This is more of an overall observation: do you think you could make 1 function that would handle your first five questions?  This would make your code much DRYer and easier to read.  Think about how your five questions are similar (the things that could be abstracted into a function) and different (the things you might pass into a function as a parameter).

### remember to address both sets of comments  :)


Yeah my bad, I jumped the gun. Embarrassing.


Ah, good to know. Time for some refactoring!


These don't fit with our capitalization as used elsewhere including in the footer: we've got "System information," but "User Manual" and "Developer Documentation"

Also I'm not sure we want to link to developer documentation... the issue, or at least the animating comment, called for the manual and the forums.

@mebrett?


Do you play the drums? If not you should consider it :) haha!


@ibilon the "or version not installed" part was about trying to be as much backward compatible as possible. I agree this is not ideal but I fail to see how being more respectful of user explicitness makes haxelib worse.


Code chunk horizontal scroll bar will now only appear when needed.


Well **crap** -- that's not supposed to be here! :( Yeah, I had to put that in when developing because I was never on a system where the JVM name wasn't formatted "as expected." Well that's unfortunate - great eyes!


@rlorenzo Yes, I'll delete it.


Created multidev environment [dgreat#pr-nids](https://dashboard.pantheon.io/sites/41cad7fe-472d-43a9-a470-d391b9622376#pr-nids).

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WHAT THE FUCK IS THIS SHIT JGRAY


I think you'll probably need to work through the use of `stageId` / `stage` throughout the plugin; just changing this line isn't enough to get things going.


Thanks for catching that - I have pushed a fix. 1c23550bd32314528ab2eb84602c51f0b0b90388


Remind me, does VW currently support C++98? If so, should we opt to provide that as the default compilation instead of C++11 or higher?


Created multidev environment [dgreat#pr-tandem-o](https://dashboard.pantheon.io/sites/41cad7fe-472d-43a9-a470-d391b9622376#pr-tandem-o).

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The following doc(s) have been deployed to the [plat321ne](https://plat321ne-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/sftp](https://plat321ne-static-docs.pantheonsite.io/docs/sftp)


Thanks amit


Well you want to test a new lib from haxelib in a quick project, for its dependency it downloads the version you didn't have.
And suddenly without touching it, your main project which used a dev, suddenly doesn't work anymore.

It's not more respectful of user explicitness if you ignore it on non explicit conditions.
At least the previous behavior was simple, you have a dev set then it'll use that.

The real problem is that you can't mix well between versions from haxelib and dev sources,
it'd need something like allowing path in set, or a command like `haxelib add-local libname versionname path` so you could do `haxelib add-local heaps dev /path/to/clone` + `haxe -lib heaps:dev`.
Without the big problems, though sometimes useful, that comes with the global override of the current dev command.

And a new command/way of doing this wouldn't break the current use of people with dev version who upgrade their haxelib version.


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Created multidev environment [sfgov#pr-65](https://dashboard.pantheon.io/sites/91d50373-c4cf-40e4-a646-cb73e16a140c#pr-65).

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