[R/assertions.R:210:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/assertions.R#L210) *style:* **Lines should not be more than 100 characters.**
```r
      stop("2 or more species share the same label under the 'EN_generic_short' or 'Leading' columns of sim$sppEquiv.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assertions.R:214:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/assertions.R#L214) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/cohorts.R:47:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L47) *style:* **Lines should not be more than 100 characters.**
```r
#' @param treedFirePixelTableSinceLastDisp A data.table with at least 2 columns, \code{pixelIndex} and \code{pixelGroup}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:71:48:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L71) *style:* **Variable and function names should not be longer than 30 characters.**
```r
                             speciesEcoregion, treedFirePixelTableSinceLastDisp = NULL,
                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:92:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L92) *style:* **Lines should not be more than 100 characters.**
```r
      message(crayon::green("  Regenerating only open pixels (e.g., likely resprouting & serotiny only)"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:93:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L93) *style:* **Lines should not be more than 100 characters.**
```r
    columnsForPG <- c("ecoregionGroup", "speciesCode", "age") # no Biomass because they all have zero
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:94:31:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L94) *style:* **Commas should always have a space after.**
```r
    cd <- newPixelCohortData[,c("pixelIndex", columnsForPG), with = FALSE]
                              ^
```
[R/cohorts.R:122:30:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    allCohortData <- cohorts[ , .(ecoregionGroup = ecoregionGroup[1],
                             ^
```
[R/cohorts.R:122:31:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L122) *style:* **Commas should never have a space before.**
```r
    allCohortData <- cohorts[ , .(ecoregionGroup = ecoregionGroup[1],
                             ~^
```
[R/cohorts.R:145:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L145) *style:* **Commented code should be removed.**
```r
  # newPixelCohortData[, sumB := sum(B, na.rm = TRUE), by = pixelGroup]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:221:3:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L221) *style:* **Variable or function name should be lowerCamelCase.**
```r
  specieseco_current <- speciesEcoregionLatestYear(speciesEcoregion, time)
  ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:222:3:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L222) *style:* **Variable or function name should be lowerCamelCase.**
```r
  specieseco_current <- setkey(specieseco_current[, .(speciesCode, maxANPP, maxB, ecoregionGroup)],
  ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:227:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L227) *style:* **Lines should not be more than 100 characters.**
```r
  #missingNewPixelCohortData <- newPixelCohortData[!specieseco_current, on = uniqueSpeciesEcoregionDefinition]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:227:4:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L227) *style:* **Commented code should be removed.**
```r
  #missingNewPixelCohortData <- newPixelCohortData[!specieseco_current, on = uniqueSpeciesEcoregionDefinition]
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:228:3:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L228) *style:* **Variable or function name should be lowerCamelCase.**
```r
  specieseco_current <- specieseco_current[!is.na(maxB)]
  ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:229:24:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L229) *style:* **Variable or function name should be lowerCamelCase.**
```r
  specieseco_current[, maxB_eco := max(maxB), by = ecoregionGroup]
                       ^~~~~~~~
```
[R/cohorts.R:230:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L230) *style:* **Lines should not be more than 100 characters.**
```r
  newPixelCohortData <- specieseco_current[newPixelCohortData, on = uniqueSpeciesEcoregionDefinition]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:236:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L236) *style:* **Commented code should be removed.**
```r
  # set(newPixelCohortData, NULL, "sumB", 0L)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:243:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L243) *style:* **Lines should not be more than 100 characters.**
```r
  set(newPixelCohortData, which(is.na(newPixelCohortData$oldSumB)), "oldSumB", 0)   ## faster than [:=]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:248:26:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L248) *style:* **Variable or function name should be lowerCamelCase.**
```r
    newPixelCohortData[, B := NULL]
                         ^
```
[R/cohorts.R:252:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L252) *style:* **Lines should not be more than 100 characters.**
```r
  set(newPixelCohortData, NULL, "B", asInteger(pmin(newPixelCohortData$maxANPP, newPixelCohortData$B)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:258:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L258) *style:* **Lines should not be more than 100 characters.**
```r
    if (isTRUE(NROW(unique(newPixelCohortData, by = uniqueCohortDefinition)) != NROW(newPixelCohortData)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:263:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L263) *style:* **Commented code should be removed.**
```r
  # cohortData[, sumB := sum(B, na.rm = TRUE), by = "pixelGroup"]  ## recalculate sumB
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:265:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L265) *style:* **Commented code should be removed.**
```r
  #   set(cohortData, NULL, "sumB", asInteger(cohortData[["sumB"]]))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:295:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L295) *style:* **Lines should not be more than 100 characters.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:295:67:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L295) *style:* **Commas should always have a space after.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
                                                                  ^
```
[R/cohorts.R:295:70:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L295) *style:* **Commented code should be removed.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
                                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:296:4:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L296) *style:* **Commented code should be removed.**
```r
  #pgsStillInPGMGoneFromCD <- setdiff(unique(pgmVals$pixelGroup), unique(cohortData$pixelGroup))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:298:64:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L298) *style:* **Commas should always have a space after.**
```r
  pgsStillInPGMGoneFromCD <- pgmVals[whPgsStillInPGMGoneFromCD,]
                                                               ^
```
[R/cohorts.R:349:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L349) *style:* **Lines should not be more than 100 characters.**
```r
  # concatenate within rows -- e.g., ecoregionCode_speciesCode_age_biomass or 647_11_Abie_sp_100_2000
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:353:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L353) *style:* **Lines should not be more than 100 characters.**
```r
  pcd[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"), by = "pixelIndex"]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:353:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L353) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  pcd[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"), by = "pixelIndex"]
      ^
```
[R/cohorts.R:353:8:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L353) *style:* **Commas should never have a space before.**
```r
  pcd[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"), by = "pixelIndex"]
      ~^
```
[R/cohorts.R:354:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L354) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  pcd[ , c("pixelGroup") := as.integer(maxPixelGroup) + as.integer(factor(uniqueComboByPixelIndex))]
      ^
```
[R/cohorts.R:354:8:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L354) *style:* **Commas should never have a space before.**
```r
  pcd[ , c("pixelGroup") := as.integer(maxPixelGroup) + as.integer(factor(uniqueComboByPixelIndex))]
      ~^
```
[R/cohorts.R:356:38:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L356) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (getOption("LandR.assertions")) { # old algorithm
                                     ^
```
[R/cohorts.R:360:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L360) *style:* **Lines should not be more than 100 characters.**
```r
    pcd[, pixelGroup2 := mapvalues(pixelGroup, from = unique(pixelGroup), to = as.character(seq_along(unique(pixelGroup))))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:366:12:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L366) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pcdOld[ , c(columns2) := lapply(.SD, function(x) {
           ^
```
[R/cohorts.R:366:13:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L366) *style:* **Commas should never have a space before.**
```r
    pcdOld[ , c(columns2) := lapply(.SD, function(x) {
           ~^
```
[R/cohorts.R:370:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L370) *style:* **Lines should not be more than 100 characters.**
```r
    # concatenate within rows -- e.g., ecoregionCode_speciesCode_age_biomass or 647_11_Abie_sp_100_2000
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:371:52:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L371) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pcdOld[, uniqueComboByRow := as.integer(factor( do.call(paste, as.list(.SD)))),
                                                   ^
```
[R/cohorts.R:375:12:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L375) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pcdOld[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"),
           ^
```
[R/cohorts.R:375:13:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L375) *style:* **Commas should never have a space before.**
```r
    pcdOld[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"),
           ~^
```
[R/cohorts.R:377:12:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L377) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pcdOld[ , c("pixelGroup") := as.integer(maxPixelGroup) +
           ^
```
[R/cohorts.R:377:13:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L377) *style:* **Commas should never have a space before.**
```r
    pcdOld[ , c("pixelGroup") := as.integer(maxPixelGroup) +
           ~^
```
[R/cohorts.R:382:25:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L382) *style:* **Put spaces around all infix operators.**
```r
    pcdOld[, pixelGroup2:=mapvalues(pixelGroup, from = unique(pixelGroup),
                       ~^~~
```
[R/cohorts.R:427:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L427) *style:* **Variable and function names should not be longer than 30 characters.**
```r
uniqueSpeciesEcoregionDefinition <- c("speciesCode", "ecoregionGroup")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:440:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L440) *style:* **Lines should not be more than 100 characters.**
```r
  message(magenta("Pixels with non-NA cover:, ", cohortData[!is.na(cover), length(unique(pixelIndex))]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:448:86:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L448) *style:* **Put spaces around all infix operators.**
```r
    pixelsZero <- NROW(cohortData[, all(get(val) == 0), by = "pixelIndex"][get("V1") ==TRUE])
                                                                                ^~~
```
[R/cohorts.R:449:40:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L449) *style:* **Commas should always have a space after.**
```r
    message(magenta("Pixels with all(",val," == 0): ", format(pixelsZero, big.mark = ",")))
                                       ^
```
[R/cohorts.R:449:44:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L449) *style:* **Commas should always have a space after.**
```r
    message(magenta("Pixels with all(",val," == 0): ", format(pixelsZero, big.mark = ",")))
                                           ^
```
[R/cohorts.R:450:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L450) *style:* **Lines should not be more than 100 characters.**
```r
    pixelsBiomassNonZero <- NROW(cohortData[, any(get(val) > 0), by = "pixelIndex"][get("V1") ==TRUE])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:450:95:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L450) *style:* **Put spaces around all infix operators.**
```r
    pixelsBiomassNonZero <- NROW(cohortData[, any(get(val) > 0), by = "pixelIndex"][get("V1") ==TRUE])
                                                                                ^~~
```
[R/cohorts.R:451:40:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L451) *style:* **Commas should always have a space after.**
```r
    message(magenta("Pixels with all(",val," > 0): ", format(pixelsBiomassNonZero, big.mark = ",")))
                                       ^
```
[R/cohorts.R:451:44:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L451) *style:* **Commas should always have a space after.**
```r
    message(magenta("Pixels with all(",val," > 0): ", format(pixelsBiomassNonZero, big.mark = ",")))
                                           ^
```
[R/cohorts.R:452:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L452) *style:* **Lines should not be more than 100 characters.**
```r
    out <- list(pixelsNA = pixelsNA, pixelsZero = pixelsZero, pixelsBiomassNonZero = pixelsBiomassNonZero)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:518:32:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L518) *style:* **Variable or function name should be lowerCamelCase.**
```r
                               availableERC_by_Sp, theUnwantedPixels,
                               ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:530:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L530) *style:* **Variable or function name should be lowerCamelCase.**
```r
      availableERC_by_Sp <- as.data.table(availableERC_by_Sp)
      ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:554:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L554) *style:* **Commented code should be removed.**
```r
  #   numChar <- max(nchar(availableERC_by_Sp$initialEcoregionCode), na.rm = TRUE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:556:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L556) *style:* **Lines should not be more than 100 characters.**
```r
  #                      initialEcoregionCode := paste0("1_", paddedFloatToChar(as.integer(initialEcoregionCode), numChar))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:560:16:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L560) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (FALSE) { # This is old section... can be deleted soon (April 10, 2019, Eliot)
               ^
```
[R/cohorts.R:575:8:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L575) *style:* **Commented code should be removed.**
```r
    #  stop("values of 34 and 35 on pixelCohortData and sim$LCC2005 don't match")
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:604:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L604) *style:* **Lines should not be more than 100 characters.**
```r
    out <- out[initialPixels != pixels] # rm pixels which are same as initialPixels --> these are known wrong
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:607:42:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L607) *style:* **Put spaces around all infix operators.**
```r
    out[lcc %in% c(classesToReplace), lcc:=NA]
                                        ~^~~
```
[R/cohorts.R:610:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L610) *style:* **Lines should not be more than 100 characters.**
```r
                               on = c("pixelIndex" = "initialPixels"), nomatch = NA] # join the availableERC_by_Sp which has initialEcoregionCode
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:614:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L614) *style:* **Lines should not be more than 100 characters.**
```r
                               paddedFloatToChar(as.integer(lcc), padL = numCharLCCCodes, padR = 0))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:618:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L618) *style:* **Lines should not be more than 100 characters.**
```r
    out7 <- out5[availableERG2, on = c("speciesCode", "possERC" = "initialEcoregionCode"), nomatch = NA]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:668:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L668) *style:* **Commented code should be removed.**
```r
    # setnames(out3, c("initialPixels", "initialEcoregionCode"), c("pixelIndex", "ecoregionGroup"))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:670:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L670) *style:* **Commented code should be removed.**
```r
    # out3 <- unique(out3, by = c("pixelIndex", "ecoregionGroup"))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:693:6:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L693) *style:* **Commented code should be removed.**
```r
    #describeCohortData(cohortData)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:709:18:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L709) *style:* **Variable or function name should be lowerCamelCase.**
```r
    cohortData[, V1 := NULL]
                 ^~
```
[R/cohorts.R:711:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L711) *style:* **Commented code should be removed.**
```r
  # cohortData[cover == 0, `:=`(age = 0L, logAge = -Inf, B = 0)]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:717:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L717) *style:* **Commented code should be removed.**
```r
  # cohortData[speciesCode == "Popu_sp", cover := asInteger(cover / 2)]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:719:14:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L719) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  cohortData[ , cover := {
             ^
```
[R/cohorts.R:719:15:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L719) *style:* **Commas should never have a space before.**
```r
  cohortData[ , cover := {
             ~^
```
[R/cohorts.R:732:16:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L732) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
               ^
```
[R/cohorts.R:732:17:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L732) *style:* **Commas should never have a space before.**
```r
    cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
               ~^
```
[R/cohorts.R:732:19:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L732) *style:* **Variable or function name should be lowerCamelCase.**
```r
    cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
                  ^
```
[R/cohorts.R:734:16:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L734) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
               ^
```
[R/cohorts.R:734:17:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L734) *style:* **Commas should never have a space before.**
```r
    cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
               ~^
```
[R/cohorts.R:734:19:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L734) *style:* **Variable or function name should be lowerCamelCase.**
```r
    cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
                  ^
```
[R/cohorts.R:736:16:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L736) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    cohortData[ , totalBiomass := asInteger(totalBiomass)]
               ^
```
[R/cohorts.R:736:17:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L736) *style:* **Commas should never have a space before.**
```r
    cohortData[ , totalBiomass := asInteger(totalBiomass)]
               ~^
```
[R/cohorts.R:843:36:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L843) *style:* **Variable or function name should be lowerCamelCase.**
```r
  cohortData[cover > 0 & age == 0, B := 0L]
                                   ^
```
[R/cohorts.R:849:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L849) *style:* **Commented code should be removed.**
```r
  # cohortData[ , coverProp := (cover/100 * (NROW(cohortData) - 1) + 0.5) / NROW(cohortData)]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:861:22:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L861) *style:* **Variable or function name should be lowerCamelCase.**
```r
subsetDT <- function(DT, by, doSubset = TRUE) {
                     ^~
```
[R/cohorts.R:866:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L866) *style:* **Lines should not be more than 100 characters.**
```r
              "using maximum of ", sam, " samples per combination of ecoregionGroup and speciesCode. ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:871:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/cohorts.R#L871) *style:* **Variable or function name should be lowerCamelCase.**
```r
      DT <- DT[a$lineNum]
      ^~
```
[R/ecoregionProducer.R:37:4:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/ecoregionProducer.R#L37) *style:* **Commented code should be removed.**
```r
  #ecoregionMapInStudy <- raster::intersect(ecoregionMapFull, fixErrors(aggregate(studyArea)))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:54:3:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/ecoregionProducer.R#L54) *style:* **Variable or function name should be lowerCamelCase.**
```r
  NAs <- rtmNAs | rstEcoregionNAs
  ^~~
```
[R/ecoregionProducer.R:71:4:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/ecoregionProducer.R#L71) *style:* **Commented code should be removed.**
```r
  #ecoregionFactorValues <- na.omit(unique(rstEcoregion[]))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:73:4:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/ecoregionProducer.R#L73) *style:* **Commented code should be removed.**
```r
  #ecoregionTable <- raster::levels(rstEcoregion)[[1]]
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:81:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/ecoregionProducer.R#L81) *style:* **Lines should not be more than 100 characters.**
```r
    # rstEcoregion[] <- plyr::mapvalues(rstEcoregion[], from = ecoregionTable$ecoregion, to = ecoregionTable$mapcode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:81:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/ecoregionProducer.R#L81) *style:* **Commented code should be removed.**
```r
    # rstEcoregion[] <- plyr::mapvalues(rstEcoregion[], from = ecoregionTable$ecoregion, to = ecoregionTable$mapcode)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:96:37:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/ecoregionProducer.R#L96) *style:* **Commas should always have a space after.**
```r
  ecoregionTable <- ecoregionTable[,.(active = "yes", mapcode, ecoregion)]
                                    ^
```
[R/LANDIS-II-tables.R:76:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L76) *style:* **Lines should not be more than 100 characters.**
```r
    sppEquiv <- data.table(utils::data("sppEquivalencies_CA", package = "LandR", envir = environment()))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:84:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L84) *style:* **Lines should not be more than 100 characters.**
```r
  speciesTable <- speciesTable[species %in% equivalentName(sppNameVector, sppEquiv, "LANDIS_traits", multi = TRUE) &
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:101:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L101) *style:* **Lines should not be more than 100 characters.**
```r
#' (\url{https://raw.githubusercontent.com/dcyr/LANDIS-II_IA_generalUseFiles/master/speciesTraits.csv}).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:105:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L105) *style:* **Lines should not be more than 100 characters.**
```r
#' @param species a \code{data.table} that has species traits such as longevity, shade tolerance, etc.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:122:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L122) *style:* **Lines should not be more than 100 characters.**
```r
    sppEquiv <- data.table(utils::data("sppEquivalencies_CA", package = "LandR", envir = environment()))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:144:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L144) *style:* **Lines should not be more than 100 characters.**
```r
  speciesTableShort[species == "PSEU.MEN", longevity := 525] ## only in MC area, corresponding to var. glauca
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:153:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L153) *style:* **Lines should not be more than 100 characters.**
```r
  speciesTableShort <- speciesTableShort[species %in% equivalentName(sppNameVector, sppEquiv, "LANDIS_traits", multi = TRUE)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:170:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L170) *style:* **Lines should not be more than 100 characters.**
```r
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession_test.txt"}).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:190:17:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L190) *style:* **Commented code should be removed.**
```r
  maxcol <- 13 #max(count.fields(file.path(dPath, "species.txt"), sep = ""))
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:211:13:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L211) *style:* **Only use double-quotes.**
```r
  species[, ':='(seeddistance_eff = gsub(",", "", seeddistance_eff),
            ^~~~
```
[R/LANDIS-II-tables.R:211:17:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  species[, ':='(seeddistance_eff = gsub(",", "", seeddistance_eff),
                ^
```
[R/LANDIS-II-tables.R:224:18:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L224) *style:* **Only use double-quotes.**
```r
  speciesAddon[, ':='(leaflongevity = as.numeric(leaflongevity),
                 ^~~~
```
[R/LANDIS-II-tables.R:224:22:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L224) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  speciesAddon[, ':='(leaflongevity = as.numeric(leaflongevity),
                     ^
```
[R/LANDIS-II-tables.R:236:13:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L236) *style:* **Only use double-quotes.**
```r
  species[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
            ^~~~
```
[R/LANDIS-II-tables.R:236:17:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L236) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  species[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
                ^
```
[R/LANDIS-II-tables.R:240:13:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L240) *style:* **Only use double-quotes.**
```r
  species[, ':='(species1 = NULL, species2 = NULL)]
            ^~~~
```
[R/LANDIS-II-tables.R:240:17:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L240) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  species[, ':='(species1 = NULL, species2 = NULL)]
                ^
```
[R/LANDIS-II-tables.R:268:39:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L268) *style:* **Commas should always have a space after.**
```r
  mainInput <- mainInput[col1 != ">>",]
                                      ^
```
[R/LANDIS-II-tables.R:278:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L278) *style:* **Lines should not be more than 100 characters.**
```r
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/ecoregion.txt"}).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:295:16:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L295) *style:* **Commented code should be removed.**
```r
  maxcol <- 5 #max(count.fields(file.path(dPath, "ecoregions.txt"), sep = ""))
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:311:47:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L311) *style:* **Commas should always have a space after.**
```r
  ecoregion <- ecoregion[col1 != "LandisData",]
                                              ^
```
[R/LANDIS-II-tables.R:312:39:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L312) *style:* **Commas should always have a space after.**
```r
  ecoregion <- ecoregion[col1 != ">>",]
                                      ^
```
[R/LANDIS-II-tables.R:324:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L324) *style:* **Lines should not be more than 100 characters.**
```r
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession-dynamic-inputs_test.txt"}).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:356:61:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L356) *style:* **Commas should always have a space after.**
```r
  speciesEcoregion <- speciesEcoregion[col1 != "LandisData",]
                                                            ^
```
[R/LANDIS-II-tables.R:357:53:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L357) *style:* **Commas should always have a space after.**
```r
  speciesEcoregion <- speciesEcoregion[col1 != ">>",]
                                                    ^
```
[R/LANDIS-II-tables.R:368:22:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L368) *style:* **Only use double-quotes.**
```r
  speciesEcoregion[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
                     ^~~~
```
[R/LANDIS-II-tables.R:368:26:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L368) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  speciesEcoregion[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
                         ^
```
[R/LANDIS-II-tables.R:371:22:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L371) *style:* **Only use double-quotes.**
```r
  speciesEcoregion[, ':='(species1 = NULL, species2 = NULL)]
                     ^~~~
```
[R/LANDIS-II-tables.R:371:26:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/LANDIS-II-tables.R#L371) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  speciesEcoregion[, ':='(species1 = NULL, species2 = NULL)]
                         ^
```
[R/maps.R:22:29:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L22) *style:* **Variable or function name should be lowerCamelCase.**
```r
defineFlammable <- function(LandCoverClassifiedMap = NULL,
                            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:177:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L177) *style:* **Variable and function names should not be longer than 30 characters.**
```r
vegTypeMapGenerator.RasterStack <- function(x, ...) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:177:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L177) *style:* **Variable or function name should be lowerCamelCase.**
```r
vegTypeMapGenerator.RasterStack <- function(x, ...) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:188:14:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L188) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (FALSE) { # This is the old version -- Eliot & Alex July 11, 2019
             ^
```
[R/maps.R:198:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L198) *style:* **Lines should not be more than 100 characters.**
```r
      whMixed <- which(sum(speciesStack < (100 * vegLeadingProportion))[] == numLayers(speciesStack))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:199:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L199) *style:* **Variable or function name should be lowerCamelCase.**
```r
      MixedRas <- speciesStack[[1]]
      ^~~~~~~~
```
[R/maps.R:203:20:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L203) *style:* **Variable or function name should be lowerCamelCase.**
```r
      speciesStack$Mixed <- MixedRas
                   ^~~~~
```
[R/maps.R:232:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L232) *style:* **Variable or function name should be lowerCamelCase.**
```r
vegTypeMapGenerator.data.table <- function(x, pixelGroupMap, vegLeadingProportion = 0.8,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:279:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L279) *style:* **Lines should not be more than 100 characters.**
```r
    # 1. Find length of each pixelGroup -- don't include pixelGroups in "by" that have only 1 cohort: N = 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:289:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L289) *style:* **Lines should not be more than 100 characters.**
```r
      pixelGroupData1[N != 1, (totalOfLeadingBasedOn) := sum(cover, na.rm = TRUE), by = pixelGroupColName]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:290:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L290) *style:* **Lines should not be more than 100 characters.**
```r
      pixelGroupData1 <- pixelGroupData1[, list(sum(cover, na.rm = TRUE), totalcover[1]), by = pgdAndSc]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:292:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L292) *style:* **Lines should not be more than 100 characters.**
```r
      pixelGroupData1[N != 1, (totalOfLeadingBasedOn) := sum(B, na.rm = TRUE), by = pixelGroupColName]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:295:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L295) *style:* **Lines should not be more than 100 characters.**
```r
    setnames(pixelGroupData1, old = c("V1", "V2"), new = c(speciesOfLeadingBasedOn, totalOfLeadingBasedOn))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:314:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L314) *style:* **Commented code should be removed.**
```r
    # setorderv(x, pixelGroupColName)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:317:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L317) *style:* **Variable or function name should be lowerCamelCase.**
```r
    N <- rep.int(pixelGroupData2$N, pixelGroupData2$N)
    ^
```
[R/maps.R:321:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L321) *style:* **Lines should not be more than 100 characters.**
```r
        totalBNot1 <- cohortData2[!wh1, list(N = .N, totalcover = sum(cover, na.rm = TRUE)), by = pixelGroupColName]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:323:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L323) *style:* **Lines should not be more than 100 characters.**
```r
        totalBNot1 <- cohortData2[!wh1, list(N = .N, totalB = sum(B, na.rm = TRUE)), by = pixelGroupColName]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:330:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L330) *style:* **Variable or function name should be lowerCamelCase.**
```r
      GT1 <- (b > 1)
      ^~~
```
[R/maps.R:335:10:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L335) *style:* **Commented code should be removed.**
```r
        #pixelGroupData2List[[2]] <- cohortData2[!GT1]
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:336:10:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L336) *style:* **Commented code should be removed.**
```r
        #pixelGroupData2 <- rbindlist(pixelGroupData2List)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:338:11:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L338) *style:* **Commented code should be removed.**
```r
        # cols <- c(pixelGroupColName, "speciesCode", "speciesProportion")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:339:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L339) *style:* **Lines should not be more than 100 characters.**
```r
        set(cohortData2, NULL, "speciesProportion", cohortData2[[leadingBasedOn]] / cohortData2[[totalOfLeadingBasedOn]])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:340:11:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L340) *style:* **Commented code should be removed.**
```r
        # pixelGroupData2[[NROW(pixelGroupData2) + 1]] <- cohortData2[!GT1, ..cols]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:398:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L398) *style:* **Lines should not be more than 100 characters.**
```r
    ## 2. sort on pixelGroup and speciesProportion, reverse so that 1st row of each pixelGroup is the largest
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:412:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L412) *style:* **Commented code should be removed.**
```r
    # a2 <- Sys.time()
      ^~~~~~~~~~~~~~~~
```
[R/maps.R:413:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L413) *style:* **Lines should not be more than 100 characters.**
```r
    # pixelGroupData2 <- pixelGroupData[, list(mixed = all(speciesProportion < vegLeadingProportion),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:416:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L416) *style:* **Commented code should be removed.**
```r
    # pixelGroupData2[mixed == TRUE, leading := "Mixed"]
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:417:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L417) *style:* **Commented code should be removed.**
```r
    # b2 <- Sys.time()
      ^~~~~~~~~~~~~~~~
```
[R/maps.R:439:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L439) *style:* **Lines should not be more than 100 characters.**
```r
    pixelGroupData3 <- pixelGroupData3[, .SD[1], by = pixelGroupColName] ## sp. w/ highest prop. per pixelGroup
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:447:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L447) *style:* **Lines should not be more than 100 characters.**
```r
  if ("pixelIndex" %in% colnames(pixelGroupData3)) { #(!any(duplicated(pixelGroupData3[[pixelGroupColName]]))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:447:52:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L447) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if ("pixelIndex" %in% colnames(pixelGroupData3)) { #(!any(duplicated(pixelGroupData3[[pixelGroupColName]]))) {
                                                   ^
```
[R/maps.R:492:14:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L492) *style:* **Variable or function name should be lowerCamelCase.**
```r
    pgTest[, Type := equivalentName(speciesCode, sppEquiv, "Type")]
             ^~~~
```
[R/maps.R:630:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L630) *style:* **Lines should not be more than 100 characters.**
```r
  ## select which archives/targetFiles to extract -- because there was "multi" above, need unique here
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:637:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L637) *style:* **Lines should not be more than 100 characters.**
```r
                    archive2 = file.path(dPath, paste0("NFI_MODIS250m_kNN_Species_", kNNnames, "_v0.zip")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:640:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L640) *style:* **Lines should not be more than 100 characters.**
```r
  if (!all(reproducible::basename2(file_path_sans_ext(names(archives))) == file_path_sans_ext(targetFiles)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:647:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L647) *style:* **Lines should not be more than 100 characters.**
```r
    message("This looks like a lot of species; did you mean to pass only a subset of this to sppEquiv?",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:665:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L665) *style:* **Lines should not be more than 100 characters.**
```r
                         prepInputs, quick = TRUE) # don't need to digest all the "targetFile" and "archives"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:667:79:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L667) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  noDataLayers <- sapply(speciesLayers, function(xx) if (maxValue(xx) < thresh ) FALSE else TRUE)
                                                                              ^
```
[R/maps.R:670:76:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L670) *style:* **Commas should always have a space after.**
```r
    message("removing ", sum(!noDataLayers), " species because they had <",thresh,
                                                                           ^
```
[R/maps.R:672:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L672) *style:* **Lines should not be more than 100 characters.**
```r
            "\n  These species are retained (and could be further culled manually, if desired):\n  ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:694:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L694) *style:* **Commented code should be removed.**
```r
  # layerData <- Cache(sapply, X = speciesLayers, function(xx) sum(xx[] > 0, na.rm = TRUE))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:696:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L696) *style:* **Commented code should be removed.**
```r
  # ## remove layers that had < thresh pixels with biomass
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:697:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L697) *style:* **Commented code should be removed.**
```r
  # belowThresh <- layerData < thresh
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:699:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L699) *style:* **Commented code should be removed.**
```r
  #   message(names(belowThresh)[belowThresh], " was removed because it had no data")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:700:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L700) *style:* **Commented code should be removed.**
```r
  #   speciesLayers[belowThresh] <- NULL
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:799:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L799) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRastName <- basename(tempfile(fileext = ".tif"))
      ^~~~~~~~~~
```
[R/maps.R:801:9:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L801) *style:* **Variable or function name should be lowerCamelCase.**
```r
        LQCurName <- basename(tempfile(fileext = ".tif"))
        ^~~~~~~~~
```
[R/maps.R:808:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L808) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRastInHQcrs <- projectExtent(lowQualityStack, crs = crs(highQualityStack))
      ^~~~~~~~~~~~~
```
[R/maps.R:821:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L821) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- raster(LQRastName)
      ^~~~~~
```
[R/maps.R:839:9:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L839) *style:* **Variable or function name should be lowerCamelCase.**
```r
        HQRast <- raster(tmpHQName)
        ^~~~~~
```
[R/maps.R:844:9:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L844) *style:* **Variable or function name should be lowerCamelCase.**
```r
        HQRast <- highQualityStack[[SPP]]
        ^~~~~~
```
[R/maps.R:847:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L847) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- lowQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:848:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L848) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:855:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L855) *style:* **Variable or function name should be lowerCamelCase.**
```r
    NAs <- is.na(HQRast[])
    ^~~
```
[R/maps.R:859:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L859) *style:* **Variable or function name should be lowerCamelCase.**
```r
    HQRast <- writeRaster(HQRast, datatype = "INT1U",
    ^~~~~~
```
[R/maps.R:869:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L869) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:873:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L873) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- lowQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:877:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L877) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:909:4:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/maps.R#L909) *style:* **Commented code should be removed.**
```r
  #names(sppMerges) <- equivalentName(names(sppMerges), sppEquiv,  column = sppEquivCol)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/misc.R:23:1:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/misc.R#L23) *style:* **Lines should not be more than 100 characters.**
```r
#' Essentially a wrapper around \code{round}, rather than \code{truncate}, which is what \code{as.integer}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:47:25:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L47) *style:* **Variable or function name should be lowerCamelCase.**
```r
overlayLCCs <- function(LCCs, forestedList, outputLayer,
                        ^~~~
```
[R/overlayLCCs.R:48:25:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L48) *style:* **Variable or function name should be lowerCamelCase.**
```r
                        NAcondition, NNcondition, remapTable = NULL,
                        ^~~~~~~~~~~
```
[R/overlayLCCs.R:48:38:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L48) *style:* **Variable or function name should be lowerCamelCase.**
```r
                        NAcondition, NNcondition, remapTable = NULL,
                                     ^~~~~~~~~~~
```
[R/overlayLCCs.R:49:43:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L49) *style:* **Variable or function name should be lowerCamelCase.**
```r
                        classesToReplace, availableERC_by_Sp,
                                          ^~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:65:5:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L65) *style:* **Variable or function name should be lowerCamelCase.**
```r
    LCCs <- stack(LCCs)
    ^~~~
```
[R/overlayLCCs.R:81:7:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L81) *style:* **Variable or function name should be lowerCamelCase.**
```r
      availableERC_by_Sp <- data.table(initialEcoregionCode = LCCs[[outputLayer]][])
      ^~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:90:14:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L90) *style:* **Variable or function name should be lowerCamelCase.**
```r
        dt[, NAs := eval(parse(text = NAcondition)), with = TRUE]
             ^~~
```
[R/overlayLCCs.R:92:14:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L92) *style:* **Variable or function name should be lowerCamelCase.**
```r
        dt[, NAs := NULL]
             ^~~
```
[R/overlayLCCs.R:96:14:](https://github.com/PredictiveEcology/LandR/blob/c34c917f58b5cac19076b6a8e20d8dba968ff49e/R/overlayLCCs.R#L96) *style:* **Variable or function name should be lowerCamelCase.**
```r
        dt[, NNcondition := eval(parse(text = NNcondition))]
             ^~~~~~~~~~~
```


全般的にリテラル値は設定ファイル系にまとめておくと良いと思うよ。


why did you remove this blank line? I liked it!


Collaborator: Review for this commit was created. [Link to review](http://tests-a.collabdevteam.net:8080/ui#review:id=47)


Collaborator: Review for this commit was created. [Link to review](http://tests-a.collabdevteam.net:8080/ui#review:id=49)


Collaborator: Review for this commit was created. [Link to review](http://tests-a.collabdevteam.net:8080/ui#review:id=50)


Aaah. That explains it.

I'm stupid. Thanks for dealing with my stupid. 🙃


Successfully aliased the URL <https://seatsmart-ck9afpqxm.now.sh> to the following aliases:

* https://seatsmart.tech
* https://seatsmart.now.sh
* https://seatsmart.thaddeusmccleary.now.sh
* https://seatsmart-git-master.thaddeusmccleary.now.sh


Here you are making an assumption if the dictionary does'nt start with IpPermissions Array.

But the issue in #307  was that the IpPermission itself was in another array. The solution to issue would ideally be having a check between whether

```
pyjq.first('select(.IpPermissions[]|.IpProtocol=="-1")|.GroupId', ingress, None)

```

or

```
pyjq.first('.[] | select(.IpPermissions[]|.IpProtocol=="-1")| .GroupId', ingress, None)

```
format.

There is a difference in both formats.

This current check would just ignore the latter case instead of considering it. The issue here is not lack of securitygroup. The issue here is securitygroup being present in the output in a different format than previously assumed format.

Would suggest reconsidering  the commit.


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

* `objectionjs_database_url` (in env: `DATABASE_URL)`
* `objectionjs_graphql_endpoint` (in env: `GRAPHQL_ENDPOINT)`

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


余力があればボタンやラベルコントロール名もそれぞれ意味をなすような名前にしておくと良いと思う。


I’m just modify existing patch


Collaborator: Review for this commit was created. [Link to review](http://tests-a.collabdevteam.net:8080/ui#review:id=54)


Collaborator: Review for this commit was created. [Link to review](http://tests-a.collabdevteam.net:8080/ui#review:id=56)