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mergeRaster when triggering mosaic now takes function from user #55

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@tati-micheletti tati-micheletti commented Jan 8, 2019

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@lintr-bot lintr-bot commented Jan 23, 2019

inst/examples/example_distanceFromEachPoint.R:37:2: style: Commented code should be removed.

#beginCluster(3) # can do parallel
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_distanceFromEachPoint.R:40:2: style: Commented code should be removed.

#endCluster() # if beginCluster was run
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:83:11: style: Do not place spaces around code in parentheses or square brackets.

if ( method != "RMexp") {
          ^

R/initialize.R:88:1: style: Lines should not be more than 100 characters.

map <- raster(RandomFields::RFsimulate(model, y = 1:ncSpeedup, x = 1:nrSpeedup, grid = TRUE, ...))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:223:1: style: Variable or function name should be lowerCamelCase.

randomPolygon.SpatialPoints <- function(x, hectares, area) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:247:4: style: Commented code should be removed.

#y <- spTransform(x, areaCRS)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:263:3: style: Variable or function name should be lowerCamelCase.

X <- c(jitter(sort(rbeta(nPoints, betaPar, betaPar) * (maxX - minX) + minX)),
  ^

R/initialize.R:265:3: style: Variable or function name should be lowerCamelCase.

Y <- c(jitter(sort(rbeta(nPoints / 2, betaPar, betaPar) * (maxY - meanY) + meanY)),
  ^

R/initialize.R:269:3: style: Variable or function name should be lowerCamelCase.

Sr1 <- Polygon(cbind(X + xAdd, Y + yAdd))
  ^~~

R/initialize.R:270:3: style: Variable or function name should be lowerCamelCase.

Srs1 <- Polygons(list(Sr1), "s1")
  ^~~~

R/initialize.R:283:1: style: Variable or function name should be lowerCamelCase.

randomPolygon.matrix <- function(x, hectares, area) {
^~~~~~~~~~~~~~~~~~~~

R/initialize.R:300:1: style: Variable or function name should be lowerCamelCase.

randomPolygon.SpatialPolygons <- function(x, hectares, area) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:307:8: style: Place a space before left parenthesis, except in a function call.

while(need) {
       ^

R/initialize.R:407:3: style: Commented code should be removed.

# ### INCORPORATE RELEVANT PARTS OF THIS OLD INIT FUNCTION INTO INITCOORDS()
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:412:3: style: Commented code should be removed.

# #'                      (currently only \code{RasterLayer} or
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:413:3: style: Commented code should be removed.

# #'                      \code{SpatialPolygonsDataFrame}) accepted.
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:423:7: style: Commented code should be removed.

#     ext <- extent(agentlocation)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:425:9: style: Commented code should be removed.

#       #            nonNAs <- !is.na(getvalue(probinit))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:426:9: style: Commented code should be removed.

#       nonNAs <- !is.na(getValues(probinit))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:427:9: style: Commented code should be removed.

#       wh.nonNAs <- which(nonNAs)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:428:9: style: Commented code should be removed.

#       #            ProbInit.v <- cumsum(getvalue(probinit)[nonNAs])
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:429:9: style: Commented code should be removed.

#       ProbInit.v <- cumsum(getValues(probinit)[nonNAs])
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:431:11: style: Commented code should be removed.

#         ran <- runif(numagents,0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:432:11: style: Commented code should be removed.

#         fI <- findInterval(ran, ProbInit.v)+1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:433:11: style: Commented code should be removed.

#         fI2 <- wh.nonNAs[fI]
          ^~~~~~~~~~~~~~~~~~~~

R/initialize.R:434:11: style: Commented code should be removed.

#         last.ran <- runif(numagents,0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:435:11: style: Commented code should be removed.

#         last.fI <- findInterval(last.ran, ProbInit.v)+1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:436:11: style: Commented code should be removed.

#         last.fI2 <- wh.nonNAs[last.fI]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:438:11: style: Commented code should be removed.

#         #                va <- getvalue(probinit)[nonNAs]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:439:11: style: Commented code should be removed.

#         va <- getValues(probinit)[nonNAs]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:440:11: style: Commented code should be removed.

#         ran <- runif(length(va), 0, 1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:441:11: style: Commented code should be removed.

#         fI2 <- wh.nonNAs[ran<va]
          ^~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:443:11: style: Commented code should be removed.

#         last.ran <- runif(length(fI2), 0, 1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:444:11: style: Commented code should be removed.

#         last.fI <- findInterval(last.ran, ProbInit.v) + 1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:445:11: style: Commented code should be removed.

#         last.fI2 <- wh.nonNAs[last.fI]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:447:11: style: Commented code should be removed.

#         #                last.ran <- runif(length(fI2),0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:448:11: style: Commented code should be removed.

#         #                last.fI2 <- wh.nonNAs[last.ran<va]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:451:11: style: Commented code should be removed.

#         position <- xyFromCell(agentlocation,fI2,spatial = TRUE)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:453:11: style: Commented code should be removed.

#         position <- coordinates(agentlocation)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:455:11: style: Commented code should be removed.

#         stop("need raster layer or Spatial Points object")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:457:9: style: Commented code should be removed.

#       numagents <- length(position)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:465:13: style: Commented code should be removed.

#           colnames(xy) = c("x", "y")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:466:13: style: Commented code should be removed.

#           position <- SpatialPoints(xy)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:467:13: style: Commented code should be removed.

#           position <- SpatialPoints(sampleRandom(agentlocation, numagents, xy = TRUE, sp = TRUE))
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:469:13: style: Commented code should be removed.

#           sam <- sample(1:length(agentlocation),numagents)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:470:13: style: Commented code should be removed.

#           position <- SpatialPoints(agentlocation[sam,])
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:472:13: style: Commented code should be removed.

#           stop("need raster layer or Spatial Points object")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:479:13: style: Commented code should be removed.

#           position <- SpatialPoints(agentlocation)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:481:13: style: Commented code should be removed.

#           stop("need raster layer or Spatial Points object")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:483:11: style: Commented code should be removed.

#         numagents <- length(position)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:491:11: style: Commented code should be removed.

#         numagents <- length(position)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:495:7: style: Commented code should be removed.

#     stop("Need to provide agentlocation, which can be a map layer")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:497:5: style: Commented code should be removed.

#   heading1 <- runif(numagents, 0, 360)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:498:5: style: Commented code should be removed.

#   distance <- runif(numagents, 0.1, 10)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:500:5: style: Commented code should be removed.

#   .Object@ID <- as.character(1:numagents)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:501:5: style: Commented code should be removed.

#   .Object@spatial <- position
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:502:5: style: Commented code should be removed.

#   .Object@heading <- heading1
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:503:5: style: Commented code should be removed.

#   .Object@distance <- distance
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:505:5: style: Commented code should be removed.

#   return(.Object)
    ^~~~~~~~~~~~~~~

R/initialize.R:510:32: style: Commas should always have a space after.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                               ^

R/initialize.R:510:37: style: Commas should always have a space after.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                                    ^

R/initialize.R:510:52: style: Commas should always have a space after.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                                                   ^

R/initialize.R:510:55: style: Put spaces around all infix operators.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                                                     ~^~

R/initialize.R:510:56: style: Only use double-quotes.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                                                       ^~

R/initialize.R:514:22: style: Put spaces around all infix operators.

​  (floor((long + 180)/6) %% 60) + 1
                    ~^~

R/mapReduce.R:53:3: style: Variable or function name should be lowerCamelCase.

BsumVec <- reduced[fullRasterVals] # join
  ^~~~~~~

R/neighbourhood.R:114:21: style: Variable or function name should be lowerCamelCase.

match.adjacent = FALSE, cutoff.for.data.table = 2e3,
                    ^~~~~~~~~~~~~~

R/neighbourhood.R:114:45: style: Variable or function name should be lowerCamelCase.

match.adjacent = FALSE, cutoff.for.data.table = 2e3,
                                            ^~~~~~~~~~~~~~~~~~~~~

R/neighbourhood.R:233:1: style: Lines should not be more than 100 characters.

​              ((adj[, "from"] %% numCol + adj[, "to"] %% numCol) == 1)) # | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/neighbourhood.R:238:1: style: Lines should not be more than 100 characters.

​              ((adj[, "from"] %% numCol + adj[, "to"] %% numCol) == 1)) # | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/neighbourhood.R:297:1: style: Lines should not be more than 100 characters.

​              ((from %% numCol + to %% numCol) == 1))# | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/neighbourhood.R:806:29: style: Variable or function name should be lowerCamelCase.

setGeneric("wrap", function(X, bounds, withHeading) {
                            ^

R/neighbourhood.R:815:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:832:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:842:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:843:5: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds))
    ^

R/neighbourhood.R:852:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:853:5: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds))
    ^

R/neighbourhood.R:862:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:865:7: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds))
      ^

R/neighbourhood.R:877:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds, withHeading) {
                        ^

R/neighbourhood.R:902:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds, withHeading) {
                        ^

R/neighbourhood.R:903:7: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds), withHeading = withHeading)
      ^

R/neighbourhood.R:912:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds, withHeading) {
                        ^

R/neighbourhood.R:915:7: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds), withHeading = withHeading)
      ^

R/neighbourhood.R:1052:40: style: Commas should always have a space after.

cc <- cbind(pureCircle2[, "x"] - xy[,"x"], pureCircle2[, "y"] - xy[, "y"])
                                       ^

R/probability.R:41:35: style: Place a space before left parenthesis, except in a function call.

1 / sqrt(var * 2 * pi) * exp(-((theta - mu + 2 * pi * k) ^ 2) / (2 * var))
                                  ^

R/probability.R:44:3: style: Variable or function name should be lowerCamelCase.

Next <- term(theta, mu, var, k)
  ^~~~

R/probability.R:45:3: style: Variable or function name should be lowerCamelCase.

Last <- Next
  ^~~~

R/RcppExports.R:68:20: style: Variable or function name should be lowerCamelCase.

runifC <- function(N) {
                   ^

R/RcppExports.R:71:1: style: Trailing blank lines are superfluous.

^

R/SELES.R:53:23: style: Variable or function name should be lowerCamelCase.

numAgents <- function(N, probInit) {
                      ^

R/splitRaster.R:116:1: style: Lines should not be more than 100 characters.

​      clusterApplyLB(cl = cl, x = seq_along(extents), fun = croppy, e = extents, r = r, path = path, rType = rType)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread.R:538:8: style: Commented code should be removed.

#isNASpreadProb <- is.na(spreadProb[])
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread.R:540:11: style: Commented code should be removed.

#   isNASpreadProb <- is.na(spreadProb[])
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread.R:541:11: style: Commented code should be removed.

#   spreadProb[isNASpreadProb] <- 0L
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread.R:942:41: style: Place a space before left parenthesis, except in a function call.

notDupsEvents <- notDups[-(1:(nrSpreads - nrPotentials))]
                                        ^

R/spread2.R:5:1: style: Lines should not be more than 100 characters.

"quantityAdj", "quantityAdj2", "state", "size", "tooBigByNCells", "V1", "proportion"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:674:12: style: Commented code should be removed.

#pureCircle <- unique(pureCircle)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:759:13: style: Commented code should be removed.

# colnamesDtPot <- colnames(dtPotential)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:760:13: style: Commented code should be removed.

# ll <-  lapply(colnamesDtPot, function(x) dtPotential[[x]][!spreadProbNA])
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:761:13: style: Commented code should be removed.

# names(ll) <- colnamesDtPot
            ^~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:762:13: style: Commented code should be removed.

# dtPotential <- as.data.table(ll)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:772:1: style: Lines should not be more than 100 characters.

.I[sample.int(length(numNeighs), size = numNeighs, prob = spreadProbRel)],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:787:7: style: Variable or function name should be lowerCamelCase.

NAaSP <- !is.na(actualSpreadProb)
      ^~~~~

R/spread2.R:789:42: style: Commas should always have a space after.

dtPotential <- dtPotential[NAaSP,]
                                         ^

R/spread2.R:830:1: style: Lines should not be more than 100 characters.

# 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: style: Lines should not be more than 100 characters.

#successCells <- na.omit(successCells[!dupsWithinDtPotential]) # remove the dupsWithinDtPotential
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:848:10: style: Commented code should be removed.

#successCells <- na.omit(successCells[!dupsWithinDtPotential]) # remove the dupsWithinDtPotential
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-examples.R:6:11: style: Commented code should be removed.

​    cat("#START##############\n", file = tmpExFile, append = FALSE)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-examples.R:17:5: style: Commas should never have a space before.

​  } , add = TRUE)
   ~^

tests/testthat/test-mapReduce.R:23:4: style: Commented code should be removed.

#expect_equal(sort(unique(getValues(biomass))), sort(reducedDT$biomass))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:27:5: style: Commented code should be removed.

#   library(data.table)
    ^~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:28:5: style: Commented code should be removed.

#   library(raster)
    ^~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:31:6: style: Commented code should be removed.

#    detach("package:data.table")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:35:5: style: Commented code should be removed.

#   ras <- raster(extent(0,15,0,15), res=1)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:36:5: style: Commented code should be removed.

#   fullRas <- randomPolygons(ras, numTypes=5, speedup=1, p=0.3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:37:5: style: Commented code should be removed.

#   names(fullRas) <- "mapcodeAll"
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:38:5: style: Commented code should be removed.

#   uniqueComms <- raster::unique(fullRas)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:42:7: style: Commented code should be removed.

#     biomass=rnbinom(length(uniqueComms), mu=4000, 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:44:5: style: Commented code should be removed.

#   biomass <- rasterizeReduced(reducedDT, fullRas, "biomass")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:46:5: style: Commented code should be removed.

#   expect_equal(sort(unique(getValues(biomass))), sort(reducedDT$biomass))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:47:5: style: Commented code should be removed.

#   expect_equal(length(unique(getValues(biomass))), length(unique(getValues(fullRas))))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:49:5: style: Commented code should be removed.

#   setkey(reducedDT, biomass)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:50:5: style: Commented code should be removed.

#   communities <- rasterizeReduced(reducedDT, fullRas, "communities")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:51:5: style: Commented code should be removed.

#   expect_equal(sort(unique(getValues(communities))), sort(reducedDT$communities))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:52:5: style: Commented code should be removed.

#   expect_equal(length(unique(getValues(communities))), length(unique(getValues(fullRas))))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:56:5: style: Commented code should be removed.

#   library(data.table)
    ^~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:57:5: style: Commented code should be removed.

#   library(raster)
    ^~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:60:6: style: Commented code should be removed.

#    detach("package:data.table")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:64:5: style: Commented code should be removed.

#   ras <- raster(extent(0, 15, 0, 15), res = 1)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:65:5: style: Commented code should be removed.

#   fullRas <- randomPolygons(ras, numTypes = 5, speedup = 1, p = 0.3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:67:5: style: Commented code should be removed.

#   uniqueComms <- raster::unique(fullRas)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:71:7: style: Commented code should be removed.

#     biomass=rnbinom(length(uniqueComms), mu = 4000, 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:73:5: style: Commented code should be removed.

#   biomass <- rasterizeReduced(reducedDT, fullRas, "biomass")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:75:5: style: Commented code should be removed.

#   setkey(reducedDT, biomass)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:76:5: style: Commented code should be removed.

#   communities <- rasterizeReduced(reducedDT, fullRas, "communities")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:77:5: style: Commented code should be removed.

#   expect_equal(sort(unique(getValues(communities))), sort(reducedDT$communities))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:81:5: style: Commented code should be removed.

#   library(data.table)
    ^~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:82:5: style: Commented code should be removed.

#   library(raster)
    ^~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:85:6: style: Commented code should be removed.

#    detach("package:data.table")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:89:5: style: Commented code should be removed.

#   ras <- raster(extent(0,15,0,15), res=1)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:90:5: style: Commented code should be removed.

#   fullRas <- randomPolygons(ras, numTypes=5, speedup=1, p=0.3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:91:5: style: Commented code should be removed.

#   names(fullRas) <- "mapcodeAll"
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:92:5: style: Commented code should be removed.

#   uniqueComms <- raster::unique(fullRas)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:96:7: style: Commented code should be removed.

#     biomass=rnbinom(length(uniqueComms), mu=4000, 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:98:5: style: Commented code should be removed.

#   biomass <- rasterizeReduced(reducedDT, fullRas, "biomass")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R💯5: style: Commented code should be removed.

#   setkey(reducedDT, biomass)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:101:5: style: Commented code should be removed.

#   communities <- rasterizeReduced(reducedDT, fullRas, "communities")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:102:5: style: Commented code should be removed.

#   expect_equal(length(unique(getValues(communities))), length(unique(getValues(fullRas))))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mergeRaster.R:4:6: style: Use <-, not =, for assignment.

nx = 3
     ^

tests/testthat/test-mergeRaster.R:5:6: style: Use <-, not =, for assignment.

ny = 3
     ^

tests/testthat/test-mergeRaster.R:10:54: style: Commas should never have a space before.

vals = round(runif(n = 14400 , min = 1, max = 10)))
                                                    ~^

tests/testthat/test-mergeRaster.R:13:29: style: Put spaces around all infix operators.

​  expect_length(splitted, nx*ny)
                           ~^~

tests/testthat/test-mergeRaster.R:33:6: style: Use <-, not =, for assignment.

nx = 3
     ^

tests/testthat/test-mergeRaster.R:34:6: style: Use <-, not =, for assignment.

ny = 3
     ^

tests/testthat/test-mergeRaster.R:39:54: style: Commas should never have a space before.

vals = round(runif(n = 14400 , min = 1, max = 10)))
                                                    ~^

tests/testthat/test-mergeRaster.R:42:29: style: Put spaces around all infix operators.

​  expect_length(splitted, nx*ny)
                           ~^~

tests/testthat/test-mergeRaster.R:52:54: style: Commas should never have a space before.

vals = round(runif(n = 14400 , min = 1, max = 10)))
                                                    ~^

tests/testthat/test-mergeRaster.R:55:1: style: Lines should not be more than 100 characters.

​test_that("mergeRaster will use mosaic with default mean if rasters are resampled and fun if passed", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mergeRaster.R:58:6: style: Use <-, not =, for assignment.

nx = 3
     ^

tests/testthat/test-mergeRaster.R:59:6: style: Use <-, not =, for assignment.

ny = 3
     ^

tests/testthat/test-mergeRaster.R:64:54: style: Commas should never have a space before.

vals = round(runif(n = 14400 , min = 1, max = 10)))
                                                    ~^

tests/testthat/test-mergeRaster.R:67:29: style: Put spaces around all infix operators.

​  expect_length(splitted, nx*ny)
                           ~^~

tests/testthat/test-randomPolygon.R:24:60: style: Put spaces around all infix operators.

​  expect_true(base::abs(base::abs(polyArea - area)) <  area/4) ## TODO: why is this area/4?
                                                          ~^~

tests/testthat/test-randomPolygon.R:28:3: style: Variable or function name should be lowerCamelCase.

centerSP_UTM <- sp::spTransform(centerSP, CRSobj = raster::crs(poly1InUTM))
  ^~~~~~~~~~~~

tests/testthat/test-randomPolygon.R:30:1: style: Lines should not be more than 100 characters.

​  expect_true(raster::pointDistance(centerSP_UTM, polyCenter, lonlat = FALSE) < 100) ## TODO: appropriate test?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:148:38: style: Commas should always have a space after.

​  expect_identical(dataType(y4[[1]]),"INT1U")
                                     ^

tests/testthat/test-splitRaster.R:165:1: style: Lines should not be more than 100 characters.

tmpdir <- file.path(tempdir(), "splitRaster-test-parallel") %>% reproducible::checkPath(create = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:168:8: style: Commented code should be removed.

#detach("package:raster")
       ^~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:226:1: style: Lines should not be more than 100 characters.

tmpdir <- file.path(tempdir(), "splitRaster-test-large") %>% reproducible::checkPath(create = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:264:4: style: Commented code should be removed.

#expect_equal(min(values(m)), min(values(r))) ## Error: cannot allocate vector of size 4.8 Gb
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:283:4: style: Commented code should be removed.

#expect_equal(max(values(m1)), max(values(r)))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:284:4: style: Commented code should be removed.

#expect_equal(min(values(m1)), min(values(r)))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread.R:209:1: style: Lines should not be more than 100 characters.

if (interactive()) Plot(circEdge, addTo = "circs", cols = c("transparent", rainbow(numCircs)[whCirc]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:148:4: style: Commented code should be removed.

#quickDT <- data.table(id = seq_along(sams), initialPixels = sams, key = "id")
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:150:4: style: Commented code should be removed.

#cirOut <- quickDT[cirOut, on = ]
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:473:1: style: Lines should not be more than 100 characters.

##                                    expr       min        lq      mean   median        uq       max neval
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:474:1: style: Lines should not be more than 100 characters.

##         iterativeFun(ras, FALSE, n, sp)  3.096979 12.642477  73.02248 35.17520  91.10528  764.4073   300
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:475:1: style: Lines should not be more than 100 characters.

##      nonIterativeFun(ras, FALSE, n, sp)  1.509484  6.555565  31.18444 14.91066  42.78317  158.5237   300
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:476:1: style: Lines should not be more than 100 characters.

##           origSpread(ras, FALSE, n, sp)  5.154006  7.555631  14.87158 11.49005  17.50599  231.5487   300
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:477:1: style: Lines should not be more than 100 characters.

## origSpreadIterations(ras, FALSE, n, sp) 10.754669 51.524368 141.48620 93.61996 169.10808 2110.2683   300
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:688:38: style: Place a space before left parenthesis, except in a function call.

ciCentre[seq_len(ncell(ciCentre))[-(ncell(ciCentre) / 2 - ncol(ciCentre) / 2)]] <- NA_integer_
                                     ^

tests/testthat/test-spread2.R:884:1: style: Lines should not be more than 100 characters.

spreadProb = 0.23, persistProb = 0, iterations = 10, directions = 8L, plot.it = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:886:1: style: Lines should not be more than 100 characters.

spreadProb = 0.23, persistProb = 0.8, iterations = 10, directions = 8L, plot.it = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:891:3: style: Variable or function name should be lowerCamelCase.

M <- matrix(0.8, nrow = 50, ncol = 50)
  ^

tests/testthat/test-spread2.R:898:35: style: Put spaces around all infix operators.

start <- c(50, length(landscape)-49)
                                 ~^~

tests/testthat/test-spread2.R:902:1: style: Lines should not be more than 100 characters.

spreadProb = 0.23, persistProb = persistRas, iterations = 10, directions = 8L,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:916:14: style: Use <-, not =, for assignment.

spreadProb = landscape
             ^

tests/testthat/test-spread2.R:918:72: style: Commas should always have a space after.

​  expect_silent(spread2(landscape = landscape, spreadProb = spreadProb,start = start,
                                                                       ^

@lintr-bot
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@lintr-bot lintr-bot commented Jan 28, 2019

inst/examples/example_distanceFromEachPoint.R:37:2: style: Commented code should be removed.

#beginCluster(3) # can do parallel
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_distanceFromEachPoint.R:40:2: style: Commented code should be removed.

#endCluster() # if beginCluster was run
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:83:11: style: Do not place spaces around code in parentheses or square brackets.

if ( method != "RMexp") {
          ^

R/initialize.R:88:1: style: Lines should not be more than 100 characters.

map <- raster(RandomFields::RFsimulate(model, y = 1:ncSpeedup, x = 1:nrSpeedup, grid = TRUE, ...))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:223:1: style: Variable or function name should be lowerCamelCase.

randomPolygon.SpatialPoints <- function(x, hectares, area) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:247:4: style: Commented code should be removed.

#y <- spTransform(x, areaCRS)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:263:3: style: Variable or function name should be lowerCamelCase.

X <- c(jitter(sort(rbeta(nPoints, betaPar, betaPar) * (maxX - minX) + minX)),
  ^

R/initialize.R:265:3: style: Variable or function name should be lowerCamelCase.

Y <- c(jitter(sort(rbeta(nPoints / 2, betaPar, betaPar) * (maxY - meanY) + meanY)),
  ^

R/initialize.R:269:3: style: Variable or function name should be lowerCamelCase.

Sr1 <- Polygon(cbind(X + xAdd, Y + yAdd))
  ^~~

R/initialize.R:270:3: style: Variable or function name should be lowerCamelCase.

Srs1 <- Polygons(list(Sr1), "s1")
  ^~~~

R/initialize.R:283:1: style: Variable or function name should be lowerCamelCase.

randomPolygon.matrix <- function(x, hectares, area) {
^~~~~~~~~~~~~~~~~~~~

R/initialize.R:300:1: style: Variable or function name should be lowerCamelCase.

randomPolygon.SpatialPolygons <- function(x, hectares, area) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:307:8: style: Place a space before left parenthesis, except in a function call.

while(need) {
       ^

R/initialize.R:407:3: style: Commented code should be removed.

# ### INCORPORATE RELEVANT PARTS OF THIS OLD INIT FUNCTION INTO INITCOORDS()
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:412:3: style: Commented code should be removed.

# #'                      (currently only \code{RasterLayer} or
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:413:3: style: Commented code should be removed.

# #'                      \code{SpatialPolygonsDataFrame}) accepted.
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:423:7: style: Commented code should be removed.

#     ext <- extent(agentlocation)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:425:9: style: Commented code should be removed.

#       #            nonNAs <- !is.na(getvalue(probinit))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:426:9: style: Commented code should be removed.

#       nonNAs <- !is.na(getValues(probinit))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:427:9: style: Commented code should be removed.

#       wh.nonNAs <- which(nonNAs)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:428:9: style: Commented code should be removed.

#       #            ProbInit.v <- cumsum(getvalue(probinit)[nonNAs])
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:429:9: style: Commented code should be removed.

#       ProbInit.v <- cumsum(getValues(probinit)[nonNAs])
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:431:11: style: Commented code should be removed.

#         ran <- runif(numagents,0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:432:11: style: Commented code should be removed.

#         fI <- findInterval(ran, ProbInit.v)+1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:433:11: style: Commented code should be removed.

#         fI2 <- wh.nonNAs[fI]
          ^~~~~~~~~~~~~~~~~~~~

R/initialize.R:434:11: style: Commented code should be removed.

#         last.ran <- runif(numagents,0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:435:11: style: Commented code should be removed.

#         last.fI <- findInterval(last.ran, ProbInit.v)+1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:436:11: style: Commented code should be removed.

#         last.fI2 <- wh.nonNAs[last.fI]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:438:11: style: Commented code should be removed.

#         #                va <- getvalue(probinit)[nonNAs]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:439:11: style: Commented code should be removed.

#         va <- getValues(probinit)[nonNAs]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:440:11: style: Commented code should be removed.

#         ran <- runif(length(va), 0, 1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:441:11: style: Commented code should be removed.

#         fI2 <- wh.nonNAs[ran<va]
          ^~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:443:11: style: Commented code should be removed.

#         last.ran <- runif(length(fI2), 0, 1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:444:11: style: Commented code should be removed.

#         last.fI <- findInterval(last.ran, ProbInit.v) + 1
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:445:11: style: Commented code should be removed.

#         last.fI2 <- wh.nonNAs[last.fI]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:447:11: style: Commented code should be removed.

#         #                last.ran <- runif(length(fI2),0,1)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:448:11: style: Commented code should be removed.

#         #                last.fI2 <- wh.nonNAs[last.ran<va]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:451:11: style: Commented code should be removed.

#         position <- xyFromCell(agentlocation,fI2,spatial = TRUE)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:453:11: style: Commented code should be removed.

#         position <- coordinates(agentlocation)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:455:11: style: Commented code should be removed.

#         stop("need raster layer or Spatial Points object")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:457:9: style: Commented code should be removed.

#       numagents <- length(position)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:465:13: style: Commented code should be removed.

#           colnames(xy) = c("x", "y")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:466:13: style: Commented code should be removed.

#           position <- SpatialPoints(xy)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:467:13: style: Commented code should be removed.

#           position <- SpatialPoints(sampleRandom(agentlocation, numagents, xy = TRUE, sp = TRUE))
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:469:13: style: Commented code should be removed.

#           sam <- sample(1:length(agentlocation),numagents)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:470:13: style: Commented code should be removed.

#           position <- SpatialPoints(agentlocation[sam,])
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:472:13: style: Commented code should be removed.

#           stop("need raster layer or Spatial Points object")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:479:13: style: Commented code should be removed.

#           position <- SpatialPoints(agentlocation)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:481:13: style: Commented code should be removed.

#           stop("need raster layer or Spatial Points object")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:483:11: style: Commented code should be removed.

#         numagents <- length(position)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:491:11: style: Commented code should be removed.

#         numagents <- length(position)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:495:7: style: Commented code should be removed.

#     stop("Need to provide agentlocation, which can be a map layer")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:497:5: style: Commented code should be removed.

#   heading1 <- runif(numagents, 0, 360)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:498:5: style: Commented code should be removed.

#   distance <- runif(numagents, 0.1, 10)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:500:5: style: Commented code should be removed.

#   .Object@ID <- as.character(1:numagents)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:501:5: style: Commented code should be removed.

#   .Object@spatial <- position
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:502:5: style: Commented code should be removed.

#   .Object@heading <- heading1
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:503:5: style: Commented code should be removed.

#   .Object@distance <- distance
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/initialize.R:505:5: style: Commented code should be removed.

#   return(.Object)
    ^~~~~~~~~~~~~~~

R/initialize.R:510:32: style: Commas should always have a space after.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                               ^

R/initialize.R:510:37: style: Commas should always have a space after.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                                    ^

R/initialize.R:510:52: style: Commas should always have a space after.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                                                   ^

R/initialize.R:510:55: style: Put spaces around all infix operators.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                                                     ~^~

R/initialize.R:510:56: style: Only use double-quotes.

​  CRS(paste("+proj=utm +zone=",zone," ellps=WGS84",sep=''))
                                                       ^~

R/initialize.R:514:22: style: Put spaces around all infix operators.

​  (floor((long + 180)/6) %% 60) + 1
                    ~^~

R/mapReduce.R:53:3: style: Variable or function name should be lowerCamelCase.

BsumVec <- reduced[fullRasterVals] # join
  ^~~~~~~

R/neighbourhood.R:114:21: style: Variable or function name should be lowerCamelCase.

match.adjacent = FALSE, cutoff.for.data.table = 2e3,
                    ^~~~~~~~~~~~~~

R/neighbourhood.R:114:45: style: Variable or function name should be lowerCamelCase.

match.adjacent = FALSE, cutoff.for.data.table = 2e3,
                                            ^~~~~~~~~~~~~~~~~~~~~

R/neighbourhood.R:233:1: style: Lines should not be more than 100 characters.

​              ((adj[, "from"] %% numCol + adj[, "to"] %% numCol) == 1)) # | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/neighbourhood.R:238:1: style: Lines should not be more than 100 characters.

​              ((adj[, "from"] %% numCol + adj[, "to"] %% numCol) == 1)) # | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/neighbourhood.R:297:1: style: Lines should not be more than 100 characters.

​              ((from %% numCol + to %% numCol) == 1))# | #right & left edge cells, with neighbours wrapped
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/neighbourhood.R:806:29: style: Variable or function name should be lowerCamelCase.

setGeneric("wrap", function(X, bounds, withHeading) {
                            ^

R/neighbourhood.R:815:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:832:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:842:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:843:5: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds))
    ^

R/neighbourhood.R:852:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:853:5: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds))
    ^

R/neighbourhood.R:862:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds) {
                        ^

R/neighbourhood.R:865:7: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds))
      ^

R/neighbourhood.R:877:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds, withHeading) {
                        ^

R/neighbourhood.R:902:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds, withHeading) {
                        ^

R/neighbourhood.R:903:7: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds), withHeading = withHeading)
      ^

R/neighbourhood.R:912:25: style: Variable or function name should be lowerCamelCase.

definition = function(X, bounds, withHeading) {
                        ^

R/neighbourhood.R:915:7: style: Variable or function name should be lowerCamelCase.

X <- wrap(X, bounds = extent(bounds), withHeading = withHeading)
      ^

R/neighbourhood.R:1052:40: style: Commas should always have a space after.

cc <- cbind(pureCircle2[, "x"] - xy[,"x"], pureCircle2[, "y"] - xy[, "y"])
                                       ^

R/probability.R:41:35: style: Place a space before left parenthesis, except in a function call.

1 / sqrt(var * 2 * pi) * exp(-((theta - mu + 2 * pi * k) ^ 2) / (2 * var))
                                  ^

R/probability.R:44:3: style: Variable or function name should be lowerCamelCase.

Next <- term(theta, mu, var, k)
  ^~~~

R/probability.R:45:3: style: Variable or function name should be lowerCamelCase.

Last <- Next
  ^~~~

R/RcppExports.R:68:20: style: Variable or function name should be lowerCamelCase.

runifC <- function(N) {
                   ^

R/RcppExports.R:71:1: style: Trailing blank lines are superfluous.

^

R/SELES.R:53:23: style: Variable or function name should be lowerCamelCase.

numAgents <- function(N, probInit) {
                      ^

R/splitRaster.R:116:1: style: Lines should not be more than 100 characters.

​      clusterApplyLB(cl = cl, x = seq_along(extents), fun = croppy, e = extents, r = r, path = path, rType = rType)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread.R:538:8: style: Commented code should be removed.

#isNASpreadProb <- is.na(spreadProb[])
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread.R:540:11: style: Commented code should be removed.

#   isNASpreadProb <- is.na(spreadProb[])
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread.R:541:11: style: Commented code should be removed.

#   spreadProb[isNASpreadProb] <- 0L
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread.R:942:41: style: Place a space before left parenthesis, except in a function call.

notDupsEvents <- notDups[-(1:(nrSpreads - nrPotentials))]
                                        ^

R/spread2.R:5:1: style: Lines should not be more than 100 characters.

"quantityAdj", "quantityAdj2", "state", "size", "tooBigByNCells", "V1", "proportion"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:674:12: style: Commented code should be removed.

#pureCircle <- unique(pureCircle)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:759:13: style: Commented code should be removed.

# colnamesDtPot <- colnames(dtPotential)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:760:13: style: Commented code should be removed.

# ll <-  lapply(colnamesDtPot, function(x) dtPotential[[x]][!spreadProbNA])
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:761:13: style: Commented code should be removed.

# names(ll) <- colnamesDtPot
            ^~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:762:13: style: Commented code should be removed.

# dtPotential <- as.data.table(ll)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:772:1: style: Lines should not be more than 100 characters.

.I[sample.int(length(numNeighs), size = numNeighs, prob = spreadProbRel)],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:787:7: style: Variable or function name should be lowerCamelCase.

NAaSP <- !is.na(actualSpreadProb)
      ^~~~~

R/spread2.R:789:42: style: Commas should always have a space after.

dtPotential <- dtPotential[NAaSP,]
                                         ^

R/spread2.R:830:1: style: Lines should not be more than 100 characters.

# 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: style: Lines should not be more than 100 characters.

#successCells <- na.omit(successCells[!dupsWithinDtPotential]) # remove the dupsWithinDtPotential
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/spread2.R:848:10: style: Commented code should be removed.

#successCells <- na.omit(successCells[!dupsWithinDtPotential]) # remove the dupsWithinDtPotential
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-examples.R:6:11: style: Commented code should be removed.

​    cat("#START##############\n", file = tmpExFile, append = FALSE)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-examples.R:17:5: style: Commas should never have a space before.

​  } , add = TRUE)
   ~^

tests/testthat/test-mapReduce.R:23:4: style: Commented code should be removed.

#expect_equal(sort(unique(getValues(biomass))), sort(reducedDT$biomass))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:27:5: style: Commented code should be removed.

#   library(data.table)
    ^~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:28:5: style: Commented code should be removed.

#   library(raster)
    ^~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:31:6: style: Commented code should be removed.

#    detach("package:data.table")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:35:5: style: Commented code should be removed.

#   ras <- raster(extent(0,15,0,15), res=1)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:36:5: style: Commented code should be removed.

#   fullRas <- randomPolygons(ras, numTypes=5, speedup=1, p=0.3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:37:5: style: Commented code should be removed.

#   names(fullRas) <- "mapcodeAll"
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:38:5: style: Commented code should be removed.

#   uniqueComms <- raster::unique(fullRas)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:42:7: style: Commented code should be removed.

#     biomass=rnbinom(length(uniqueComms), mu=4000, 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:44:5: style: Commented code should be removed.

#   biomass <- rasterizeReduced(reducedDT, fullRas, "biomass")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:46:5: style: Commented code should be removed.

#   expect_equal(sort(unique(getValues(biomass))), sort(reducedDT$biomass))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:47:5: style: Commented code should be removed.

#   expect_equal(length(unique(getValues(biomass))), length(unique(getValues(fullRas))))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:49:5: style: Commented code should be removed.

#   setkey(reducedDT, biomass)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:50:5: style: Commented code should be removed.

#   communities <- rasterizeReduced(reducedDT, fullRas, "communities")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:51:5: style: Commented code should be removed.

#   expect_equal(sort(unique(getValues(communities))), sort(reducedDT$communities))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:52:5: style: Commented code should be removed.

#   expect_equal(length(unique(getValues(communities))), length(unique(getValues(fullRas))))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:56:5: style: Commented code should be removed.

#   library(data.table)
    ^~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:57:5: style: Commented code should be removed.

#   library(raster)
    ^~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:60:6: style: Commented code should be removed.

#    detach("package:data.table")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:64:5: style: Commented code should be removed.

#   ras <- raster(extent(0, 15, 0, 15), res = 1)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:65:5: style: Commented code should be removed.

#   fullRas <- randomPolygons(ras, numTypes = 5, speedup = 1, p = 0.3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:67:5: style: Commented code should be removed.

#   uniqueComms <- raster::unique(fullRas)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:71:7: style: Commented code should be removed.

#     biomass=rnbinom(length(uniqueComms), mu = 4000, 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:73:5: style: Commented code should be removed.

#   biomass <- rasterizeReduced(reducedDT, fullRas, "biomass")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:75:5: style: Commented code should be removed.

#   setkey(reducedDT, biomass)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:76:5: style: Commented code should be removed.

#   communities <- rasterizeReduced(reducedDT, fullRas, "communities")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:77:5: style: Commented code should be removed.

#   expect_equal(sort(unique(getValues(communities))), sort(reducedDT$communities))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:81:5: style: Commented code should be removed.

#   library(data.table)
    ^~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:82:5: style: Commented code should be removed.

#   library(raster)
    ^~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:85:6: style: Commented code should be removed.

#    detach("package:data.table")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:89:5: style: Commented code should be removed.

#   ras <- raster(extent(0,15,0,15), res=1)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:90:5: style: Commented code should be removed.

#   fullRas <- randomPolygons(ras, numTypes=5, speedup=1, p=0.3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:91:5: style: Commented code should be removed.

#   names(fullRas) <- "mapcodeAll"
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:92:5: style: Commented code should be removed.

#   uniqueComms <- raster::unique(fullRas)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:96:7: style: Commented code should be removed.

#     biomass=rnbinom(length(uniqueComms), mu=4000, 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:98:5: style: Commented code should be removed.

#   biomass <- rasterizeReduced(reducedDT, fullRas, "biomass")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R💯5: style: Commented code should be removed.

#   setkey(reducedDT, biomass)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:101:5: style: Commented code should be removed.

#   communities <- rasterizeReduced(reducedDT, fullRas, "communities")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mapReduce.R:102:5: style: Commented code should be removed.

#   expect_equal(length(unique(getValues(communities))), length(unique(getValues(fullRas))))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mergeRaster.R:4:6: style: Use <-, not =, for assignment.

nx = 3
     ^

tests/testthat/test-mergeRaster.R:5:6: style: Use <-, not =, for assignment.

ny = 3
     ^

tests/testthat/test-mergeRaster.R:10:54: style: Commas should never have a space before.

vals = round(runif(n = 14400 , min = 1, max = 10)))
                                                    ~^

tests/testthat/test-mergeRaster.R:13:29: style: Put spaces around all infix operators.

​  expect_length(splitted, nx*ny)
                           ~^~

tests/testthat/test-mergeRaster.R:33:6: style: Use <-, not =, for assignment.

nx = 3
     ^

tests/testthat/test-mergeRaster.R:34:6: style: Use <-, not =, for assignment.

ny = 3
     ^

tests/testthat/test-mergeRaster.R:39:54: style: Commas should never have a space before.

vals = round(runif(n = 14400 , min = 1, max = 10)))
                                                    ~^

tests/testthat/test-mergeRaster.R:42:29: style: Put spaces around all infix operators.

​  expect_length(splitted, nx*ny)
                           ~^~

tests/testthat/test-mergeRaster.R:52:54: style: Commas should never have a space before.

vals = round(runif(n = 14400 , min = 1, max = 10)))
                                                    ~^

tests/testthat/test-mergeRaster.R:55:1: style: Lines should not be more than 100 characters.

​test_that("mergeRaster will use mosaic with default mean if rasters are resampled and fun if passed", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mergeRaster.R:58:6: style: Use <-, not =, for assignment.

nx = 3
     ^

tests/testthat/test-mergeRaster.R:59:6: style: Use <-, not =, for assignment.

ny = 3
     ^

tests/testthat/test-mergeRaster.R:64:54: style: Commas should never have a space before.

vals = round(runif(n = 14400 , min = 1, max = 10)))
                                                    ~^

tests/testthat/test-mergeRaster.R:67:29: style: Put spaces around all infix operators.

​  expect_length(splitted, nx*ny)
                           ~^~

tests/testthat/test-randomPolygon.R:24:60: style: Put spaces around all infix operators.

​  expect_true(base::abs(base::abs(polyArea - area)) <  area/4) ## TODO: why is this area/4?
                                                          ~^~

tests/testthat/test-randomPolygon.R:28:3: style: Variable or function name should be lowerCamelCase.

centerSP_UTM <- sp::spTransform(centerSP, CRSobj = raster::crs(poly1InUTM))
  ^~~~~~~~~~~~

tests/testthat/test-randomPolygon.R:30:1: style: Lines should not be more than 100 characters.

​  expect_true(raster::pointDistance(centerSP_UTM, polyCenter, lonlat = FALSE) < 100) ## TODO: appropriate test?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:148:38: style: Commas should always have a space after.

​  expect_identical(dataType(y4[[1]]),"INT1U")
                                     ^

tests/testthat/test-splitRaster.R:165:1: style: Lines should not be more than 100 characters.

tmpdir <- file.path(tempdir(), "splitRaster-test-parallel") %>% reproducible::checkPath(create = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:168:8: style: Commented code should be removed.

#detach("package:raster")
       ^~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:226:1: style: Lines should not be more than 100 characters.

tmpdir <- file.path(tempdir(), "splitRaster-test-large") %>% reproducible::checkPath(create = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:264:4: style: Commented code should be removed.

#expect_equal(min(values(m)), min(values(r))) ## Error: cannot allocate vector of size 4.8 Gb
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:283:4: style: Commented code should be removed.

#expect_equal(max(values(m1)), max(values(r)))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-splitRaster.R:284:4: style: Commented code should be removed.

#expect_equal(min(values(m1)), min(values(r)))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread.R:209:1: style: Lines should not be more than 100 characters.

if (interactive()) Plot(circEdge, addTo = "circs", cols = c("transparent", rainbow(numCircs)[whCirc]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:148:4: style: Commented code should be removed.

#quickDT <- data.table(id = seq_along(sams), initialPixels = sams, key = "id")
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:150:4: style: Commented code should be removed.

#cirOut <- quickDT[cirOut, on = ]
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:473:1: style: Lines should not be more than 100 characters.

##                                    expr       min        lq      mean   median        uq       max neval
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:474:1: style: Lines should not be more than 100 characters.

##         iterativeFun(ras, FALSE, n, sp)  3.096979 12.642477  73.02248 35.17520  91.10528  764.4073   300
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:475:1: style: Lines should not be more than 100 characters.

##      nonIterativeFun(ras, FALSE, n, sp)  1.509484  6.555565  31.18444 14.91066  42.78317  158.5237   300
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:476:1: style: Lines should not be more than 100 characters.

##           origSpread(ras, FALSE, n, sp)  5.154006  7.555631  14.87158 11.49005  17.50599  231.5487   300
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:477:1: style: Lines should not be more than 100 characters.

## origSpreadIterations(ras, FALSE, n, sp) 10.754669 51.524368 141.48620 93.61996 169.10808 2110.2683   300
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:688:38: style: Place a space before left parenthesis, except in a function call.

ciCentre[seq_len(ncell(ciCentre))[-(ncell(ciCentre) / 2 - ncol(ciCentre) / 2)]] <- NA_integer_
                                     ^

tests/testthat/test-spread2.R:884:1: style: Lines should not be more than 100 characters.

spreadProb = 0.23, persistProb = 0, iterations = 10, directions = 8L, plot.it = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:886:1: style: Lines should not be more than 100 characters.

spreadProb = 0.23, persistProb = 0.8, iterations = 10, directions = 8L, plot.it = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:891:3: style: Variable or function name should be lowerCamelCase.

M <- matrix(0.8, nrow = 50, ncol = 50)
  ^

tests/testthat/test-spread2.R:898:35: style: Put spaces around all infix operators.

start <- c(50, length(landscape)-49)
                                 ~^~

tests/testthat/test-spread2.R:902:1: style: Lines should not be more than 100 characters.

spreadProb = 0.23, persistProb = persistRas, iterations = 10, directions = 8L,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-spread2.R:916:14: style: Use <-, not =, for assignment.

spreadProb = landscape
             ^

tests/testthat/test-spread2.R:918:72: style: Commas should always have a space after.

​  expect_silent(spread2(landscape = landscape, spreadProb = spreadProb,start = start,
                                                                       ^

@eliotmcintire eliotmcintire merged commit 181d195 into PredictiveEcology:development Jan 28, 2019
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