LandWeb/13-old.R at master · fRI-Research/LandWeb · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
  ##########################################################
  # Reporting Polygons
  ##########################################################
  ml2 <- mapAdd(map = ml, layerName = "AB Natural Sub Regions",
                url = "https://drive.google.com/file/d/1mCEynahKnFkStJUJC8ho5ndRD41olz9F/view?usp=sharing",
                columnNameForLabels = "Name")

  ##########################################################
  # Load other maps
  ##########################################################

  ml <- mapAdd(map = ml,
               destinationPath = "~/GitHub/LandWeb/inputs/FMA_Boundaries/DMI/",
               targetCRS = targetCRS,
               targetFile = "DMI_Full.shp", #studyArea = studyArea(ml, 1),
               layerName = "DMI Full", overwrite = TRUE, isStudyArea = TRUE,
               columnNameForLabels = "Name", administrative = TRUE)

  ml <- mapAdd(map = ml, layerName = "AB Natural Sub Regions", overwrite = TRUE,
               url = "https://drive.google.com/file/d/1mCEynahKnFkStJUJC8ho5ndRD41olz9F/view?usp=sharing",
               columnNameForLabels = "Name", filename2 = NULL)

  ml <- mapAdd(url = "https://drive.google.com/open?id=1JnKeXrw0U9LmrZpixCDooIm62qiv4_G1",
               map = ml, leaflet = TRUE, #studyArea = studyArea(ml, 2),
               #targetFile = "age1.tif", overwrite = TRUE,
               filename2 = NULL,
               layerName = "Age") # dots include things like method = "ngb" for projectRaster

  ################################
  # set some options
  #################################
  source("appInfo.R")

  # Options
  originalOpts <- options("spades.moduleCodeChecks" = FALSE, "reproducible.quick" = FALSE,
                          reproducible.verbose = FALSE, reproducible.useMemoise = TRUE,
                          spades.browserOnError = FALSE)

  # Google Authentication setup
  options(googleAuthR.scopes.selected = c("https://www.googleapis.com/auth/userinfo.email",
                                          "https://www.googleapis.com/auth/userinfo.profile"))

  if (Sys.info()["nodename"] == "landweb.ca") {
    ## LandWeb.ca (live version)
    options(googleAuthR.webapp.client_id = "680957910261-kmlslu6vu0fo9129oj1fckksapg94gja.apps.googleusercontent.com")
    options(googleAuthR.webapp.client_secret = "Qe0TE327wRf9DYM-BEhDxe4a")
  } else {
    ## LandWeb.org (Alex's development version)
    options(googleAuthR.webapp.client_id = "869088473060-a7o2bc7oit2vn11gj3ieh128eh8orb04.apps.googleusercontent.com")
    options(googleAuthR.webapp.client_secret = "FR-4jL12j_ynAtsl-1Yk_cEL")
  }
  options(httr_oob_default = TRUE)

  appURL <- "http://landweb.ca"

  ##########################################################
  # Set paths
  ##########################################################
  paths <- list(
    cachePath = "cache",
    modulePath = "m", # short name because shinyapps.io can't handle longer than 100 characters
    inputPath = "inputs",
    outputPath = "outputs"
  )
  do.call(setPaths, paths) # Set them here so that we don't have to specify at each call to Cache

  ##########################################################
  # source auxiliary functions
  ##########################################################
  source("R/functions.R")
  ## source additional shiny modules
  vapply(list.files("shiny-modules", "[.]R", full.names = TRUE), source, vector("list", 2))

  # This needs simInit call to be run already
  # a few map details for shiny app
  message("Preparing polygon maps for reporting histograms")
  source(file.path("R", "colorPaletteForShiny.R"))
  labelColumn <- "shinyLabel"


  # leaflet parameters
  leafletZoomInit <- 5

  # Some shinycssloaders options
  options("spinner.type" = 5)

  # This will search for gdal utilities. If it finds nothing, and you are on Windows,
  #   you should install the GDAL that comes with QGIS -- use OSGeo4W Network Installer 64 bit
  #   may be still here: http://www.qgis.org/en/site/forusers/download.html
  options(gdalUtils_gdalPath = Cache(gdalSet, cacheRepo = paths$cachePath))

  ########################################
  # simInit
  ########################################
  # Time steps
  fireTimestep <- 1
  successionTimestep <- 10

  ## spades module variables -- creates
  # eventCaching, maxAge, vegLeadingProportion
  # ageClasses, ageClassCutOffs, ageClas0s0Zones
  source("R/LandWeb user parameters.R")
  landisInputs <- readRDS(file.path(paths$inputPath, "landisInputs.rds"))
  spEcoReg <- readRDS(file.path(paths$inputPath, "SpEcoReg.rds"))

  # The CRS for the Study -- spTransform converts this first one to the second one, they are identical geographically
  # crsStudyArea <- CRS(paste("+proj=lcc +lat_1=49 +lat_2=77 +lat_0=0 +lon_0=-95 +x_0=0 +y_0=0",
  #                         "+datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"))
  crsStudyArea <- CRS(paste("+proj=lcc +lat_1=49 +lat_2=77 +lat_0=0 +lon_0=-95 +x_0=0 +y_0=0",
                              "+ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs"))


  ######################################################
  ml <- mapAdd(map = ml,
               url = "https://drive.google.com/file/d/1Oz2vSor3oIKf2uGv3KRtLoLRWEfX5Mas/view?usp=sharing",
               layerName = "Mountain Northern Caribou Ranges",
               columnNameForLabels = "Name")

  ml <- mapAdd(map = ml, layerName = "Provincial Parks",
               url = "https://drive.google.com/file/d/1GHgTI4JY-YhAXvWkgV20vugbvLNqEEGH/view?usp=sharing",
               columnNameForLabels = "Name")
  ml <- mapAdd(map = ml, layerName = "NWT Ecoregions",
               url = "https://drive.google.com/file/d/1iRAQfARkmS6-XVHFnTkB-iltzMNPAczC/view?usp=sharing",
               columnNameForLabels = "Name")
  ml <- mapAdd(map = ml, layerName = "National Parks",
               url = "https://drive.google.com/file/d/1B3VUU8PDn4NPveAyF76OBPY0vZkxScEt/view?usp=sharing",
               columnNameForLabels = "Name")
  ml <- mapAdd(map = ml, layerName = "AB Natural Sub Regions",
               url = "https://drive.google.com/file/d/1mCEynahKnFkStJUJC8ho5ndRD41olz9F/view?usp=sharing",
               columnNameForLabels = "Name")
  # "LP MASTERFILE June62012",
  #   url = "https://drive.google.com/file/d/1J38DKQQavjBV9F3z2gGzHNuNE0s2rmhh/view?usp=sharing",
  #   columnNameForLabels = "Name"),
  ml <- mapAdd(map = ml, layerName = "BC Bio Geoclimatic Zones",
               url = "https://drive.google.com/file/d/1VAwsax63l2akOM2j_O4Je9p0ZiYg8Hl-/view?usp=sharing",
               columnNameForLabels = "ZONE_NAME")
  ml <- mapAdd(map = ml, layerName = "FMU Alberta 2015-11",
               url = "https://drive.google.com/file/d/1JiCLcHh5fsBAy8yAx8NgtK7fxaZ4Tetl/view?usp=sharing",
               columnNameForLabels = "FMU_NAME")
  ml <- mapAdd(map = ml, layerName = "FMA Boundary Updated",
               url = "https://drive.google.com/file/d/1nTFOcrdMf1hIsxd_yNCSTr8RrYNHHwuc/view?usp=sharing",
               columnNameForLabels = "Name")
  ml <- mapAdd(map = ml, layerName = "Boreal Caribou Ranges",
               url = "https://drive.google.com/file/d/1PYLou8J1wcrme7Z2tx1wtA4GvaWnU1Jy/view?usp=sharing",
               columnNameForLabels = "Name")


  ### RASTERS
  # STOPPED HERE
  # Current Condition
  preProcess(url = "https://drive.google.com/file/d/1JnKeXrw0U9LmrZpixCDooIm62qiv4_G1/view?usp=sharing")

  ml <- mapAdd(map = ml, url = "https://drive.google.com/file/d/1Oz2vSor3oIKf2uGv3KRtLoLRWEfX5Mas/view?usp=sharing",
               layerName = "Mountain Northern Caribou Ranges",
               columnNameForLabels = "Name")