Using the caret and xgboost packages and this tutorial, I am running an XGBoost regression (XGBR) and I want to extract the residuals of the XGBR. I hyper-tuned the model using the caret package and then, using the 'best' model parameters I used the xgboost package to perform the regression.
My dataset has the ntl, pop, tirs, agbh variables stored in data.frame (ntl is the dependent variable while the other three are the independent). Assuming that my XGBR model is called m and my data.frame is called block.data, I did:
library(caret)
library(raster)
library(xgboost)
xgb_m <- xgb.DMatrix(data = data.matrix(block.data), label = block.data$ntl)
m = xgboost(data = xgb_m,
max.depth = xgb_tune5$bestTune$max_depth,
nrounds = xgb_tune5$bestTune$nrounds,
min_child_weight = xgb_tune5$bestTune$min_child_weight,
subsample = xgb_tune5$bestTune$subsample,
eta = xgb_tune5$bestTune$eta,
gamma = xgb_tune5$bestTune$gamma,
colsample_bytree = xgb_tune5$bestTune$colsample_bytree,
objective = "reg:squarederror")
# export xgb residuals
p = predict(m, xgb_m, na.rm = TRUE)
xgb_resids = s$ntl - p # s is a raster stack containing my variables
plot(xgb_resids)
The plot looks like this:
Obviously, I am doing something very wrong. How can I export the residuals of an XGBR as a single raster?
Here is a very small sample of my dataset:
block.data = structure(list(x = c(11880750L, 11879250L, 11879750L, 11880250L,
11880750L, 11881250L, 11879250L, 11879750L, 11880250L, 11880750L,
11881250L, 11878750L, 11879250L, 11879750L, 11880250L, 11880750L,
11881250L, 11879250L, 11879750L, 11880250L, 11880750L, 11881250L,
11881750L, 11882250L, 11879250L, 11879750L, 11880250L, 11880750L,
11881250L, 11881750L, 11882250L, 11882750L, 11879250L, 11879750L
), y = c(1802250L, 1801750L, 1801750L, 1801750L, 1801750L, 1801750L,
1801250L, 1801250L, 1801250L, 1801250L, 1801250L, 1800750L, 1800750L,
1800750L, 1800750L, 1800750L, 1800750L, 1800250L, 1800250L, 1800250L,
1800250L, 1800250L, 1800250L, 1800250L, 1799750L, 1799750L, 1799750L,
1799750L, 1799750L, 1799750L, 1799750L, 1799750L, 1799250L, 1799250L
), ntl = c(18.7969169616699, 25.7222957611084, 23.4188251495361,
25.4322757720947, 16.4593601226807, 12.7868213653564, 30.9337253570557,
29.865758895874, 30.4080600738525, 29.5479888916016, 24.3493347167969,
35.2427635192871, 38.989933013916, 34.6536979675293, 29.4607238769531,
30.7469024658203, 34.3946380615234, 42.8660278320312, 34.7930717468262,
30.9516315460205, 32.20654296875, 39.999755859375, 46.6002235412598,
38.6480979919434, 60.5214920043945, 33.1799964904785, 31.8498134613037,
30.9209423065186, 32.2269744873047, 53.7062034606934, 45.5225944519043,
38.3570976257324, 123.040382385254, 73.0528182983398), pop = c(19.6407718658447,
610.009216308594, 654.812622070312, 426.475830078125, 66.3839492797852,
10.6471328735352, 443.848846435547, 602.677429199219, 488.478454589844,
387.470947265625, 58.2341117858887, 413.888488769531, 315.057678222656,
354.082946777344, 602.827758789062, 463.518829345703, 296.713928222656,
923.920593261719, 434.436645507812, 799.562927246094, 404.709564208984,
265.043304443359, 366.697235107422, 399.851684570312, 952.2314453125,
870.356994628906, 673.406616210938, 493.521606445312, 273.841888427734,
371.428619384766, 383.057830810547, 320.986755371094, 991.131225585938,
1148.87768554688), tirs = c(39.7242431640625, 44.9583969116211,
41.4048385620117, 42.6056709289551, 40.0976028442383, 38.7490005493164,
44.2747650146484, 43.5645370483398, 41.6180191040039, 40.3799781799316,
38.8664817810059, 44.9089202880859, 44.414306640625, 44.560977935791,
43.1288986206055, 40.9315185546875, 38.8918418884277, 46.3063850402832,
45.5805702209473, 44.9196586608887, 42.2495613098145, 39.3051452636719,
38.7914810180664, 38.6069412231445, 44.6782455444336, 46.4024772644043,
44.4720573425293, 41.7361183166504, 42.3378067016602, 41.0018348693848,
39.3579216003418, 41.6303863525391, 43.8207550048828, 46.0460357666016
), agbh = c(3.32185006141663, 4.98925733566284, 4.35699367523193,
4.94798421859741, 3.14325952529907, 2.93211793899536, 4.52736520767212,
4.99723243713379, 5.13944292068481, 3.92965626716614, 3.43465113639832,
3.55617475509644, 3.4659411907196, 5.24469566345215, 5.36995029449463,
4.61549234390259, 4.82002925872803, 4.20452928543091, 4.71502685546875,
5.20452785491943, 5.05676746368408, 5.9952244758606, 6.16778612136841,
4.69053316116333, 2.62325501441956, 4.74775457382202, 4.93133020401001,
5.02366256713867, 5.74016952514648, 6.28353786468506, 4.67424774169922,
4.56812858581543, 1.88153350353241, 4.31531000137329)), class = "data.frame", row.names = c(NA,
-34L))
My raster layer:
r = new("RasterBrick", file = new(".RasterFile", name = "", datanotation = "FLT4S",
byteorder = "little", nodatavalue = -Inf, NAchanged = FALSE,
nbands = 1L, bandorder = "BIL", offset = 0L, toptobottom = TRUE,
blockrows = 0L, blockcols = 0L, driver = "", open = FALSE),
data = new(".MultipleRasterData", values = structure(c(NA,
NA, NA, NA, 18.7969169616699, NA, NA, NA, NA, NA, 25.7222957611084,
23.4188251495361, 25.4322757720947, 16.4593601226807, 12.7868213653564,
NA, NA, NA, NA, 30.9337253570557, 29.865758895874, 30.4080600738525,
29.5479888916016, 24.3493347167969, NA, NA, NA, 35.2427635192871,
38.989933013916, 34.6536979675293, 29.4607238769531, 30.7469024658203,
34.3946380615234, NA, NA, NA, NA, 42.8660278320312, 34.7930717468262,
30.9516315460205, 32.20654296875, 39.999755859375, 46.6002235412598,
38.6480979919434, NA, NA, 60.5214920043945, 33.1799964904785,
31.8498134613037, 30.9209423065186, 32.2269744873047, 53.7062034606934,
45.5225944519043, 38.3570976257324, NA, 123.040382385254,
73.0528182983398, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
19.6407718658447, NA, NA, NA, NA, NA, 610.009216308594, 654.812622070312,
426.475830078125, 66.3839492797852, 10.6471328735352, NA,
NA, NA, NA, 443.848846435547, 602.677429199219, 488.478454589844,
387.470947265625, 58.2341117858887, NA, NA, NA, 413.888488769531,
315.057678222656, 354.082946777344, 602.827758789062, 463.518829345703,
296.713928222656, NA, NA, NA, NA, 923.920593261719, 434.436645507812,
799.562927246094, 404.709564208984, 265.043304443359, 366.697235107422,
399.851684570312, NA, NA, 952.2314453125, 870.356994628906,
673.406616210938, 493.521606445312, 273.841888427734, 371.428619384766,
383.057830810547, 320.986755371094, NA, 991.131225585938,
1148.87768554688, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
39.7242431640625, NA, NA, NA, NA, NA, 44.9583969116211, 41.4048385620117,
42.6056709289551, 40.0976028442383, 38.7490005493164, NA,
NA, NA, NA, 44.2747650146484, 43.5645370483398, 41.6180191040039,
40.3799781799316, 38.8664817810059, NA, NA, NA, 44.9089202880859,
44.414306640625, 44.560977935791, 43.1288986206055, 40.9315185546875,
38.8918418884277, NA, NA, NA, NA, 46.3063850402832, 45.5805702209473,
44.9196586608887, 42.2495613098145, 39.3051452636719, 38.7914810180664,
38.6069412231445, NA, NA, 44.6782455444336, 46.4024772644043,
44.4720573425293, 41.7361183166504, 42.3378067016602, 41.0018348693848,
39.3579216003418, 41.6303863525391, NA, 43.8207550048828,
46.0460357666016, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
3.32185006141663, NA, NA, NA, NA, NA, 4.98925733566284, 4.35699367523193,
4.94798421859741, 3.14325952529907, 2.93211793899536, NA,
NA, NA, NA, 4.52736520767212, 4.99723243713379, 5.13944292068481,
3.92965626716614, 3.43465113639832, NA, NA, NA, 3.55617475509644,
3.4659411907196, 5.24469566345215, 5.36995029449463, 4.61549234390259,
4.82002925872803, NA, NA, NA, NA, 4.20452928543091, 4.71502685546875,
5.20452785491943, 5.05676746368408, 5.9952244758606, 6.16778612136841,
4.69053316116333, NA, NA, 2.62325501441956, 4.74775457382202,
4.93133020401001, 5.02366256713867, 5.74016952514648, 6.28353786468506,
4.67424774169922, 4.56812858581543, NA, 1.88153350353241,
4.31531000137329, NA, NA, NA, NA, NA, NA), .Dim = c(63L,
4L)), offset = 0, gain = 1, inmemory = TRUE, fromdisk = FALSE,
nlayers = 4L, dropped = NULL, isfactor = c(FALSE, FALSE,
FALSE, FALSE), attributes = list(), haveminmax = TRUE,
min = c(12.7868213653564, 10.6471328735352, 38.6069412231445,
1.88153350353241), max = c(123.040382385254, 1148.87768554688,
46.4024772644043, 6.28353786468506), unit = "", names = c("ntl",
"pop", "tirs", "agbh")), legend = new(".RasterLegend",
type = character(0), values = logical(0), color = logical(0),
names = logical(0), colortable = logical(0)), title = character(0),
extent = new("Extent", xmin = 11878500, xmax = 11883000,
ymin = 1799000, ymax = 1802500), rotated = FALSE, rotation = new(".Rotation",
geotrans = numeric(0), transfun = function ()
NULL), ncols = 9L, nrows = 7L, crs = new("CRS", projargs = NA_character_),
srs = character(0), history = list(), z = list())