Merges two hyperSpec objects and base::cbind()s their spectra
matrices, or merges additional extra data into a hyperSpec object.
# S4 method for hyperSpec,hyperSpec
merge(x, y, ...)
# S4 method for hyperSpec,data.frame
merge(x, y, ...)
# S4 method for data.frame,hyperSpec
merge(x, y, ...)a hyperSpec object or data.frame
a hyperSpec object or data.frame
(including derived classes like tibble)
handed to base::merge.data.frame()
After merging, the spectra matrix can contain duplicates, and is not ordered according to the wavelength.
If the wavelength axis should be ordered, use wl_sort().
If a hyperSpec object and a data.frame are merged, the result is
of the class of the first (x) object.
collapse() combines hyperSpec objects that do not share the wavelength axis.
merge(faux_cell[1:10, , 600], faux_cell[5:15, , 600], by = c("x", "y"))$.
#> x y region.x .nx region.y .ny spc.1 spc.2
#> 1 -2.55 -4.77 matrix 10 matrix 6 NA NA
#> 2 -3.55 -4.77 matrix 9 matrix 5 NA NA
#> 3 -4.55 -4.77 matrix 8 matrix 4 NA NA
#> 4 -5.55 -4.77 matrix 7 matrix 3 NA NA
#> 5 -6.55 -4.77 matrix 6 matrix 2 NA NA
#> 6 -7.55 -4.77 matrix 5 matrix 1 NA NA
tmp <- merge(faux_cell[1:10, , 610], faux_cell[5:15, , 610],
by = c("x", "y"), all = TRUE
)
tmp$.
#> x y region.x .nx region.y .ny spc.1 spc.2
#> 1 -11.55 -4.77 matrix 1 <NA> NA 15 NA
#> 2 -10.55 -4.77 matrix 2 <NA> NA 159 NA
#> 3 -9.55 -4.77 matrix 3 <NA> NA 99 NA
#> 4 -8.55 -4.77 matrix 4 <NA> NA 39 NA
#> 5 -7.55 -4.77 matrix 5 matrix 1 1 1
#> 6 -6.55 -4.77 matrix 6 matrix 2 90 90
#> 7 -5.55 -4.77 matrix 7 matrix 3 79 79
#> 8 -4.55 -4.77 matrix 8 matrix 4 59 59
#> 9 -3.55 -4.77 matrix 9 matrix 5 152 152
#> 10 -2.55 -4.77 matrix 10 matrix 6 163 163
#> 11 -1.55 -4.77 <NA> NA matrix 7 NA 176
#> 12 -0.55 -4.77 <NA> NA matrix 8 NA 33
#> 13 0.45 -4.77 <NA> NA matrix 9 NA 11
#> 14 1.45 -4.77 <NA> NA matrix 10 NA 66
#> 15 2.45 -4.77 <NA> NA matrix 11 NA 84
wl(tmp)
#> [1] 610 610
## remove duplicated wavelengths:
approxfun <- function(y, wl, new.wl) {
approx(wl, y, new.wl,
method = "constant",
ties = function(x) mean(x, na.rm = TRUE)
)$y
}
merged <- merge(faux_cell[1:7, , 610 ~ 620], faux_cell[5:10, , 615 ~ 625], all = TRUE)
merged$.
#> x y region .nx .ny spc.1 spc.2 spc.3 spc.4 spc.5 spc.6 spc.7
#> 1 -11.55 -4.77 matrix 1 NA 15 13 15 NA NA NA NA
#> 2 -10.55 -4.77 matrix 2 NA 159 175 160 NA NA NA NA
#> 3 -9.55 -4.77 matrix 3 NA 99 115 119 NA NA NA NA
#> 4 -8.55 -4.77 matrix 4 NA 39 25 34 NA NA NA NA
#> 5 -7.55 -4.77 matrix 5 1 1 2 2 2 2 2 2
#> 6 -6.55 -4.77 matrix 6 2 90 87 105 87 105 100 98
#> 7 -5.55 -4.77 matrix 7 3 79 93 96 93 96 108 103
#> 8 -4.55 -4.77 matrix NA 4 NA NA NA 71 58 66 59
#> 9 -3.55 -4.77 matrix NA 5 NA NA NA 142 130 136 141
#> 10 -2.55 -4.77 matrix NA 6 NA NA NA 164 144 163 153
merged <- apply(merged, 1, approxfun,
wl = wl(merged), new.wl = unique(wl(merged)),
new.wavelength = "new.wl"
)
merged$.
#> x y region .nx .ny spc.1 spc.2 spc.3 spc.4 spc.5
#> 1 -11.55 -4.77 matrix 1 NA 15 13 15 NA NA
#> 2 -10.55 -4.77 matrix 2 NA 159 175 160 NA NA
#> 3 -9.55 -4.77 matrix 3 NA 99 115 119 NA NA
#> 4 -8.55 -4.77 matrix 4 NA 39 25 34 NA NA
#> 5 -7.55 -4.77 matrix 5 1 1 2 2 2 2
#> 6 -6.55 -4.77 matrix 6 2 90 87 105 100 98
#> 7 -5.55 -4.77 matrix 7 3 79 93 96 108 103
#> 8 -4.55 -4.77 matrix NA 4 NA 71 58 66 59
#> 9 -3.55 -4.77 matrix NA 5 NA 142 130 136 141
#> 10 -2.55 -4.77 matrix NA 6 NA 164 144 163 153
## merging data.frame into hyperSpec object => hyperSpec object
y <- data.frame(filename = sample(flu$filename, 4, replace = TRUE), cpred = 1:4)
y
#> filename cpred
#> 1 rawdata/flu2.txt 1
#> 2 rawdata/flu3.txt 2
#> 3 rawdata/flu1.txt 3
#> 4 rawdata/flu2.txt 4
tmp <- merge(flu, y)
tmp$..
#> filename c cpred
#> 1 rawdata/flu1.txt 0.05 3
#> 2 rawdata/flu2.txt 0.10 1
#> 3 rawdata/flu2.txt 0.10 4
#> 4 rawdata/flu3.txt 0.15 2
## merging hyperSpec object into data.frame => data.frame
merge(y, flu)
#> filename cpred spc.405 spc.405.5 spc.406 spc.406.5 spc.407
#> 1 rawdata/flu1.txt 3 27.15000 32.34467 33.37867 34.41933 36.53133
#> 2 rawdata/flu2.txt 1 66.80133 63.71533 66.71200 69.58233 72.52967
#> 3 rawdata/flu2.txt 4 66.80133 63.71533 66.71200 69.58233 72.52967
#> 4 rawdata/flu3.txt 2 93.14433 103.06767 106.19367 110.18633 113.24867
#> spc.407.5 spc.408 spc.408.5 spc.409 spc.409.5 spc.410 spc.410.5
#> 1 37.64767 38.13700 39.17700 40.73567 41.38133 44.25133 44.12633
#> 2 74.55833 77.04800 80.25967 82.53867 84.49167 88.15167 91.08533
#> 3 74.55833 77.04800 80.25967 82.53867 84.49167 88.15167 91.08533
#> 4 119.17300 121.31333 124.67533 129.56867 134.11733 139.98667 145.02333
#> spc.411 spc.411.5 spc.412 spc.412.5 spc.413 spc.413.5 spc.414
#> 1 46.98067 49.08167 50.27433 50.10967 52.23167 53.03967 54.51900
#> 2 95.37233 95.53033 98.99533 101.03433 103.55800 107.02667 109.54533
#> 3 95.37233 95.53033 98.99533 101.03433 103.55800 107.02667 109.54533
#> 4 147.10367 150.53400 151.91733 158.18767 162.47900 167.57967 170.99567
#> spc.414.5 spc.415 spc.415.5 spc.416 spc.416.5 spc.417 spc.417.5
#> 1 56.22033 57.71933 59.51433 58.74500 60.09467 61.84067 62.16867
#> 2 111.67233 113.98733 117.03267 119.83500 123.49433 123.32367 127.00167
#> 3 111.67233 113.98733 117.03267 119.83500 123.49433 123.32367 127.00167
#> 4 176.37600 181.19767 181.86833 187.98933 192.12267 194.55600 198.58033
#> spc.418 spc.418.5 spc.419 spc.419.5 spc.420 spc.420.5 spc.421
#> 1 66.04933 65.24500 65.79900 66.94333 69.13600 70.92467 73.83400
#> 2 130.68067 132.35800 136.16467 138.39933 140.22433 141.04333 143.13133
#> 3 130.68067 132.35800 136.16467 138.39933 140.22433 141.04333 143.13133
#> 4 204.04367 208.43300 212.51867 215.81567 219.50867 222.67767 227.59000
#> spc.421.5 spc.422 spc.422.5 spc.423 spc.423.5 spc.424 spc.424.5
#> 1 74.38567 74.17333 75.53067 76.42967 76.13200 77.89067 79.36867
#> 2 147.17967 150.01200 153.69333 155.72800 158.47200 159.50067 160.81567
#> 3 147.17967 150.01200 153.69333 155.72800 158.47200 159.50067 160.81567
#> 4 229.54900 234.28167 236.97767 241.06967 245.41933 249.38867 251.92200
#> spc.425 spc.425.5 spc.426 spc.426.5 spc.427 spc.427.5 spc.428
#> 1 79.42733 82.02833 83.87833 83.81367 85.50667 86.50233 88.93733
#> 2 163.90967 166.25500 169.59233 170.82833 172.08767 175.21133 178.47067
#> 3 163.90967 166.25500 169.59233 170.82833 172.08767 175.21133 178.47067
#> 4 256.41200 261.64400 264.58433 268.46033 274.54733 275.68967 279.99767
#> spc.428.5 spc.429 spc.429.5 spc.430 spc.430.5 spc.431 spc.431.5
#> 1 88.99533 89.51500 90.55667 91.70633 93.57900 94.01300 94.21033
#> 2 179.68100 181.82867 184.42933 187.75600 187.93767 191.05700 192.50900
#> 3 179.68100 181.82867 184.42933 187.75600 187.93767 191.05700 192.50900
#> 4 283.71833 285.21700 290.15667 292.75667 294.99133 299.22533 301.33567
#> spc.432 spc.432.5 spc.433 spc.433.5 spc.434 spc.434.5 spc.435
#> 1 96.44200 96.62733 98.96233 98.84767 100.56833 100.44933 99.91600
#> 2 192.80100 195.55600 197.89067 198.78200 200.99467 201.52233 200.20600
#> 3 192.80100 195.55600 197.89067 198.78200 200.99467 201.52233 200.20600
#> 4 301.46200 309.15933 309.92833 310.05567 312.86500 314.62367 318.42200
#> spc.435.5 spc.436 spc.436.5 spc.437 spc.437.5 spc.438 spc.438.5
#> 1 99.71900 100.88633 101.44533 102.64267 104.22967 103.11133 104.75800
#> 2 204.13200 204.90433 203.98833 205.75600 204.81700 206.09100 208.60733
#> 3 204.13200 204.90433 203.98833 205.75600 204.81700 206.09100 208.60733
#> 4 323.17967 324.57933 325.85133 326.61767 324.63700 326.96700 327.78933
#> spc.439 spc.439.5 spc.440 spc.440.5 spc.441 spc.441.5 spc.442
#> 1 103.15833 103.94267 105.37100 105.86333 103.67967 104.09000 104.65400
#> 2 210.79667 210.58400 210.19033 210.54233 209.85933 212.82733 212.52067
#> 3 210.79667 210.58400 210.19033 210.54233 209.85933 212.82733 212.52067
#> 4 329.90967 328.28167 328.56567 331.69100 330.74933 335.06767 334.62533
#> spc.442.5 spc.443 spc.443.5 spc.444 spc.444.5 spc.445 spc.445.5
#> 1 105.22633 104.80433 105.81033 104.75800 103.88300 105.36167 105.01500
#> 2 212.41967 211.22233 215.56367 213.42467 211.15933 212.97533 213.98933
#> 3 212.41967 211.22233 215.56367 213.42467 211.15933 212.97533 213.98933
#> 4 334.27133 332.64733 333.62633 332.72400 330.82933 332.14667 334.25567
#> spc.446 spc.446.5 spc.447 spc.447.5 spc.448 spc.448.5 spc.449
#> 1 105.05933 105.34933 103.98700 105.43867 104.19667 105.09800 104.72333
#> 2 214.17200 213.47633 212.48867 211.74100 212.70467 212.94033 212.12933
#> 3 214.17200 213.47633 212.48867 211.74100 212.70467 212.94033 212.12933
#> 4 333.93800 332.78600 331.55400 331.97367 334.16567 334.10633 333.85700
#> spc.449.5 spc.450 spc.450.5 spc.451 spc.451.5 spc.452 spc.452.5
#> 1 106.66733 106.94967 104.75467 105.08267 105.30000 105.21300 104.78100
#> 2 213.77267 213.49733 213.46400 213.17067 212.83600 211.96333 208.79867
#> 3 213.77267 213.49733 213.46400 213.17067 212.83600 211.96333 208.79867
#> 4 336.50567 333.77567 334.70633 333.20267 333.36967 332.16600 330.79900
#> spc.453 spc.453.5 spc.454 spc.454.5 spc.455 spc.455.5 spc.456
#> 1 104.53867 105.13267 105.16967 104.05700 106.38533 104.07967 104.40133
#> 2 211.50633 209.47700 211.85967 213.26200 212.28367 211.77333 209.39067
#> 3 211.50633 209.47700 211.85967 213.26200 212.28367 211.77333 209.39067
#> 4 332.47633 332.63667 330.23200 329.06333 327.73533 327.03167 326.89333
#> spc.456.5 spc.457 spc.457.5 spc.458 spc.458.5 spc.459 spc.459.5
#> 1 102.18133 103.44167 101.79700 102.87167 102.38867 100.41900 101.16167
#> 2 208.85600 208.34033 206.50633 206.77733 206.64500 205.25500 201.74700
#> 3 208.85600 208.34033 206.50633 206.77733 206.64500 205.25500 201.74700
#> 4 327.08800 326.73833 324.45733 322.25233 318.61333 319.23467 318.66567
#> spc.460 spc.460.5 spc.461 spc.461.5 spc.462 spc.462.5 spc.463
#> 1 98.61133 98.42933 98.57600 98.34100 98.46733 95.14900 94.71100
#> 2 201.98800 199.57000 200.55100 198.76767 197.03300 194.14467 193.38300
#> 3 201.98800 199.57000 200.55100 198.76767 197.03300 194.14467 193.38300
#> 4 314.18900 313.58533 310.74700 311.77633 306.24567 305.31367 303.65067
#> spc.463.5 spc.464 spc.464.5 spc.465 spc.465.5 spc.466 spc.466.5
#> 1 95.27433 94.88433 93.62133 92.46567 92.11533 91.30867 89.53900
#> 2 193.66467 192.51267 190.63300 186.45567 186.05433 182.30533 182.33367
#> 3 193.66467 192.51267 190.63300 186.45567 186.05433 182.30533 182.33367
#> 4 299.22133 301.25333 296.55200 294.46667 291.52000 288.69967 286.65467
#> spc.467 spc.467.5 spc.468 spc.468.5 spc.469 spc.469.5 spc.470
#> 1 88.28100 86.13633 86.16200 86.81733 85.95767 84.06700 86.21200
#> 2 180.56933 180.50633 180.21267 175.21100 171.65000 170.41667 170.37400
#> 3 180.56933 180.50633 180.21267 175.21100 171.65000 170.41667 170.37400
#> 4 283.82400 282.00933 279.39100 274.85267 271.53567 268.85467 265.92933
#> spc.470.5 spc.471 spc.471.5 spc.472 spc.472.5 spc.473 spc.473.5
#> 1 83.68333 82.56867 82.70533 81.26033 78.75233 76.67533 77.95300
#> 2 169.40700 164.89000 164.14133 163.17333 160.98933 159.66533 157.74633
#> 3 169.40700 164.89000 164.14133 163.17333 160.98933 159.66533 157.74633
#> 4 261.68533 260.63400 258.69100 254.81867 250.93133 247.61267 247.52033
#> spc.474 spc.474.5 spc.475 spc.475.5 spc.476 spc.476.5 spc.477
#> 1 77.50700 76.16400 75.64600 76.43700 74.57033 72.87900 72.80267
#> 2 155.13467 153.23933 151.52300 149.19667 147.49467 147.49000 145.43367
#> 3 155.13467 153.23933 151.52300 149.19667 147.49467 147.49000 145.43367
#> 4 244.78833 241.26000 240.24000 238.41733 233.56600 231.26300 229.50400
#> spc.477.5 spc.478 spc.478.5 spc.479 spc.479.5 spc.480 spc.480.5
#> 1 71.05200 70.21367 69.60533 69.98967 68.78000 68.34233 67.68467
#> 2 144.81900 142.43867 142.68967 142.88100 139.83767 135.47933 135.25267
#> 3 144.81900 142.43867 142.68967 142.88100 139.83767 135.47933 135.25267
#> 4 228.82800 225.52900 221.65767 218.32400 216.50633 213.21500 215.24567
#> spc.481 spc.481.5 spc.482 spc.482.5 spc.483 spc.483.5 spc.484
#> 1 67.27700 67.04833 65.31300 64.50900 63.50567 62.18367 62.04500
#> 2 135.84567 133.55900 133.31767 132.82400 128.93033 125.20300 124.73967
#> 3 135.84567 133.55900 133.31767 132.82400 128.93033 125.20300 124.73967
#> 4 208.54933 208.86967 210.30900 205.67467 203.98400 200.07500 197.68767
#> spc.484.5 spc.485 spc.485.5 spc.486 spc.486.5 spc.487 spc.487.5
#> 1 62.02733 61.79900 60.52800 59.34200 59.12500 57.74800 57.44667
#> 2 124.71667 121.67833 120.90167 121.40600 117.66767 117.04100 115.94100
#> 3 124.71667 121.67833 120.90167 121.40600 117.66767 117.04100 115.94100
#> 4 197.21600 193.02933 191.21133 190.76267 186.57933 183.09267 182.39100
#> spc.488 spc.488.5 spc.489 spc.489.5 spc.490 spc.490.5 spc.491
#> 1 57.74267 56.27500 55.49233 54.40933 53.83267 53.26333 52.45733
#> 2 112.22900 112.72433 111.67267 109.69833 107.64067 108.05067 105.22000
#> 3 112.22900 112.72433 111.67267 109.69833 107.64067 108.05067 105.22000
#> 4 179.87400 177.13400 176.43600 173.72833 170.26000 168.65033 166.09067
#> spc.491.5 spc.492 spc.492.5 spc.493 spc.493.5 spc.494 spc.494.5
#> 1 52.14000 49.78433 49.62300 48.33800 47.30400 47.16267 46.41233
#> 2 102.95300 102.75833 100.62800 97.96500 97.35333 96.60167 96.20600
#> 3 102.95300 102.75833 100.62800 97.96500 97.35333 96.60167 96.20600
#> 4 164.44633 160.81267 158.91100 156.76133 154.92067 149.53900 148.52667
#> spc.495 c
#> 1 45.25633 0.05
#> 2 94.61033 0.10
#> 3 94.61033 0.10
#> 4 145.79333 0.15