CSV-file used for this script: ~/Data/brushing_v2.csv
This script formats the output of the resulting CSV-file from applying a template computing ISO25178 parameters in ConfoMap. The script will:
All files will be saved in a subfolder “Data” within the directory of the present Rmd file, i.e. “~/Data”.
imp.info <- file.info(params$data)
imp.data <- read.csv(params$data, header=FALSE, stringsAsFactors=FALSE, na.strings="*****")The imported file is: “~/Data/brushing_v2.csv”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2019-10-23 18:30:50”, “2019-10-24 09:45:18” and “2019-10-24 09:45:18”.
head.keep <- unlist(imp.data[2, keep.col])
names(data.keep) <- gsub("\\.+", "\\.", make.names(head.keep))
names(data.keep) <- gsub("\\.$", "", names(data.keep))
names(data.keep)[1:3] <- c("Measurement.date", "Analysis.date","Analysis.time")
names(data.keep) [1] "Measurement.date"
[2] "Analysis.date"
[3] "Analysis.time"
[4] "Name.of.the.studiable"
[5] "Axis.length.X"
[6] "Axis.size.X"
[7] "Axis.spacing.X"
[8] "Axis.length.Y"
[9] "Axis.size.Y"
[10] "Axis.spacing.Y"
[11] "Axis.length.Z"
[12] "Axis.size.Z"
[13] "Axis.spacing.Z"
[14] "NMP.ratio.Z"
[15] "Length.scale.anisotropy.epLsar"
[16] "Fractal.complexity.Asfc"
[17] "Scale.of.max.complexity.Smfc"
[18] "HAsfc9.HAsfc9"
[19] "HAsfc81.HAsfc81"
[20] "Sq"
[21] "Ssk"
[22] "Sku"
[23] "Sp"
[24] "Sv"
[25] "Sz"
[26] "Sa"
[27] "Smr.c.1000.nm.under.the.highest.peak"
[28] "Smc.p.10"
[29] "Sxp.p.50.q.97.5"
[30] "Sal.s.0.2"
[31] "Str.s.0.2"
[32] "Std.Reference.angle.0"
[33] "Sdq"
[34] "Sdr"
[35] "Vm.p.10"
[36] "Vv.p.10"
[37] "Vmp.p.10"
[38] "Vmc.p.10.q.80"
[39] "Vvc.p.10.q.80"
[40] "Vvv.p.80"
[41] "Maximum.depth.of.furrows"
[42] "Mean.depth.of.furrows"
[43] "Mean.density.of.furrows"
[44] "Isotropy"
[45] "First.Direction"
[46] "Second.Direction"
[47] "Third.Direction"
[48] "Isotropy"
[49] "Periodicity"
[50] "Period"
[51] "Direction.of.period"
[52] "Sq"
[53] "Ssk"
[54] "Sku"
[55] "Sp"
[56] "Sv"
[57] "Sz"
[58] "Sa"
[59] "Smr.c.1000.nm.under.the.highest.peak"
[60] "Smc.p.10"
[61] "Sxp.p.50.q.97.5"
[62] "Sal.s.0.2"
[63] "Str.s.0.2"
[64] "Std.Reference.angle.0"
[65] "Sdq"
[66] "Sdr"
[67] "Vm.p.10"
[68] "Vv.p.10"
[69] "Vmp.p.10"
[70] "Vmc.p.10.q.80"
[71] "Vvc.p.10.q.80"
[72] "Vvv.p.80"
[73] "Maximum.depth.of.furrows"
[74] "Mean.depth.of.furrows"
[75] "Mean.density.of.furrows"
[76] "Isotropy"
[77] "First.Direction"
[78] "Second.Direction"
[79] "Third.Direction"
[80] "Isotropy"
[81] "Periodicity"
[82] "Period"
[83] "Direction.of.period" Warning: NAs introduced by coercionvar.num <- c(ID, SSFA, SL.ISO, SL.furrow, SL.diriso)
units.var <- unlist(imp.data[3, keep.col])[var.num] #extract 'unit' line for considered columns
names(units.var) <- head.keep[var.num] #get names associated to the units
units.var.table <- data.frame(variable=names(units.var), unit=units.var) #put all of it into a data.framenames(data.keep)[c(SL.ISO, SF.ISO)] <- sapply(strsplit(names(data.keep)[c(SL.ISO, SF.ISO)], ".", fixed=TRUE), `[[`, 1)
names(data.keep)[SSFA] <- c("epLsar", "Asfc", "Smfc", "HAsfc9", "HAsfc81")
names(data.keep)[c(SL.ISO,SL.furrow,SL.diriso)] <- paste0(names(data.keep)[c(SL.ISO,SL.furrow,SL.diriso)], ".SL")
names(data.keep)[c(SF.ISO,SF.furrow,SF.diriso)] <- paste0(names(data.keep)[c(SF.ISO,SF.furrow,SF.diriso)], ".SF")data.final[["Before.after"]] <- factor(ifelse(data.final[["Mode"]]=="LSM2", "After", "Before"), labels=c("Before","After"))
data.final[["Material"]] <- factor(ifelse(grepl(pattern="FLT", data.final[["Sample"]]), "Flint", "Quartzite"))
data.final[data.final$Sample %in% c("FLT3-8","QTZ3-2","FLT3-13","QTZ3-3"), "Brush"] <- "No"
data.final[data.final$Sample %in% c("FLT3-9","QTZ3-5","FLT3-10","QTZ3-13"), "Brush"] <- "Yes"
data.final[data.final$Sample %in% c("FLT3-8","QTZ3-2","FLT3-9","QTZ3-5"), "Dirt"] <- "No"
data.final[data.final$Sample %in% c("FLT3-13","QTZ3-3","FLT3-10","QTZ3-13"), "Dirt"] <- "Yes"
data.final[["Brush"]] <- factor(data.final[["Brush"]])
data.final[["Dirt"]] <- factor(data.final[["Dirt"]])Type comment(data.final) to check the units of the columns.
'data.frame': 30 obs. of 89 variables:
$ Material : Factor w/ 2 levels "Flint","Quartzite": 1 1 1 1 1 1 1 2 2 2 ...
$ Sample : Factor w/ 8 levels "FLT3-10","FLT3-13",..: 1 1 2 2 3 4 4 5 5 6 ...
$ Brush : Factor w/ 2 levels "No","Yes": 2 2 1 1 1 2 2 2 2 1 ...
$ Dirt : Factor w/ 2 levels "No","Yes": 2 2 2 2 1 1 1 2 2 1 ...
$ Before.after : Factor w/ 2 levels "Before","After": 2 2 2 2 2 2 2 2 2 2 ...
$ Area : Factor w/ 2 levels "Area1","Area2": 1 2 1 2 2 1 2 1 2 1 ...
$ Objective : Factor w/ 1 level "50x-0.95": 1 1 1 1 1 1 1 1 1 1 ...
$ Measurement.date : POSIXct, format: "2019-03-28 15:19:32" "2019-03-28 16:11:01" ...
$ Analysis.date : Date, format: "2019-10-23" "2019-10-23" ...
$ Analysis.time : 'times' num 12:25:46 12:35:13 12:44:37 12:54:02 13:18:27 ...
..- attr(*, "format")= chr "h:m:s"
$ Axis.length.X : num 255 255 255 255 255 ...
$ Axis.size.X : num 3000 3000 3000 3000 3000 3000 3000 3000 3000 3000 ...
$ Axis.spacing.X : num 0.0852 0.0852 0.0852 0.0852 0.0852 ...
$ Axis.length.Y : num 255 255 255 255 255 ...
$ Axis.size.Y : num 3000 3000 3000 3000 3000 3000 3000 3000 3000 3000 ...
$ Axis.spacing.Y : num 0.0852 0.0852 0.0852 0.0852 0.0852 ...
$ Axis.length.Z : num 22180 24153 16689 18953 22314 ...
$ Axis.size.Z : num 65532 65532 65531 65531 65532 ...
$ Axis.spacing.Z : num 0.338 0.369 0.255 0.289 0.341 ...
$ NMP.ratio.Z : num 0 0 0 0.134 0.142 ...
$ epLsar : num 0.0171 0.0174 0.0175 0.0174 0.0174 ...
$ Asfc : num 19.6 17.2 21 18.7 20.6 ...
$ Smfc : num 0.233 0.233 0.169 0.169 0.233 ...
$ HAsfc9 : num 0.1801 0.2036 0.0725 0.0941 0.2992 ...
$ HAsfc81 : num 0.251 0.264 0.119 0.134 0.323 ...
$ Sq.SL : num 1548 1336 1294 1102 1334 ...
$ Ssk.SL : num 0.279 -0.957 -0.023 0.106 -0.577 ...
$ Sku.SL : num 6.29 5.08 4.95 4.06 4.77 ...
$ Sp.SL : num 6781 4282 5693 4320 4841 ...
$ Sv.SL : num 7249 6431 6070 4502 6343 ...
$ Sz.SL : num 14030 10713 11762 8821 11183 ...
$ Sa.SL : num 1092 995 972 847 994 ...
$ Smr.SL : num 0.36 0.294 0.374 0.754 0.313 ...
$ Smc.SL : num 1665 1454 1528 1312 1575 ...
$ Sxp.SL : num 2840 3486 2624 2122 3097 ...
$ Sal.SL : num 19.5 19.3 15 15.9 16.3 ...
$ Str.SL : num 0.543 0.583 0.613 0.793 0.605 ...
$ Std.SL : num 93 65 155.2 106.8 86.5 ...
$ Sdq.SL : num 0.718 0.695 0.713 0.663 0.75 ...
$ Sdr.SL : num 16.7 15.4 17.7 15.8 17.8 ...
$ Vm.SL : num 0.135 0.0528 0.0763 0.0689 0.0602 ...
$ Vv.SL : num 1.8 1.51 1.6 1.38 1.63 ...
$ Vmp.SL : num 0.135 0.0528 0.0763 0.0689 0.0602 ...
$ Vmc.SL : num 1.06 1.058 1.031 0.924 1.064 ...
$ Vvc.SL : num 1.61 1.28 1.44 1.25 1.44 ...
$ Vvv.SL : num 0.188 0.227 0.162 0.129 0.198 ...
$ Maximum.depth.of.furrows.SL: num 6038 6970 6609 4969 5851 ...
$ Mean.depth.of.furrows.SL : num 1875 1612 1791 1518 1784 ...
$ Mean.density.of.furrows.SL : num 7781 7577 7787 7703 7753 ...
$ Isotropy.SL : num 54.3 58.3 61.3 79.3 60.5 ...
$ First.Direction.SL : num 90.009 90.005 90.002 0.184 90.02 ...
$ Second.Direction.SL : num 44.985 45.019 0.172 89.982 0.209 ...
$ Third.Direction.SL : num 135.019 0.213 45.003 135.031 45.019 ...
$ Isotropy.SL.1 : num 68.7 70.2 80.8 78.9 75.5 ...
$ Periodicity.SL : num NA NA NA NA NA NA NA NA NA NA ...
$ Period.SL : num NA NA NA NA NA NA NA NA NA NA ...
$ Direction.of.period.SL : num NA NA NA NA NA NA NA NA NA NA ...
$ Sq.SF : num 607 367 400 284 528 ...
$ Ssk.SF : num -0.03013 0.10126 0.00249 0.14301 0.66318 ...
$ Sku.SF : num 2.72 3.52 3.02 2.43 2.82 ...
$ Sp.SF : num 1676 1023 1038 677 1543 ...
$ Sv.SF : num 1390 1232 1175 665 843 ...
$ Sz.SF : num 3067 2255 2214 1342 2386 ...
$ Sa.SF : num 490 284 314 232 433 ...
$ Smr.SF : num 12.7 45.6 46.3 86.9 16.6 ...
$ Smc.SF : num 775 496 498 395 742 ...
$ Sxp.SF : num 1307 712 802 503 677 ...
$ Sal.SF : num 48.9 35.4 43.2 43.9 46.8 ...
$ Str.SF : num 0.58 0.595 0.671 0.492 0.666 ...
$ Std.SF : num 85.7 23.8 15.5 104.2 54.5 ...
$ Sdq.SF : num 0.0201 0.0161 0.0161 0.0114 0.0207 ...
$ Sdr.SF : num 0.0202 0.0129 0.013 0.0065 0.0215 ...
$ Vm.SF : num 0.0283 0.0206 0.023 0.011 0.0319 ...
$ Vv.SF : num 0.803 0.516 0.52 0.406 0.774 ...
$ Vmp.SF : num 0.0283 0.0206 0.023 0.011 0.0319 ...
$ Vmc.SF : num 0.603 0.297 0.36 0.26 0.483 ...
$ Vvc.SF : num 0.741 0.475 0.474 0.378 0.746 ...
$ Vvv.SF : num 0.062 0.0412 0.0462 0.0288 0.0283 ...
$ Maximum.depth.of.furrows.SF: num 322 382 333 271 345 ...
$ Mean.depth.of.furrows.SF : num 160 136 133 96 179 ...
$ Mean.density.of.furrows.SF : num 104 123 110 120 105 ...
$ Isotropy.SF : num 58 59.5 67.1 49.2 66.6 ...
$ First.Direction.SF : num 85.5 8.75 37 104.25 45.5 ...
$ Second.Direction.SF : num 94.5 171.3 104.2 53 111.5 ...
$ Third.Direction.SF : num 18.2 176.2 21.5 175.5 54.3 ...
$ Isotropy.SF.1 : num 78.9 40.9 77 82.6 56.9 ...
$ Periodicity.SF : num 27.8 39.8 25.1 NA 30.6 ...
$ Period.SF : num 99.5 126.9 148.1 NA 140.3 ...
$ Direction.of.period.SF : num 143 22.5 52.9 NA 134.8 ...
- attr(*, "comment")= Named chr "µm" "points" "µm" "µm" ...
..- attr(*, "names")= chr "Axis length - X" "Axis size - X" "Axis spacing - X" "Axis length - Y" ... Material Sample Brush Dirt Before.after Area Objective Measurement.date
4 Flint FLT3-10 Yes Yes After Area1 50x-0.95 2019-03-28 15:19:32
5 Flint FLT3-10 Yes Yes After Area2 50x-0.95 2019-03-28 16:11:01
6 Flint FLT3-13 No Yes After Area1 50x-0.95 2019-03-28 11:44:28
7 Flint FLT3-13 No Yes After Area2 50x-0.95 2019-03-28 14:08:52
9 Flint FLT3-8 No No After Area2 50x-0.95 2019-03-21 14:31:50
10 Flint FLT3-9 Yes No After Area1 50x-0.95 2019-03-21 15:53:59
Analysis.date Analysis.time Axis.length.X Axis.size.X Axis.spacing.X
4 2019-10-23 12:25:46 255.4748 3000 0.08518666
5 2019-10-23 12:35:13 255.4748 3000 0.08518666
6 2019-10-23 12:44:37 255.4748 3000 0.08518666
7 2019-10-23 12:54:02 255.4748 3000 0.08518666
9 2019-10-23 13:18:27 255.4748 3000 0.08518666
10 2019-10-23 13:28:07 255.4748 3000 0.08518666
Axis.length.Y Axis.size.Y Axis.spacing.Y Axis.length.Z Axis.size.Z
4 255.4748 3000 0.08518666 22180.42 65532
5 255.4748 3000 0.08518666 24153.08 65532
6 255.4748 3000 0.08518666 16689.44 65531
7 255.4748 3000 0.08518666 18953.32 65531
9 255.4748 3000 0.08518666 22314.21 65532
10 255.4748 3000 0.08518666 17853.52 65532
Axis.spacing.Z NMP.ratio.Z epLsar Asfc Smfc HAsfc9
4 0.3384670 0.0000000 0.01714716 19.56945 0.2332067 0.18005092
5 0.3685692 0.0000000 0.01735469 17.23687 0.2332067 0.20357394
6 0.2546801 0.0000000 0.01748232 21.01142 0.1693019 0.07250272
7 0.2892268 0.1338556 0.01735057 18.70799 0.1693019 0.09413337
9 0.3405086 0.1417000 0.01737891 20.55407 0.2332067 0.29923168
10 0.2724396 0.0000000 0.01744802 20.87535 0.3212329 0.10230478
HAsfc81 Sq.SL Ssk.SL Sku.SL Sp.SL Sv.SL Sz.SL
4 0.2514574 1547.995 0.27899188 6.292930 6780.848 7249.286 14030.134
5 0.2638315 1336.182 -0.95741563 5.078233 4281.668 6431.164 10712.832
6 0.1188184 1293.781 -0.02300918 4.946463 5692.610 6069.791 11762.401
7 0.1342448 1102.412 0.10567406 4.060327 4319.603 4501.816 8821.419
9 0.3227291 1333.949 -0.57722755 4.772413 4840.670 6342.654 11183.324
10 0.1751943 1327.697 0.27391767 7.594889 6635.540 7074.713 13710.253
Sa.SL Smr.SL Smc.SL Sxp.SL Sal.SL Str.SL Std.SL Sdq.SL
4 1092.3567 0.3600017 1665.410 2839.798 19.48807 0.5433402 92.99391 0.7179665
5 995.0547 0.2944130 1454.259 3486.000 19.29139 0.5825679 65.01043 0.6946692
6 972.4787 0.3738135 1528.417 2624.185 15.04753 0.6133658 155.24925 0.7130941
7 846.8755 0.7540504 1311.523 2122.182 15.91403 0.7932008 106.75015 0.6633986
9 994.2861 0.3131865 1574.797 3096.992 16.27671 0.6047282 86.49890 0.7498406
10 934.3642 0.3670132 1448.824 2296.308 18.46236 0.8210036 35.98873 0.7981448
Sdr.SL Vm.SL Vv.SL Vmp.SL Vmc.SL Vvc.SL Vvv.SL
4 16.71961 0.13498926 1.800286 0.13498926 1.0597621 1.612096 0.1881894
5 15.43765 0.05280878 1.507006 0.05280878 1.0575692 1.280265 0.2267406
6 17.70261 0.07630900 1.604746 0.07630900 1.0307427 1.442711 0.1620358
7 15.80641 0.06887440 1.380449 0.06887440 0.9239193 1.251934 0.1285151
9 17.75498 0.06015525 1.634807 0.06015525 1.0642306 1.437145 0.1976610
10 16.75480 0.10536882 1.554121 0.10536882 0.9448575 1.396761 0.1573595
Maximum.depth.of.furrows.SL Mean.depth.of.furrows.SL
4 6037.574 1875.439
5 6969.644 1611.658
6 6609.204 1790.851
7 4968.628 1517.898
9 5850.704 1784.425
10 7377.666 1827.509
Mean.density.of.furrows.SL Isotropy.SL First.Direction.SL
4 7780.699 54.33402 90.0093393
5 7576.945 58.25679 90.0045412
6 7787.424 61.33658 90.0023654
7 7703.471 79.32008 0.1836484
9 7753.074 60.47282 90.0199459
10 8036.763 82.10036 90.0028614
Second.Direction.SL Third.Direction.SL Isotropy.SL.1 Periodicity.SL
4 44.9853711 135.0186951 68.70564 NA
5 45.0192443 0.2125054 70.23738 NA
6 0.1721761 45.0032528 80.78772 NA
7 89.9820795 135.0313277 78.86668 NA
9 0.2094917 45.0186261 75.49428 NA
10 44.9955354 135.0064403 80.84302 NA
Period.SL Direction.of.period.SL Sq.SF Ssk.SF Sku.SF Sp.SF
4 NA NA 607.4917 -0.030127269 2.721561 1676.0886
5 NA NA 367.3208 0.101259713 3.516685 1022.7795
6 NA NA 399.5542 0.002493731 3.024096 1038.3308
7 NA NA 283.6608 0.143007021 2.431880 677.3693
9 NA NA 528.0274 0.663177444 2.824713 1542.8444
10 NA NA 488.7831 -0.310542781 2.462864 1154.0544
Sv.SF Sz.SF Sa.SF Smr.SF Smc.SF Sxp.SF Sal.SF Str.SF
4 1390.4225 3066.511 489.7923 12.72203 775.0712 1307.1396 48.90428 0.5801547
5 1231.7583 2254.538 284.2922 45.56146 495.5479 712.4680 35.35515 0.5948142
6 1175.3487 2213.680 313.8163 46.30507 497.5722 802.4142 43.22707 0.6705867
7 664.6433 1342.013 232.3183 86.94368 395.4773 503.1003 43.87200 0.4924656
9 843.4398 2386.284 432.7235 16.56863 741.8203 676.5278 46.75734 0.6656710
10 1150.2402 2304.295 402.5779 43.17200 550.3637 1089.4114 47.56912 0.8452929
Std.SF Sdq.SF Sdr.SF Vm.SF Vv.SF Vmp.SF Vmc.SF
4 85.74960 0.02010226 0.020199438 0.02834208 0.8032595 0.02834208 0.6034480
5 23.75012 0.01606905 0.012913453 0.02061729 0.5161148 0.02061729 0.2968719
6 15.49991 0.01612422 0.013001249 0.02299213 0.5204720 0.02299213 0.3595907
7 104.24980 0.01140020 0.006497785 0.01100687 0.4063571 0.01100687 0.2601938
9 54.50003 0.02073750 0.021498439 0.03187325 0.7738147 0.03187325 0.4830335
10 58.75001 0.01788598 0.015991329 0.02002959 0.5702776 0.02002959 0.5131546
Vvc.SF Vvv.SF Maximum.depth.of.furrows.SF Mean.depth.of.furrows.SF
4 0.7412814 0.06197803 322.2206 159.80265
5 0.4749120 0.04120278 381.8377 135.90639
6 0.4742320 0.04624001 332.6122 133.18782
7 0.3775514 0.02880575 270.7163 95.97446
9 0.7455215 0.02829324 344.9352 178.64364
10 0.5185744 0.05170320 308.4017 132.88460
Mean.density.of.furrows.SF Isotropy.SF First.Direction.SF
4 103.9757 58.01547 85.501240
5 123.1478 59.48142 8.749987
6 110.1888 67.05867 37.001054
7 119.5835 49.24656 104.249854
9 104.5475 66.56710 45.500127
10 126.5249 84.52929 94.498948
Second.Direction.SF Third.Direction.SF Isotropy.SF.1 Periodicity.SF
4 94.499133 18.24953 78.86858 27.84658
5 171.252249 176.24633 40.90620 39.78308
6 104.250000 21.50003 77.02578 25.14123
7 52.999902 175.50089 82.56818 NA
9 111.499768 54.25038 56.87549 30.64392
10 4.499641 15.25028 86.29519 36.76192
Period.SF Direction.of.period.SF
4 99.47019 142.9792
5 126.91010 22.4552
6 148.12072 52.8743
7 NA NA
9 140.28410 134.8198
10 118.52956 154.8647The files will be saved as “~/Data/brushing_v2.[ext]”.
write.xlsx(list(data=data.final, units=units.var.table), file=paste0(file.out,".xlsx"))
xlsx.info <- file.info(paste0(file.out,".xlsx"))The exported XLSX-file is: “brushing_v2.xlsx”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2020-01-21 08:58:08”, “2019-10-24 11:24:36” and “2020-01-21 08:58:08”.
saveObject(data.final, file=paste0(file.out,".Rbin"))
Rbin.info <- file.info(paste0(file.out,".Rbin"))The exported Rbin-file is: “brushing_v2.Rbin”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2020-01-21 08:58:08”, “2020-01-21 08:58:08” and “2020-01-21 08:58:08”.
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] chron_2.3-54 R.utils_2.9.2 R.oo_1.23.0 R.methodsS3_1.7.1
[5] openxlsx_4.1.4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 digest_0.6.23 magrittr_1.5 evaluate_0.14
[5] zip_2.0.4 rlang_0.4.2 stringi_1.4.3 rmarkdown_2.0
[9] stringr_1.4.0 xfun_0.11 yaml_2.2.0 compiler_3.6.2
[13] htmltools_0.4.0 knitr_1.26 RStudio Version 1.2.5019
END OF SCRIPT