Rbin-file used for this script: ~/Data/CoordSys_FLT1-7_50x.Rbin
This script calculates the shift in X/Y directions from the first scan.
This script computes standard descriptive statistics for each group.
The groups are based on:
It computes the following statistics:
length)min)max)sd)dir.stats <- "Summary-stats"
dir.create(dir.stats, showWarnings=FALSE)The results will be written to XLSX-files in a subfolder “Summary-stats” within the directory of the present Rmd file, i.e. “~/Summary-stats”.
library(openxlsx)
library(R.utils)
library(tools)
library(doBy)imp.info <- file.info(params$data)
imp.data <- loadObject(params$data)The imported file is: “~/Data/CoordSys_FLT1-7_50x.Rbin”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2019-01-03 10:28:47”, “2019-01-03 10:28:47” and “2019-01-03 10:28:47”.
num.var.topo <- 19:47
num.var.shift <- 54:55
names(imp.data)[num.var.topo] [1] "Sq" "Ssk" "Sku" "Sp" "Sv" "Sz" "Sa" "Smr" "Smc" "Sxp"
[11] "Sal" "Str" "Std" "Sdq" "Sdr" "Vm" "Vv" "Vmp" "Vmc" "Vvc"
[21] "Vvv" "Sk" "Spk" "Svk" "Smr1" "Smr2" "Spq" "Svq" "Smq" names(imp.data)[num.var.shift][1] "Xshift" "Yshift"minmaxmeanmedsd <- function(x){
y <- x[!is.na(x)]
min_test <- min(y)
max_test <- max(y)
mean_test <- mean(y)
med_test <- median(y)
sd_test <- sd(y)
out <- c(min_test, max_test, mean_test, med_test, sd_test)
names(out) <- c("min", "max", "mean", "median", "sd")
return(out)
}#min, max, mean, median, sd
topo.mmmms <- summaryBy(.~Microscope, data=imp.data[c("Microscope",names(imp.data)[num.var.topo])], FUN=minmaxmeanmedsd)
#n for first variable
topo.n <- summaryBy(as.formula(paste0(names(imp.data[num.var.topo])[1],"~Microscope")), data=imp.data, FUN=length)
#combine n, min, max, mean, median and sd
topo <- merge(topo.n, topo.mmmms)
str(topo)'data.frame': 2 obs. of 137 variables:
$ Microscope : Factor w/ 2 levels "LSM","Sneox": 1 2
$ Sq.length : int 10 10
$ Sq.min : num 1.16 1.16
$ Sq.max : num 1.49 1.79
$ Sq.mean : num 1.31 1.56
$ Sq.median : num 1.31 1.62
$ Sq.sd : num 0.089 0.207
$ Ssk.min : num -0.00297 0.02434
$ Ssk.max : num 0.145 0.357
$ Ssk.mean : num 0.0769 0.1475
$ Ssk.median : num 0.0852 0.1325
$ Ssk.sd : num 0.0503 0.1061
$ Sku.min : num 3.1 3.95
$ Sku.max : num 4.42 4.82
$ Sku.mean : num 3.98 4.39
$ Sku.median : num 3.95 4.41
$ Sku.sd : num 0.408 0.286
$ Sp.min : num 5.19 6.09
$ Sp.max : num 6.24 7.04
$ Sp.mean : num 6 6.41
$ Sp.median : num 6.07 6.29
$ Sp.sd : num 0.307 0.324
$ Sv.min : num 3.91 4.15
$ Sv.max : num 7.14 7.6
$ Sv.mean : num 5.45 6.85
$ Sv.median : num 5.86 7.26
$ Sv.sd : num 1.16 1.1
$ Sz.min : num 9.11 10.23
$ Sz.max : num 13.2 14.2
$ Sz.mean : num 11.4 13.3
$ Sz.median : num 12 13.7
$ Sz.sd : num 1.39 1.24
$ Sa.min : num 0.922 0.875
$ Sa.max : num 1.12 1.37
$ Sa.mean : num 1.02 1.17
$ Sa.median : num 1.02 1.2
$ Sa.sd : num 0.0546 0.1531
$ Smr.min : num 0.0463 0.1238
$ Smr.max : num 0.293 0.558
$ Smr.mean : num 0.162 0.378
$ Smr.median : num 0.148 0.438
$ Smr.sd : num 0.0723 0.1864
$ Smc.min : num 1.49 1.34
$ Smc.max : num 1.72 2.29
$ Smc.mean : num 1.59 1.83
$ Smc.median : num 1.58 1.84
$ Smc.sd : num 0.0613 0.2942
$ Sxp.min : num 2.33 2.27
$ Sxp.max : num 3.04 3.53
$ Sxp.mean : num 2.63 3.11
$ Sxp.median : num 2.6 3.29
$ Sxp.sd : num 0.193 0.398
$ Sal.min : num 12.4 13.6
$ Sal.max : num 14.6 17.9
$ Sal.mean : num 14 15.4
$ Sal.median : num 14.1 14.8
$ Sal.sd : num 0.638 1.405
$ Str.min : num 0.512 0.635
$ Str.max : num 0.827 0.791
$ Str.mean : num 0.718 0.73
$ Str.median : num 0.72 0.745
$ Str.sd : num 0.0904 0.0536
$ Std.min : num 69 3.76
$ Std.max : num 157 144
$ Std.mean : num 100.1 65.3
$ Std.median : num 90.7 54.3
$ Std.sd : num 29.1 59.4
$ Vm.min : num 0.0546 0.0766
$ Vm.max : num 0.0974 0.1237
$ Vm.mean : num 0.0727 0.1054
$ Vm.median : num 0.0727 0.1118
$ Vm.sd : num 0.0117 0.0175
$ Vv.min : num 1.55 1.42
$ Vv.max : num 1.81 2.39
$ Vv.mean : num 1.66 1.94
$ Vv.median : num 1.65 1.96
$ Vv.sd : num 0.0725 0.3067
$ Vmp.min : num 0.0546 0.0766
$ Vmp.max : num 0.0974 0.1237
$ Vmp.mean : num 0.0727 0.1054
$ Vmp.median : num 0.0727 0.1118
$ Vmp.sd : num 0.0117 0.0175
$ Vmc.min : num 1.039 0.957
$ Vmc.max : num 1.2 1.47
$ Vmc.mean : num 1.11 1.24
$ Vmc.median : num 1.12 1.27
$ Vmc.sd : num 0.043 0.151
$ Vvc.min : num 1.41 1.29
$ Vvc.max : num 1.63 2.18
$ Vvc.mean : num 1.5 1.74
$ Vvc.median : num 1.5 1.75
$ Vvc.sd : num 0.0576 0.2833
$ Vvv.min : num 0.133 0.136
$ Vvv.max : num 0.187 0.219
$ Vvv.mean : num 0.156 0.192
$ Vvv.median : num 0.153 0.202
$ Vvv.sd : num 0.0157 0.0265
$ Sk.min : num 2.24 1.94
$ Sk.max : num 2.51 2.65
[list output truncated]#min, max, mean, median, sd
shift.mmmms <- summaryBy(.~Microscope, data=imp.data[-c(1,11), c("Microscope",names(imp.data)[num.var.shift])], FUN=minmaxmeanmedsd)
#n for first variable
shift.n <- summaryBy(as.formula(paste0(names(imp.data[num.var.shift])[1],"~Microscope")), data=imp.data[-c(1,11),], FUN=length)
#combine n, min, max, mean, median and sd
shift <- merge(shift.n, shift.mmmms)
str(shift)'data.frame': 2 obs. of 12 variables:
$ Microscope : Factor w/ 2 levels "LSM","Sneox": 1 2
$ Xshift.length: int 9 9
$ Xshift.min : num 18.85 5.01
$ Xshift.max : num 88.7 129.3
$ Xshift.mean : num 41.8 58.5
$ Xshift.median: num 33.3 50.2
$ Xshift.sd : num 20.4 41.4
$ Yshift.min : num 1.573 0.789
$ Yshift.max : num 52.1 61.4
$ Yshift.mean : num 23.6 28.1
$ Yshift.median: num 18.1 27.1
$ Yshift.sd : num 17 20.4file.out <- paste0(dir.stats, "/", basename(file_path_sans_ext(row.names(imp.info))), "_summary-stats.xlsx")
file.out[1] "Summary-stats/CoordSys_FLT1-7_50x_summary-stats.xlsx"write.xlsx(list(ISO=topo, XYshift=shift), file=file.out)
xlsx.info <- file.info(file.out)The exported XLSX-file is: “CoordSys_FLT1-7_50x_summary-stats.xlsx”
It is saved in “~/Summary-stats”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2019-01-03 10:34:13”, “2019-01-03 10:34:13” and “2019-01-03 10:34:13”.
sessionInfo()R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
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] doBy_4.6-2 R.utils_2.7.0 R.oo_1.22.0 R.methodsS3_1.7.1
[5] openxlsx_4.1.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 bindr_0.1.1 knitr_1.21 magrittr_1.5
[5] MASS_7.3-51.1 tidyselect_0.2.5 lattice_0.20-38 R6_2.3.0
[9] rlang_0.3.0.1 stringr_1.3.1 plyr_1.8.4 dplyr_0.7.8
[13] grid_3.5.2 xfun_0.4 htmltools_0.3.6 yaml_2.2.0
[17] digest_0.6.18 assertthat_0.2.0 tibble_1.4.2 crayon_1.3.4
[21] bindrcpp_0.2.2 Matrix_1.2-15 zip_1.0.0 purrr_0.2.5
[25] glue_1.3.0 evaluate_0.12 rmarkdown_1.11 stringi_1.2.4
[29] pillar_1.3.1 compiler_3.5.2 pkgconfig_2.0.2 END OF SCRIPT