data-raw/tmp/_tmp2_.R

In GegznaV/spHelper: Extension of Package `hyperSpec` and Various Convenience Functions

# # Examples
#
# ## index into the rows (spectra) -------------------------------------
# ## make some "spectra"
#
# ## numeric index
# plot (flu, "spc", lines.args = list (lty = 2))
# plot (flu[1:3], "spc", add = TRUE, col = "red")     # select spectra
# plot (flu[-(1:3)], "spc", add = TRUE, col = "blue") # delete spectra
#
# ## logic index
# plot (flu, "spc", lines.args = list (lty = 2))
# index <- rnorm (6) > 0
# index
# plot (flu[index], "spc", add = TRUE, col = "red")   # select spectra
# plot (flu[!index], "spc", add = TRUE, col = "blue") # select spectra
#
# ## index into the data columns ---------------------------------------
# range (chondro[[,"x"]])
# colnames (chondro[[,1]])
# dim (chondro[[,c(TRUE, FALSE, FALSE)]])
# chondro$x
#
#
# ## the shortcut functions --------------------------------------------
#
# ## extract the spectra matrix
# flu[[]]
#
# ## indexing via logical matrix
# summary (flu [[flu < 125]])
#
# ## indexing the spectra matrix with index matrix n by 2
# ind <- matrix (c (1, 2, 4, 406, 405.5, 409), ncol = 2)
# ind
# flu [[ind]]
#
# ind <- matrix (c (1, 2, 4, 4:6), ncol = 2)
# ind
# flu [[ind, wl.index = TRUE]]
#
# pca <- prcomp (flu[[]])
#
# ## result is data.frame, if j is given:
# result <- flu [[, 1:2, 405 ~ 410]]
# result
# class (result)
# colnames (result)
#
# ## extract the data.frame including the spectra matrix
# flu$.
# dim(flu$.)
# colnames (flu$.)
# flu$.$spc
#
# calibration <- lm (spc ~ c, data = flu[,,450]$.)
# calibration
#
# flu$..
# colnames (flu$..)
# ## replacement functions
# spc <- flu
# spc$.
# spc[, "c"] <- 16 : 11
# ## be careful:
# plot (spc)
# spc [] <- 6 : 1
# spc$..
# plot (spc)
# spc <- flu [,, 405 ~ 410]
# spc [[]]
# spc [[3]] <- -spc[[3]]
# spc [[]]
# spc [[,,405 : 410]] <- -spc[[,,405 : 410]]
# spc [[]]
# spc [[,,405 ~ 410]] <- -spc[[,,405 ~ 410]]
#
# ## indexing with logical matrix
# spc <- flu [,, min ~ 410]
# spc < 125
# spc [[spc < 125]] <- NA
# spc [[]]
#
# ## indexing with n by 2 matrix
# ind <- matrix (c (1, 2, 4, 406, 405.5, 409), ncol = 2)
# ind
# spc [[ind]] <- 3
# spc [[]]
#
# ind <- matrix (c (1, 2, 4, 4:6), ncol = 2)
# ind
# spc [[ind, wl.index = TRUE]] <- 9999
# spc [[]]
# spc$.
# spc$z <- 1 : 6
# spc
# spc$z <- list (1 : 6, "z / a.u.")
#