Merge pull request #46 from l-ramirez-lopez/v0.2.5

V0.2.5

.Rbuildignore

@@ -12,4 +12,5 @@ code_ex.R
 ^\.Rprofile$c  
 TODO
 epo.R
+NEWS.html
 

DESCRIPTION

@@ -35,7 +35,7 @@ Imports:
     mathjaxr (>= 1.0), 
     lifecycle (>= 0.2.0)
 RdMacros: mathjaxr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 NeedsCompilation: yes
 LazyData: true
 LazyDataCompression: xz

NEWS → NEWS.md

@@ -1,59 +1,62 @@
-prospectr 0.2.5
+# `prospectr`
+
+`prospectr` 0.2.5
 ===============
 
-## Improvements and fixes
+### Improvements and fixes
 
-* kenStone(): an error in a sanity check that prevented the 
+* `kenStone()`: an error in a sanity check that prevented the 
 function to run when the number of groups to be selected was smaller than the 
 total number of groups. This sanity check has been fixed. Thanks to 
-Pogs Manalili for reporting this. 
+Pogs Manalili for reporting this ([#41](https://github.com/l-ramirez-lopez/prospectr/issues/41)). 
 
-* kenStone(): this function was failing when when using the Mahalanobis distance 
-on a matrix of one column. By default the funcion transforms the matrix onto 
+* `kenStone()`: this function was failing when when using the Mahalanobis distance 
+on a matrix of one column. By default the function transforms the matrix onto 
 the Mahalanobis space using either SVD or eigendecomposition. This makes sense 
 for matrices with more than two columns. However for a matrix of one column, we 
 now assume that such space is equivalent to the variable divided by the its 
-standard deviation. Thanks to Sergio Roldán (https://github.com/sdroldan) for 
-reporting this. 
+standard deviation. Thanks to Sergio Roldan (https://github.com/sdroldan) for 
+reporting this ([#40](https://github.com/l-ramirez-lopez/prospectr/issues/40])).
+
 
-* spliceCorrection(): correcting more than one point at once  (argument splice)
+* `spliceCorrection()`: correcting more than one point at once  (argument splice)
 in the spectra was returning an error. This was a bug introduced in 
-version 0.2.4. Thanks to José Lucas Safanelli (https://github.com/zecojls) 
-for reporting this. 
+version 0.2.4. Thanks to Jose Lucas Safanelli (https://github.com/zecojls) 
+for reporting this ([#39](https://github.com/l-ramirez-lopez/prospectr/issues/39)). 
 
 
-prospectr 0.2.4
+`prospectr` 0.2.4
 ===============
 
-## Improvements and fixes
+### Improvements and fixes
 
-* baseline(): in some cases the function did not properly capture the baseline
+* `baseline()`: in some cases the function did not properly capture the baseline
 confounding maximum values of a peaks as part of the baseline. This has been 
 addressed in this version by ensuring the envelope used in the computation of the 
 convex hull (used to extract the baseline) is properly defined. At the edges, 
 this envelope has always values higher than any peak of the spectrum. 
 
-* read_nircal(): the function was wrongly identifying actual .nir files as 
+* `read_nircal()`: the function was wrongly identifying actual .nir files as 
 invalid. This preventing the function from reading any nir file. This has been 
 fixed. 
 
 
-prospectr 0.2.3
+`prospectr` 0.2.3
 ===============
 
-## New features
+### New features
 
-* The `kenStone` function now includes a new feature that allows to initialize the
+* The `kenStone()` function now includes a new feature that allows to initialize the
 calibration sample search with a user-defined subset of observations (which are 
 to be included in the final calibration subset). Thanks to Thorsten Behrens and
 Philipp Baumann for suggesting this feature. 
 
-* The gap-segment derivatives (gapDer) function now allows for high order 
+* The gap-segment derivatives (`gapDer()`) function now allows for high order 
 derivatives. In previous versions the function only allowed up to derivatives of 
 4th order, in this version the the function accepts as derivative order 
 any integer larger than 1. 
 
-## Improvements and fixes
+### Improvements and fixes
 * `binning() `a bug in the creation of the binning groups has been fixed. This bug 
 is in fact inherited from a problem in the `findInterval()` function. The breaks 
 (given in the vec arument) might get corrupted when they contain many decimal 
@@ -63,83 +66,85 @@ variable (e.g. wavelength) was exactly on the left of the bin
 range the variable was assigned to the next bin. In some cases this lead to 
 small discrepancies in the in the computation of the mean of the bins. 
 
-* `spliceCorrection()` now accepts one or two values as input for the splice
+* ``spliceCorrection()`` now accepts one or two values as input for the splice
 argument. Previously it only accepted a vector of length two. For example, now it 
 corrrects for splice steps of spectra that originates from spectrometers 
 with two detectors (i.e. it corrects for the potential abrupt transition 
 betwteen the two detectors). 
 
-* An extra sanity check has been added to the `read_nircal()` function. The 
+* An extra sanity check has been added to the ``read_nircal()`` function. The 
 function evaluaes whether it is indeed a file properly produced by the BUCHI 
 nircal software. 
 
 * There was a bug in the filter for the 3rd order derivative in gap segment 
-derivative (`gapDer`) function. One of the factors in the filter had a wrong 
+derivative (`gapDer()`) function. One of the factors in the filter had a wrong 
 negative sign. 
 
-* There was a bug in the `read_nircal` function. It emerged only in some files and 
+* There was a bug in the `read_nircal()` function. It emerged only in some files and 
 prevented the function from reading the Description field properly 
 
-## Changes
+### Changes
 * In the `msc()` function the argument `reference_spc` has been renamed to 
 `ref_spectrum` to emphasize that its input must be is a vector and not a 
 matrix of spectra. 
 
-prospectr 0.2.2
+`prospectr` 0.2.2
 ===============
 
-## New features
+### New features
 
-* a new function for baseline correction was added. See baseline()  
+* a new function for baseline correction was added. See `baseline()`  
 
-## Improvements and fixes
+### Improvements and fixes
 
 * The package was stripping some symbols for Rcpp functions in Makevars in order 
 to reduce the installation size of the package. Now these lines have been 
 commented to comply with CRAN policies
 
-* standardNormalVariate returns now a matrix (previosuly a data.frame)
+* `standardNormalVariate()` returns now a matrix (previously a data.frame)
 
 
-prospectr 0.2.1
+`prospectr` 0.2.1
 ===============
 * New license
 * The detrend function now allows to remove trends corresponding to different 
 polynomial orders. Check the new 'p' argument. 
 * New preprocessing function: multiplicative scatter correction (msc)
-* Now resample() also has a new argument (...) to pass additional arguments to the 
-splinefun() function (of stats) used within resample() when the argument 
-interpol = "spline" (the default since version 0.2.0)
-* Bug fix: in read_nircal, the description file was not being properly read
+* Now `resample()` also has a new argument (`...`) to pass additional arguments to the 
+`splinefun()` function (of stats) used within `resample()` when the argument 
+`interpol = 'spline'` (the default since version 0.2.0)
+* Bug fix: in `read_nircal()`, the description file was not being properly read
 * Now performing automatic unit tests with the package testthat
 
-prospectr 0.2.0
+`prospectr` 0.2.0
 ===============
 * New maintainer [Leo Ramirez-Lopez]
 * Updated vignette
-* A new function (read_nircal) for reading buchi NIRcal files has been added
+* A new function (`read_nircal()`) for reading buchi NIRcal files has been added
 * Documentation reviewed
-* The description of the continuum removal algorithm is was adjusted. Previously was indicated that the implemented algorithm was based on the search for a local minimum of
-the absorbance spectra the algorithm, however in fact it looks for the convex hull. Thanks to Peter Tillmann for noticing this.
+* The description of the continuum removal algorithm is was adjusted. Previously 
+was indicated that the implemented algorithm was based on the search for a 
+local minimum of the absorbance spectra the algorithm, however in fact it looks 
+for the convex hull. Thanks to Peter Tillmann for noticing this.
 
-prospectr 0.1.4
+`prospectr` 0.1.4
 ===============
-* Fix bug in kenStone and duplex when the group parameter is used
+* Fix bug in `kenStone()` and `duplex()` when the group parameter is used
 
-prospectr 0.1.3
+`prospectr` 0.1.3
 ===============
 * Fix in DESCRITPION and NAMESPACE as required by Rcpp 0.11
 
-prospectr 0.1.2
+`prospectr` 0.1.2
 ===============
-* bug fix for readASD when ASD file version = 7.0
-* add sanity check in spliceCorrection
+* bug fix for `readASD()` when ASD file version = 7.0
+* add sanity check in `spliceCorrection()`
 
-prospectr 0.1.1
+`prospectr` 0.1.1
 ===============
-* bug fix for shenkWest when rm.outlier = T 
-* bug fix for gapDer when input is a data.frame
+* bug fix for `shenkWest()` when `rm.outlier = TRUE` 
+* bug fix for `gapDer()` when input is a data.frame
 
-prospectr 0.1
+`prospectr` 0.1
 ===============
 * Initial release of the package

R/baseline.R

@@ -50,32 +50,32 @@ baseline <- function(X, wav) {
   if (is.data.frame(X)) {
     X <- as.matrix(X)
   }
-  
+
   if (missing(wav)) {
     wav <- 1:ncol(X)
   }
-  
+
   wav <- c(
     wav[1] - diff(wav[1:2]),
     wav,
     wav[length(wav)] + diff(wav[(length(wav) - 1):length(wav)])
   )
-  
+
   # make sure the edges will be well above any peak
   edges <- abs(apply(X, 1, "max")) + abs(apply(X, 1, "min"))
   edges <- edges * 2
-  
+
   X <- cbind(edges, X, edges)
   colnames(X) <- wav
-  
+
   ## simple baseline function
   simple_bs <- function(x, wav) {
     id <- sort(chull(wav, x))
     id <- id[-c(1, length(id))]
     hull_line <- approx(x = wav[id], y = x[id], xout = wav, method = "linear")$y
     return(hull_line)
   }
-  
+
   if (is.matrix(X)) {
     if (missing(wav)) {
       wav <- seq_len(ncol(X))
@@ -87,14 +87,14 @@ baseline <- function(X, wav) {
   } else {
     hull_line <- simple_bs(X, wav)
   }
-  
+
   hull_line <- hull_line[, -c(1, ncol(hull_line))]
   X <- X[, -c(1, ncol(X))]
-  
+
   baselined <- X - hull_line
-  
+
   wav <- wav[-c(1, length(wav))]
-  
+
   if (is.matrix(X)) {
     colnames(hull_line) <- colnames(baselined) <- wav
     rownames(hull_line) <- rownames(baselined) <- rownames(X)

R/cochranTest.R

@@ -39,7 +39,7 @@
 #' which can be evaluated with ('t Lam, 2010):
 #'
 #'
-#' \mjdeqn{C_{UL}(\alpha, n, N) = 1 + \[\frac{N-1}{F_{c}(\alpha/N,(n-1),(N-1)(n-1))}\]^{-1} }{C_{UL}(\alpha, n, N) = 1 + \[\frac{N-1}{F_{c}(\alpha/N,(n-1),(N-1)(n-1))}\]^{-1}}
+#' \mjdeqn{C_{UL}(\alpha, n, N) = 1 + [\frac{N-1}{F_{c}(\alpha/N,(n-1),(N-1)(n-1))}]^{-1} }{C_{UL}(\alpha, n, N) = 1 + [\frac{N-1}{F_{c}(\alpha/N,(n-1),(N-1)(n-1))}]^{-1}}
 #'
 #' where \mjeqn{\alpha}{\alpha} is the *p*-value of the test, \mjeqn{n}{n} is the (average)
 #' number of replicates and \mjeqn{F_c}{F_c} is the critical value of the Fisher's \mjeqn{F}{F} ratio.

R/e2m.R

@@ -41,7 +41,7 @@ e2m <- function(X, sm.method = c("svd", "eigen")) {
     ms_x <- X / sd(X)
   } else {
     sm_method <- match.arg(sm.method)
-    
+
     X <- as.matrix(X)
     vcv <- cov(X)
     sq_vcv <- sqrtSm(vcv, method = sm_method)

R/msc.R

@@ -15,9 +15,9 @@
 #' @param ref_spectrum a numeric vector corresponding to an "ideal" reference
 #' spectrum (e.g. free of scattering effects). By default the function uses the
 #' mean spectrum of the input \code{X}. See details. Note that this argument was
-#' previously named as `reference_spc`, however, it has been renamed to 
-#' `ref_spectrum` to emphasize that this argument is a vector and not a 
-#' matrix of spectra. 
+#' previously named as `reference_spc`, however, it has been renamed to
+#' `ref_spectrum` to emphasize that this argument is a vector and not a
+#' matrix of spectra.
 #'
 #' @details
 #' The Multiplicative Scatter Correction (MSC) is a normalization method that
@@ -47,7 +47,7 @@
 #' @examples
 #' data(NIRsoil)
 #' NIRsoil$msc_spc <- msc(X = NIRsoil$spc)
-#' 
+#'
 #' # 10 first msc spectra
 #' matplot(
 #'   x = as.numeric(colnames(NIRsoil$msc_spc)),

R/spliceCorrection.R

@@ -2,11 +2,11 @@
 #' @description
 #' Corrects steps in an input spectral matrix by linear interpolation of the
 #' values of the edges of the middle sensor
-#' 
+#'
 #' @usage
-#' 
+#'
 #' spliceCorrection(X, wav, splice = c(1000, 1830), interpol.bands = 10)
-#' 
+#'
 #' @param X a numeric matrix or vector to transform (optionally a data frame that can
 #' be coerced to a numerical matrix).
 #' @param wav a numeric vector with band positions.