Merge pull request #22 from l-ramirez-lopez/v2.0

v2.0 is now on CRAN

.Rbuildignore

@@ -1,7 +1,11 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-resemble_logo.png
 code_ex.R
 .travis.yml
 ^packrat/
 ^\.Rprofile$
+^cran-comments\.md$
+^my-comments\.md$
+logo.R
+^Rscript*
+logo_large.png

.travis.yml

@@ -22,7 +22,6 @@ r_packages:
   - covr
   - data.table
   - magrittr
-  - dplyr
   - testthat
 
 after_success:

DESCRIPTION

@@ -1,46 +1,23 @@
 Package: resemble
 Type: Package
-Title: 
-    Regression and Similarity Evaluation for Memory-Based Learning in
-    Spectral Chemometrics
+Title: Memory-Based Learning in Spectral Chemometrics
 Version: 2.0.0
-Date: 2020-10-12
-Authors@R:  
-    c(person(given = "Leonardo",
-             family = "Ramirez-Lopez",
-             role = c("aut", "cre"),
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0002-5369-5120")),
-      person(given = "Antoine",
-             family = "Stevens",
-             role = "ctb",
-             comment = c(ORCID = "0000-0002-1588-7519")),
-      person(given = "Raphael",
-             family = "Viscarra Rossel",
-             role = "ctb",
-             comment = c(ORCID = "0000-0003-1540-4748")),
-      person(given = "Craig",
-             family = "Lobsey",
-             role = "ctb",
-             comment = c(ORCID = "0000-0001-5416-8640")),
-      person(given = "Alex",
-             family = "Wadoux",
-             role = "ctb",
-             comment = c(ORCID = "0000-0001-7325-9716")),
-      person(given = "Timo",
-             family = "Breure",
-             role = "ctb",
-             comment = c(ORCID = "0000-0001-5695-8064"))
-      )
+Date: 2020-10-29
+Author: Leonardo Ramirez-Lopez [aut, cre], 
+    Antoine Stevens [aut, ctb],
+    Raphael Viscarra Rossel [ctb],
+    Craig Lobsey [ctb], 
+    Alex Wadoux [ctb],
+    Timo Breure [ctb]
 Maintainer: 
     Leonardo Ramirez-Lopez <[email protected]>
 BugReports: 
     https://github.com/l-ramirez-lopez/resemble/issues
 Description: 
-    Functions for spectral similarity/dissimilarity
-    analysis and memory-based learning (MBL) for non-linear modeling
-    in complex spectral data sets. In chemometrics MBL is also known 
-    as local modeling.
+    Functions for dissimilarity analysis and memory-based learning 
+    (MBL, a.k.a local modeling) in complex spectral data sets. 
+    Most of these functions are based the methods presented in 
+    Ramirez-Lopez et al. (2013) <doi:10.1016/j.geoderma.2012.12.014>.
 License: MIT + file LICENSE
 URL: http://l-ramirez-lopez.github.io/resemble/
 Depends:
@@ -49,26 +26,23 @@ Imports:
     foreach, 
     iterators, 
     Rcpp (>= 1.0.3), 
-    dplyr (>= 0.7.0), 
     mathjaxr (>= 1.0), 
     magrittr (>= 1.5.0), 
-    lifecycle (>= 0.2.0),
+    lifecycle (>= 0.2.0), 
     data.table (>= 1.9.8)
 Suggests: 
     prospectr, 
     parallel, 
-    doParallel,
-    testthat,
+    doParallel, 
+    testthat, 
     formatR,
-    bookdown, 
     rmarkdown,
+    bookdown,
     knitr
 LinkingTo: 
-    Rcpp, 
+    Rcpp,
     RcppArmadillo
-RdMacros: 
-    mathjaxr,
-    lifecycle
+RdMacros: mathjaxr
 VignetteBuilder: knitr
 NeedsCompilation: yes
 LazyData: true

NAMESPACE

@@ -31,8 +31,7 @@ import(grDevices)
 import(graphics)
 import(iterators)
 import(lifecycle)
-importFrom(dplyr,if_else)
-importFrom(dplyr,select)
+import(mathjaxr)
 importFrom(graphics,barplot)
 importFrom(lifecycle,deprecate_soft)
 importFrom(magrittr,"%>%")

NEWS

@@ -1,20 +1,130 @@
 # News for the resemble package
 
-## Version 2.0 (gordillo)
-
-* 11.10.2020 
-New vignette!
+## resemble 2.0 (gordillo)
 
 * 02.07.2020 
 During the recent lockdown we had the chance to inevest a enough time on the 
 development of a new version of the package resemble. This new version comes 
 with significant improvements as well as new functionality. For example, it now 
 matches the tidyverse R style guide, it includes unit tests, includes new 
-functionality for modeling, mbl is bit faster and a bit less memory-hungry, etc. 
-See changes.md file for further details.
-
-
-## Version 1.3 (never released)
+functionality for modeling, mbl is faster and a less memory-hungry.
+
+### New features
+- search_neighbors() function.
+- dissimilarity() function.
+
+## Improvements and fixes
+- mbl is faster and a less memory-hungry.
+- New vignette.
+- unit tests have been introduced using the testthat package.
+
+## Breaking changes
+
+### orthoProjection, pcProjection, plsProjection (renamed to ortho_projection, 
+pc_projection, pls_projection respectively):
+- X2 argument renamed to Xu (for consistency throughout all the fucntions)
+- Argument scaled renamed to .scale
+- Argument max.iter renamed to max_iter
+- Bug fix: when the "pca.nipals method was used and the method to select the pcs wa "opc",
+  the function was returning 1 component less than the maximum requested.
+- "pca.nipals" is now implemented in C++ via Rcpp
+- Bug fix in plsProjection: when "cumvar" was used as the pcSelection method, an 
+  error about data allocation in a matrix was retrieved
+- Argument pcSelection renamed to pc_selection
+- ... is deprecated in both pcProjection and plsProjection
+- Argument cores is deprecated, it was used to set the number of cores in some 
+c++ internal functions via OpenMP in Rcpp. 
+- Names the following outputs have been changed: X.loadings, Y.loadings, sc.sdv 
+and n.components. Their new names are: X_loadings, Y_loadings, sc_sdv and 
+n_components.
+
+### corDiss (renamed to cor_diss):
+- X2 argument renamed to Xu (for consistency throughout all the fucntions)
+- Argument scaled renamed to .scale
+- default for .scale has changed from TRUE to FALSE
+- the dimnames of the resulting matrix are now Xr_1... Xr_n (previusly Xr.1... Xr.n)
+
+### fDiss (renamed to f_diss):
+- X2 argument renamed to Xu (for consistency throughout all the fucntions)
+- Argument scaled renamed to .scale
+- default for .scale has changed from TRUE to FALSE
+- the dimnames of the resulting matrix are now Xr_1... Xr_n (previusly Xr.1... Xr.n)
+- argument method changed to diss_method
+
+### sid:
+- X2 argument renamed to Xu (for consistency throughout all the fucntions)
+- Argument scaled renamed to .scale
+- default for .scale has changed from TRUE to FALSE
+- the dimnames of the resulting matrix are now Xr_1... Xr_n (previusly Xr.1... Xr.n)
+
+
+### orthoDiss (renamed to ortho_diss):
+- X2 argument renamed to Xu (for consistency throughout all the fucntions)
+- Argument scaled renamed to .scale
+- Argument local renamed to .local
+- Argument pcSelection renamed to pc_selection
+- Argument return.all renamed to compute_all
+- Argument cores is deprecated, it wwas used to set the number of cores in some 
+c++ internal functions via OpenMP in Rcpp. 
+- When \code{.local = TRUE} a new output is produced: 'neighborhood_info' which 
+is a data.frame containing the relevant information about the neighborhood of 
+each sample (e.g. neighborhood indices, number of components used at each 
+neighborhood, etc)
+- Output global.variance.info has been renamed to global_variance_info
+
+
+### simEval (renamed to sim_eval):
+- argument sideInf renamed to side_info
+- argument lower.tri renamed to lower_triangle
+- argument cores renamed to omp_threads
+- lower_triangle is deprecated. Now if a vector is passed to d, the function assumes
+  that it is a lower triangle of a distance matrix
+- Argument cores is deprecated, it wwas used to set the number of cores in some 
+c++ internal functions via OpenMP in Rcpp.
+
+
+### mbl
+- pls.max.iter, pls.tol and noise.v were moved to mbl from mbl_control()
+- Argument scaled (from mbl_control()) renamed to .scale and moved to mbl
+- new arguments: gh and spike
+- Argument pcSelection renamed to pc_selection
+- Argument mblCtrl renamed to control
+- Argument dissUsage renamed to diss_usage
+- order of the Yr, Xr, Yu and Xu arguments has changed to Xr, Yr, Xu and Yu
+- input type for the argument method has changed. Previously it received a 
+character string  indicating the type of local regresion (i.e. "pls", 
+"wapls1" or "gpr"). Now it receives an object of class local_fit which is output 
+by the new local_fit fucntions. 
+- dissimilarityM has been deprecated. It was used to pass a dissimilarity matrix 
+computed outiside the mbl fucntion. This can be done now with the new argument 
+diss_method of mbl which was previosly named "sm" and it was in mblControl()
+
+
+### neigCleaning (now search_neighbors)
+- Function renamed to search_neighbors
+- Argument cores is deprecated, it was used to set the number of cores in some 
+c++ internal functions via OpenMP in Rcpp. 
+
+
+### mblControl (renamed to mbl_control):
+- sm argument is deprecated. Now the dissmilarity metric is an argument of the 
+mbl fucntion
+- scale and center arguments have been moved to the mbl fucntion
+- Argument range.pred.lim renamed to range_prediction_limits
+- Argument cores is deprecated, it was used to set the number of cores in some 
+c++ internal functions via OpenMP in Rcpp. 
+- k0, pcMethod, ghMethod are deprecated
+- localOptimization has been renamed to tune_locally
+- valMethod has been renamed to validation_type
+- Option "loc_crossval" in validation_type has been renamed to "local_cv"
+
+### plot.mbl
+- option "pca" was replaced by option "gh" which plots the pls projection used 
+for computing the gh distance in mbl 
+
+
+
+## resemble 1.3 (never released)
 
 * 11.04.2020 
 The option 'movcor' for the argument sm of mblControl() is deprecated. The 
@@ -37,7 +147,7 @@ differences, dividing it by the number of variables and then compute the squared
 root i.e. sqrt(mean((Xi-Xj)^2)/ncol(Xi)). This bug had no effect on the 
 computations of the nearest neighbors. 
 
-## Version 1.2.0001 (alma de coco)
+## resemble 1.2.0001 (alma de coco)
 * 13.09.2016 
 A bug in the computation of the Mahalanobis distance in the PLS space was fixed. 
 
@@ -60,7 +170,7 @@ corrected in the documentation.
 the projection Matrix (projectionM) returned by plsProjection now only contains 
 the columns corresponding only to the number components retrieved
 
-## Version 1.2 (alma de coco)
+## resemble 1.2 (alma de coco)
 * 04.03.2016 
 A patch was released for and extrange bug that prevented to run mbl 
 in parallel when the gpr method was used.
@@ -96,5 +206,5 @@ The function movcorDist was removed since. it was included by mistake in the
 previous version of the package. The corDiss function  can be used in 
 raplacement of movcorDist.
 
-## Versions 1.0 and 1.1.1
+## resemble 1.1.1
 * 19.03.2013 Hello world! Initial release of the package

R/AAA.R

@@ -2,9 +2,22 @@
 
 .onAttach <- function(lib, pkg) {
   # assign("gpclib", FALSE, envir=.RESEMBLE_CACHE)
-  resemble_v <- read.dcf(file = system.file("DESCRIPTION", package = pkg), fields = "Version")
-  packageStartupMessage(paste0("\033[34m", pkg, " version ", resemble_v, " -- 'gordillo'\033[39m"))
-  packageStartupMessage("\033[34mcheck the package repository at https://github.com/l-ramirez-lopez/resemble/\033[39m")
+  resemble_v <- read.dcf(
+    file = system.file("DESCRIPTION", package = pkg),
+    fields = "Version"
+  )
+  mss <- paste0(
+    "\033[34m",
+    pkg, " version ",
+    resemble_v,
+    " -- 'gordillo'\033[39m"
+  )
+  mss2 <- paste0(
+    "\033[34mcheck the package repository at: ",
+    "https://github.com/l-ramirez-lopez/resemble/\033[39m"
+  )
+  packageStartupMessage(mss)
+  packageStartupMessage(mss2)
 }
 
 # .onUnload <- function(libpath) {