From c14bd467b0e2013e281db3685dc4486c35e0a9d3 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Tue, 30 Aug 2022 19:19:15 +0200
Subject: [PATCH 01/17] fix(logo align with HTML5)

---
 R/resemble.R            | 2 +-
 man/resemble-package.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/resemble.R b/R/resemble.R
index 1666303..a1c4f67 100644
--- a/R/resemble.R
+++ b/R/resemble.R
@@ -18,7 +18,7 @@
 #'
 #' Functions for memory-based learning
 #'
-#' \if{html}{\figure{logo.png}{options: align='right' alt='logo' width='120'}}
+#' \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}
 #'
 #' @details
 #'
diff --git a/man/resemble-package.Rd b/man/resemble-package.Rd
index 84111dc..2ecc12a 100644
--- a/man/resemble-package.Rd
+++ b/man/resemble-package.Rd
@@ -10,7 +10,7 @@
 
 Functions for memory-based learning
 
-\if{html}{\figure{logo.png}{options: align='right' alt='logo' width='120'}}
+\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}
 }
 \details{
 This is the version \code{2.1} (\code{'piapia'}) of the package. It

From cce3f1710a41ae7f67648a994917d8d494755153 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Tue, 30 Aug 2022 19:19:21 +0200
Subject: [PATCH 02/17] Update DESCRIPTION

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 789ab57..e99d332 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -48,5 +48,5 @@ VignetteBuilder: knitr
 NeedsCompilation: yes
 LazyData: true
 Repository: CRAN
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Encoding: UTF-8

From cb85381ff508a3f6c6e3577e92bf240d20b54909 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Tue, 30 Aug 2022 19:19:44 +0200
Subject: [PATCH 03/17] fix(remove duplicated function)

---
 src/regression_methods.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/regression_methods.cpp b/src/regression_methods.cpp
index 277c14f..701293f 100644
--- a/src/regression_methods.cpp
+++ b/src/regression_methods.cpp
@@ -1159,7 +1159,6 @@ List opls_get_basics(arma::mat X,
   );
 }
 
-
 //' @title Prediction function for the \code{opls} and \code{fopls} functions
 //' @description Predicts response values based on a model generated by either by \code{opls} or the \code{fopls} functions. 
 //' For internal use only!. 

From 84d92529c78f590fb299ebc455790769661995a2 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:28:10 +0200
Subject: [PATCH 04/17] fix(works for external distance matrices) #24

---
 R/mbl.R | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/mbl.R b/R/mbl.R
index 5730bf3..313a6f8 100644
--- a/R/mbl.R
+++ b/R/mbl.R
@@ -928,6 +928,7 @@ mbl <- function(Xr, Yr, Xu, Yu = NULL,
       allow_parallel = control$allow_parallel,
       ...
     )
+  
     diss_xr_xu <- neighborhoods$dissimilarity
     if (!is.null(neighborhoods$projection)) {
       diss_xr_xu_projection <- neighborhoods$projection
@@ -946,9 +947,7 @@ mbl <- function(Xr, Yr, Xu, Yu = NULL,
         ))
       }
       diss_xr_xr <- diss_method[1:nrow(Xr), 1:nrow(Xr)]
-      diss_xr_xu <- diss_method[1:nrow(Xr), (1 + nrow(Xr)):ncol(diss_method)]
-      rm(diss_method)
-      gc()
+      diss_method <- diss_method[1:nrow(Xr), (1 + nrow(Xr)):ncol(diss_method)]
     }
     if (diss_usage %in% c("weights", "none")) {
       if (dim_diss[1] != n_xr & dim_diss[2] != n_xu) {
@@ -962,17 +961,19 @@ mbl <- function(Xr, Yr, Xu, Yu = NULL,
       }
     }
     diss_xr_xu <- diss_method
-    append(
-      neighborhoods,
-      diss_to_neighbors(diss_xr_xu,
-        k = k, k_diss = k_diss, k_range = k_range,
-        spike = NULL,
+    diss_method <- "external_matrix"
+    
+
+    neighborhoods <-
+      diss_to_neighbors(
+        diss_xr_xu,
+        k = k_max, k_diss = k_diss_max,
+        k_range = k_range,
+        spike = spike,
         return_dissimilarity = control$return_dissimilarity
       )
-    )
-
+    
     if (gh) {
-      neighborhoods <- NULL
       neighborhoods$gh$projection <- pls_projection(
         Xr = Xr, Xu = Xu,
         Yr = Yr,
@@ -980,7 +981,7 @@ mbl <- function(Xr, Yr, Xu, Yu = NULL,
         scale = scale, ...
       )
       neighborhoods$gh$gh_Xr <- f_diss(neighborhoods$gh$projection$scores,
-        Xu = t(colMeans(neighborhoods$gh$projection$scores)),
+        Xu = t(colMeans(neighborhoods$gh$projection$scores[1:nrow(Xr), ])),
         diss_method = "mahalanobis",
         center = FALSE, scale = FALSE
       )
@@ -991,7 +992,6 @@ mbl <- function(Xr, Yr, Xu, Yu = NULL,
 
     neighborhoods$diss_xr_xr <- diss_xr_xr
     rm(diss_xr_xr)
-    rm(diss_method)
     gc()
   }
 

From 9c490a650525c359c07409c03f1e8fac8797d0ab Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:28:30 +0200
Subject: [PATCH 05/17] new test for external distances

---
 tests/testthat/test-mbl.R | 74 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/tests/testthat/test-mbl.R b/tests/testthat/test-mbl.R
index 5a8609f..e977a14 100644
--- a/tests/testthat/test-mbl.R
+++ b/tests/testthat/test-mbl.R
@@ -355,3 +355,77 @@ test_that("mbl delivers expeted results", {
   expect_true(all(yuv_pls_k_diss))
   expect_true(all(yuv_wapls_k_diss))
 })
+
+
+test_that("mbl with external disstances works", {
+  tol <- 1e-10
+  nirdata <- data("NIRsoil", package = "prospectr")
+  
+  # Proprocess the data using detrend plus first derivative with Savitzky and
+  # Golay smoothing filter
+  sg_det <- savitzkyGolay(
+    detrend(NIRsoil$spc,
+            wav = as.numeric(colnames(NIRsoil$spc))
+    ),
+    m = 1,
+    p = 1,
+    w = 7
+  )
+  
+  NIRsoil$spc_pr <- sg_det
+  
+  # split into training and testing sets
+  test_x <- NIRsoil$spc_pr[NIRsoil$train == 0 & !is.na(NIRsoil$CEC), ]
+  test_y <- NIRsoil$CEC[NIRsoil$train == 0 & !is.na(NIRsoil$CEC)]
+  
+  train_y <- NIRsoil$CEC[NIRsoil$train == 1 & !is.na(NIRsoil$CEC)]
+  train_x <- NIRsoil$spc_pr[NIRsoil$train == 1 & !is.na(NIRsoil$CEC), ]
+  
+  my_control <- mbl_control(validation_type = "NNv")
+  
+  ## The neighborhood sizes to test
+  ks <- seq(40, 140, by = 20)
+  
+  ext_d <- dissimilarity(
+    rbind(train_x, test_x),  Xu = rbind(train_x, test_x),
+    diss_method = "cor",
+    center = FALSE, scale = FALSE
+  )$dissimilarity
+  
+  dim(ext_d)
+  diag(ext_d) <- 0
+  
+  
+  sbl_external_diss <- mbl(
+    Xr = train_x,
+    Yr = train_y,
+    Xu = test_x,
+    k = ks,
+    spike = 1:5,
+    method = local_fit_gpr(),
+    diss_method = ext_d,
+    diss_usage = "predictors",
+    control = my_control,
+    scale = FALSE, 
+    center = FALSE
+  )
+  
+  sbl_internal_diss <- mbl(
+    Xr = train_x,
+    Yr = train_y,
+    Xu = test_x,
+    k = ks,
+    spike = 1:5,
+    method = local_fit_gpr(),
+    diss_method = "cor",
+    diss_usage = "predictors",
+    control = my_control,
+    scale = FALSE, 
+    center = FALSE
+  )
+  
+  r_ext <- sbl_internal_diss$validation_results$nearest_neighbor_validation 
+  r_int <- sbl_external_diss$validation_results$nearest_neighbor_validation
+  
+  expect_true(sum(abs(r_ext - r-int)) < tol)
+})

From c2353636f9848c5115477009fac60dd79efbec81 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:28:38 +0200
Subject: [PATCH 06/17] Update README.md

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index a172e50..f646cdf 100644
--- a/README.md
+++ b/README.md
@@ -9,13 +9,13 @@
 
 <!-- badges: end -->
 
-_Last update: 20.03.2022_
+_Last update: 30.08.2022_
 
 <em><p align="right"> Think Globally, Fit Locally (Saul and Roweis, 2003) </p></em>
 
 ## About
 The `resemble` package provides high-performing functionality for 
-data-driven modeling (including local modeling), nearest neighbor search and 
+data-driven modeling (including local modeling), nearest-neighbor search and 
 orthogonal projections in spectral data.
 
 ## Vignette

From addf1b6d2ca3b2c3c925dc269b2f87d0d7407c10 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:29:04 +0200
Subject: [PATCH 07/17] doc(typo)

---
 R/search_neighbors.R    | 2 +-
 man/search_neighbors.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/search_neighbors.R b/R/search_neighbors.R
index bce00c6..958bcbf 100644
--- a/R/search_neighbors.R
+++ b/R/search_neighbors.R
@@ -150,7 +150,7 @@
 #' input data). Default: \code{character()}. NOTE: his is an experimental
 #' argument.
 #' @param ... further arguments to be passed to the \code{\link{dissimilarity}}
-#' fucntion. See details.
+#' function. See details.
 #' @details
 #' This function may be specially useful when the reference set (\code{Xr}) is
 #' very large. In some cases the number of observations in the reference set
diff --git a/man/search_neighbors.Rd b/man/search_neighbors.Rd
index f4edb0b..764370b 100644
--- a/man/search_neighbors.Rd
+++ b/man/search_neighbors.Rd
@@ -166,7 +166,7 @@ input data). Default: \code{character()}. NOTE: his is an experimental
 argument.}
 
 \item{...}{further arguments to be passed to the \code{\link{dissimilarity}}
-fucntion. See details.}
+function. See details.}
 }
 \value{
 a \code{list} containing the following elements:

From a9563bcb3a71da4b506a7c15ffb580e4a84a63de Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:29:12 +0200
Subject: [PATCH 08/17] Delete NEWS

---
 NEWS | 244 -----------------------------------------------------------
 1 file changed, 244 deletions(-)
 delete mode 100644 NEWS

diff --git a/NEWS b/NEWS
deleted file mode 100644
index 5d668f9..0000000
--- a/NEWS
+++ /dev/null
@@ -1,244 +0,0 @@
-# News for the resemble package
-
-## resemble 2.1 (piapia)
-23.09.2021
-
-### New features
-- A argument named "seed" was added to the mbl function. It is used to gurantee 
-reproducibility of cross-validation results. 
-
-- A modified PLS method was implemented (see local_fit_pls and local_fit_wapls).
-It uses correlation bteween response and predictors to derive the PLS weights. 
-
-## Improvements and fixes
-- A Bug in the computation of the explained variance of X for pls models was 
-detected and fixed. The pls related functions were underestimating the amount 
-of variance exmplained by each PLS component. The explained variance was being 
-computed from the matrix of scores, in this version it is computed from the 
-reconstructed spectra at each PLS iteration.
-
-- Manual selection of components in pc_projection() and pls_projection() now 
-accepts to select only 1 component (before the minimum was 2).
-
-- pls_projection() now includes a new argument (method) to allow the user to select 
-between the standard pls algorithm and a modified pls algorithm.
-
-- ortho_diss(), dissimilarity() and search_neighbors() functions include a new 
-dissimilarity method: "mpls" (modified pls).
-
-- An internal function for stratified random sampling for cross validtaion 
-purposes has been improved for computational speed. 
-
-- 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.
-
-
-## 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 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 
-'movcor' moving window correlations between spectra as dissimilarity measure. 
-Now This option can be specified by using 'cor' as the method in the argument 
-'sm' and passing a window size to the argument 'ws'of mblControl(). If 'ws' 
-is not specified, the standard correlation between spectra is computed.  
-             
-* 27.02.2020 
-The argument 'resampling' in mblControl() has been renamed to 'number'
-             
-* 18.07.2019 
-A bug in the scaling of the euclidean distances in fDiss was detected and fixed. 
-The distance ratios (between samples) were correctly calculated, but the final 
-scaling of the results was not properly done. The distance between Xi and Xj 
-were scaled by taking the squared root of the mean of the squared differences 
-and dividing it by the number of variables i.e. sqrt(mean((Xi-Xj)^2))/ncol(Xi),
-however the correct calculation is done by taking the mean of the squared 
-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. 
-
-## 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. 
-             
-* 06.09.2016 
-Thanks to Matthieu Lesnoff who found a bug in the predict.orthoProjection 
-function (an error was thrown when PCA preditions were requested). This bug has 
-been fixed. 
-             
-* 10.08.2016 
-A bug in plot.mbl was fixed. It was not possible to plot mbl results when the 
-k.diss argument (threshold distances) was used in the mbl function.   
-
-* 10.08.2016 
-Since the previous release, the "wapls1" regression (in the mbl function) 
-is actually compatible with valMethod = "loc_crossval" (in the mblControl). 
-In the previous documentation was wrongly stated otherwise. Now this has been 
-corrected in the documentation.
-
-* 09.08.2016 
-the projection Matrix (projectionM) returned by plsProjection now only contains 
-the columns corresponding only to the number components retrieved
-             
-## 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.
-
-* 19.01.2016 
-Now it is possible to locally optimize the maximum and minimum pls factors in 
-wapls1 local regressions.
-
-* 09.12.2015 
-Many thanks to Eva Ampe and Lorenzo Menichetti for their suggestions.
-
-* 08.12.2015 
-A method for better estimates of RMSE values computed for the 'wapls1' method 
-has been implemented.
-
-* 08.12.2015 
-The 'wapls2' method of the mbl function is no longer supported because of several 
-drawbacks computing reliable uncertainty estimates.
-
-* 18.11.2015 
-Several functions are now based on C++ for faster computations.
-
-* 23.04.2014 
-Added default variable names when they are missing and an error message when the 
-names of Xr do not match the names of Xu.
-
-* 23.04.2014 
-plot.mbl draws now the circles around the actual centre function when the 
-spectra is not centred for mbl.
-
-* 20.03.2013 
-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.
-
-## resemble 1.1.1
-* 19.03.2013 Hello world! Initial release of the package

From 46405aa67d9ab05f0f14c75dfdda1a319f578433 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:29:15 +0200
Subject: [PATCH 09/17] Create NEWS.md

---
 NEWS.md | 274 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 274 insertions(+)
 create mode 100644 NEWS.md

diff --git a/NEWS.md b/NEWS.md
new file mode 100644
index 0000000..c5c196c
--- /dev/null
+++ b/NEWS.md
@@ -0,0 +1,274 @@
+# `resemble`
+
+## `resemble 2.2.1 (Fix-Hodges)`
+### Improvements and fixes
+
+* Documentation is now compatible with HTML5.
+
+
+## `resemble 2.1 (piapia)`
+23.09.2021
+
+### New features
+
+- The argument `seed` was added to the mbl function. It is used to gurantee 
+reproducibility of cross-validation results. 
+
+- A modified PLS method was implemented (see `local_fit_pls()` and `local_fit_wapls()`).
+It uses correlation bteween response and predictors to derive the PLS weights. 
+
+## Improvements and fixes
+
+- A Bug in the computation of the explained variance of X for pls models was 
+detected and fixed. The pls related functions were underestimating the amount 
+of variance explained by each PLS component. The explained variance was being 
+computed from the matrix of scores, in this version it is computed from the 
+reconstructed spectra at each PLS iteration.
+
+- Manual selection of components in `pc_projection()` and `pls_projection()` now 
+accepts to select only 1 component (before the minimum was 2).
+
+- `pls_projection()` now includes a new argument (`method`) to allow the user to select 
+between the standard pls algorithm and a modified pls algorithm.
+
+- `ortho_diss()`, `dissimilarity()` and `search_neighbors()` functions include a new 
+dissimilarity method: `"mpls"` (modified pls).
+
+- An internal function for stratified random sampling for cross-validtaion 
+purposes has been improved for computational speed. 
+
+- 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.
+
+
+## `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 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 functions)
+- 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 was `"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 functions)
+- 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 functions)
+- 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 functions)
+- 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 functions)
+- 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 `.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 was 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` functions. 
+- `dissimilarityM` has been deprecated. It was used to pass a dissimilarity matrix 
+computed outside the `mbl()` function. This can be done now with the new argument 
+`diss_method` of `mbl` which was previously 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 function.
+- `scale` and `center` arguments have been moved to the `mbl()` function
+- 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 
+'movcor' moving window correlations between spectra as dissimilarity measure. 
+Now This option can be specified by using 'cor' as the method in the argument 
+'sm' and passing a window size to the argument 'ws'of mblControl(). If 'ws' 
+is not specified, the standard correlation between spectra is computed.  
+             
+* 27.02.2020 
+
+The argument 'resampling' in mblControl() has been renamed to 'number'
+             
+* 18.07.2019 
+
+A bug in the scaling of the euclidean distances in fDiss was detected and fixed. 
+The distance ratios (between samples) were correctly calculated, but the final 
+scaling of the results was not properly done. The distance between Xi and Xj 
+were scaled by taking the squared root of the mean of the squared differences 
+and dividing it by the number of variables i.e. sqrt(mean((Xi-Xj)^2))/ncol(Xi),
+however the correct calculation is done by taking the mean of the squared 
+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. 
+
+## `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. 
+             
+* 06.09.2016 
+
+Thanks to Matthieu Lesnoff who found a bug in the predict.orthoProjection 
+function (an error was thrown when PCA preditions were requested). This bug has 
+been fixed. 
+             
+* 10.08.2016 
+
+A bug in plot.mbl was fixed. It was not possible to plot mbl results when the 
+k.diss argument (threshold distances) was used in the mbl function.   
+
+* 10.08.2016 
+
+Since the previous release, the "wapls1" regression (in the mbl function) 
+is actually compatible with valMethod = "loc_crossval" (in the mblControl). 
+In the previous documentation was wrongly stated otherwise. Now this has been 
+corrected in the documentation.
+
+* 09.08.2016 
+
+the projection Matrix (projectionM) returned by plsProjection now only contains 
+the columns corresponding only to the number components retrieved
+             
+## `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.
+
+* 19.01.2016 
+Now it is possible to locally optimize the maximum and minimum pls factors in 
+wapls1 local regressions.
+
+* 09.12.2015 
+Many thanks to Eva Ampe and Lorenzo Menichetti for their suggestions.
+
+* 08.12.2015 
+A method for better estimates of RMSE values computed for the 'wapls1' method 
+has been implemented.
+
+* 08.12.2015 
+The 'wapls2' method of the mbl function is no longer supported because of several 
+drawbacks computing reliable uncertainty estimates.
+
+* 18.11.2015 
+Several functions are now based on C++ for faster computations.
+
+* 23.04.2014 
+Added default variable names when they are missing and an error message when the 
+names of Xr do not match the names of Xu.
+
+* 23.04.2014 
+plot.mbl draws now the circles around the actual centre function when the 
+spectra is not centred for mbl.
+
+* 20.03.2013 
+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.
+
+## `resemble 1.1.1`
+
+* 19.03.2013 Hello world! Initial release of the package

From 16a18b8e976cc3a4258524ee46583e71909df391 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:29:19 +0200
Subject: [PATCH 10/17] Update .Rbuildignore

---
 .Rbuildignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index 2534116..c93ac8c 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,6 +6,7 @@ code_ex.R
 ^\.Rprofile$
 ^cran-comments\.md$
 ^my-comments\.md$
+^NEWS\.html$
 logo.R
 ^Rscript*
 logo_large.png
\ No newline at end of file

From c905b4dea1e9e649ebaf708c1196072e61628e6e Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:49:08 +0200
Subject: [PATCH 11/17] fix(test external dist)

---
 tests/testthat/test-mbl.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-mbl.R b/tests/testthat/test-mbl.R
index e977a14..15b2425 100644
--- a/tests/testthat/test-mbl.R
+++ b/tests/testthat/test-mbl.R
@@ -427,5 +427,5 @@ test_that("mbl with external disstances works", {
   r_ext <- sbl_internal_diss$validation_results$nearest_neighbor_validation 
   r_int <- sbl_external_diss$validation_results$nearest_neighbor_validation
   
-  expect_true(sum(abs(r_ext - r-int)) < tol)
+  expect_true(sum(abs(r_ext - r_int)) < tol)
 })

From 6f17e0a07f95e61bd1e0a1f1da35d16f32be35e8 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:49:19 +0200
Subject: [PATCH 12/17] Update NEWS.md

---
 NEWS.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index c5c196c..f9b3f9b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,8 +2,10 @@
 
 ## `resemble 2.2.1 (Fix-Hodges)`
 ### Improvements and fixes
+- Fixed: An error was thrown when passing a pre-computed distance matrix to the 
+`diss_method` argument in `mbl()` ([#24](https://github.com/l-ramirez-lopez/resemble/issues/24)).
 
-* Documentation is now compatible with HTML5.
+- Documentation is now compatible with HTML5.
 
 
 ## `resemble 2.1 (piapia)`

From 7a8a6e693e73a7e5984ca07eaf2855500589435c Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 01:49:29 +0200
Subject: [PATCH 13/17] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f646cdf..ea40219 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ orthogonal projections in spectral data.
 
 ## Vignette
 A new vignette for `resemble` explaining its core functionality is available 
-at: https://CRAN.R-project.org/package=prospectr/vignettes/prospectr.html
+at: https://CRAN.R-project.org/package=prospectr/vignettes/vignette.html
 
 ## Core functionality 
 

From d4a42597cb509adac2546a3e8db33790c8ee95fb Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 20:08:27 +0200
Subject: [PATCH 14/17] Update DESCRIPTION

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e99d332..196131a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: resemble
 Type: Package
 Title: Memory-Based Learning in Spectral Chemometrics
 Version: 2.2.1
-Date: 2022-03-17
+Date: 2022-08-31
 Author: Leonardo Ramirez-Lopez [aut, cre], 
     Antoine Stevens [aut, ctb],
     Claudio Orellano [ctb],

From edfe2544f1af6d5cffbe8ef26a3ce54f196cd51f Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 20:08:30 +0200
Subject: [PATCH 15/17] Update my-comments.md

---
 my-comments.md | 78 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)

diff --git a/my-comments.md b/my-comments.md
index d9854e1..8a20731 100644
--- a/my-comments.md
+++ b/my-comments.md
@@ -1,5 +1,83 @@
 # resemble
 
+# version 2.2.1
+
+# submission message:
+Dear CRAN maintainers,
+I am submitting my package "resemble" to CRAN. This version accounts for 
+problems found in Rd files auto-generated with roxygen2 7.1.2 (not compatible 
+with HTML5). The new Rd files are now compatible with HTML5 (as Rd files 
+are generated with roxygen2_7.2.0 ). 
+Prior to this submission, this tarball has been checked with in the winbuilder service. Apart from that it has been also submitted to extensive tests in rhub.
+A first submission of this version failed (for "r-devel-linux-x86_64-debian-gcc"), 
+therefore following platforms were tested for a second submission using Rhub: 
+- Debian Linux, R-devel, GCC ASAN/UBSAN
+- Debian Linux, R-devel, GCC, no long double
+- Debian Linux, R-devel, clang, ISO-8859-15 locale
+- Debian Linux, R-devel, GCC
+For this second submission the package passed all the tests in the above platforms. 
+Reverse dependencies have also been checked. 
+Best regards,
+Leonardo
+
+
+
+## Package was built using: 
+```
+devtools::build(
+  pkg = ".",
+  path = NULL,
+  binary = FALSE,
+  vignettes = TRUE,
+  manual = TRUE,
+  args = NULL,
+  quiet = FALSE
+)
+```
+
+# R win builder checks for release of `resemble 2.2.1` (`Fix-Hodges`) 30.08.2022 
+passed all the checks without notes.
+
+# Rhub checks for release of `resemble 2.2.1` (`Fix-Hodges`) 30.08.2022
+The checks were conducted in the following platforms through rhub:
+
+```
+rhub::check(paste0(gsub("/resemble$", "/", getwd()), "resemble_2.2.1.tar.gz"), 
+            platform = c("fedora-gcc-devel"), 
+            email = "ramirez.lopez.leo@gmail.com")
+```
+- "linux-x86_64-rocker-gcc-san" OK
+
+- "fedora-gcc-devel" NOTE
+  installed size is 11.7Mb
+  sub-directories of 1Mb or more:
+    doc    1.6Mb
+    libs   9.5Mb
+
+- "windows-x86_64-devel" OK
+
+- "macos-highsierra-release-cran" OK
+
+- "windows-x86_64-release" OK
+
+- "ubuntu-gcc-release" NOTE
+     installed size is 13.5Mb
+     sub-directories of 1Mb or more:
+       doc    1.6Mb
+       libs  11.3Mb
+
+
+- "solaris-x86-patched-ods" Package suggested but not available: ‘testthat’
+   
+   The suggested packages are required for a complete check.
+   Checking can be attempted without them by setting the environment
+   variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
+   
+   See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+   manual.
+
+
+
 # version 2.1.1
 
 ## Package was built using: 

From 154682b7147973f3cfd66e2e7cd92c16cf379d3d Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 20:08:33 +0200
Subject: [PATCH 16/17] Update NEWS.md

---
 NEWS.md | 303 +++++++++++++++++++++++++++++++++++---------------------
 1 file changed, 190 insertions(+), 113 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index f9b3f9b..56a3ec1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,52 +1,60 @@
 # `resemble`
 
-## `resemble 2.2.1 (Fix-Hodges)`
+
+`resemble 2.2.1 (Fix-Hodges)`
+===============
+
 ### Improvements and fixes
-- Fixed: An error was thrown when passing a pre-computed distance matrix to the 
+
+* Fixed: An error was thrown when passing a pre-computed distance matrix to the 
 `diss_method` argument in `mbl()` ([#24](https://github.com/l-ramirez-lopez/resemble/issues/24)).
 
-- Documentation is now compatible with HTML5.
+* Documentation is now compatible with HTML5.
 
 
-## `resemble 2.1 (piapia)`
+`resemble 2.1 (piapia)`
+===============
+
 23.09.2021
 
 ### New features
 
-- The argument `seed` was added to the mbl function. It is used to gurantee 
+* The argument `seed` was added to the mbl function. It is used to gurantee 
 reproducibility of cross-validation results. 
 
-- A modified PLS method was implemented (see `local_fit_pls()` and `local_fit_wapls()`).
+* A modified PLS method was implemented (see `local_fit_pls()` and `local_fit_wapls()`).
 It uses correlation bteween response and predictors to derive the PLS weights. 
 
-## Improvements and fixes
+### Improvements and fixes
 
-- A Bug in the computation of the explained variance of X for pls models was 
+* A Bug in the computation of the explained variance of X for pls models was 
 detected and fixed. The pls related functions were underestimating the amount 
 of variance explained by each PLS component. The explained variance was being 
 computed from the matrix of scores, in this version it is computed from the 
 reconstructed spectra at each PLS iteration.
 
-- Manual selection of components in `pc_projection()` and `pls_projection()` now 
+* Manual selection of components in `pc_projection()` and `pls_projection()` now 
 accepts to select only 1 component (before the minimum was 2).
 
-- `pls_projection()` now includes a new argument (`method`) to allow the user to select 
+* `pls_projection()` now includes a new argument (`method`) to allow the user to select 
 between the standard pls algorithm and a modified pls algorithm.
 
-- `ortho_diss()`, `dissimilarity()` and `search_neighbors()` functions include a new 
+* `ortho_diss()`, `dissimilarity()` and `search_neighbors()` functions include a new 
 dissimilarity method: `"mpls"` (modified pls).
 
-- An internal function for stratified random sampling for cross-validtaion 
+* An internal function for stratified random sampling for cross-validtaion 
 purposes has been improved for computational speed. 
 
-- The package was stripping some symbols for Rcpp functions in Makevars in order 
+* 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.
 
 
-## `resemble 2.0 (gordillo)`
+`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 
@@ -55,133 +63,190 @@ functionality for modeling, mbl is faster and a less memory-hungry.
 
 ### New features
 
-- `search_neighbors()` function.
-- `dissimilarity()` function.
+* `search_neighbors()` function.
+
+* `dissimilarity()` function.
+
+### Improvements and fixes
+
+* `mbl` is faster and a less memory-hungry.
 
-## Improvements and fixes
+* New vignette.
 
-- `mbl` is faster and a less memory-hungry.
-- New vignette.
-- unit tests have been introduced using the testthat package.
+* unit tests have been introduced using the testthat package.
 
-## Breaking changes
 
-### `orthoProjection()`, `pcProjection()`, `plsProjection()` (renamed to `ortho_projection()`, 
+
+### Breaking changes
+
+#### `orthoProjection()`, `pcProjection()`, `plsProjection()` (renamed to `ortho_projection()`, 
 `pc_projection()`, `pls_projection()` respectively):
 
-- `X2` argument renamed to `Xu` (for consistency throughout all the functions)
-- 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 was `"opc"`,
+* `X2` argument renamed to `Xu` (for consistency throughout all the functions).
+
+* 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 was `"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 
+  
+* `"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` 
+
+* 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 functions)
-- 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)
+#### `corDiss()` (renamed to `cor_diss()`):
+
+* `X2` argument renamed to `Xu` (for consistency throughout all the functions).
+
+* 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 functions).
+
+* 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 functions).
+
+* Argument `scaled` renamed to `.scale`.
+
+* default for `.scale` has changed from `TRUE` to `FALSE`.
 
-### `fDiss()` (renamed to `f_diss()`):
+* the dimnames of the resulting matrix are now Xr_1... Xr_n (previusly Xr.1... Xr.n).
 
-- `X2` argument renamed to `Xu` (for consistency throughout all the functions)
-- 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 functions)
-- 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 functions).
 
-### orthoDiss (renamed to ortho_diss):
+* Argument `scaled` renamed to `.scale`.
 
-- `X2` argument renamed to `Xu` (for consistency throughout all the functions)
-- 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 
+* 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 `.local = TRUE` a new output is produced: `neighborhood_info` which 
+
+* When `.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`
+neighborhood, etc).
+
+* Output `global.variance.info` has been renamed to `global_variance_info`
 
 
-### `simEval()` (renamed to `sim_eval()`):
+#### `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 was used to set the number of cores in some 
+* 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 was 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 
+#### `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` functions. 
-- `dissimilarityM` has been deprecated. It was used to pass a dissimilarity matrix 
+
+* `dissimilarityM` has been deprecated. It was used to pass a dissimilarity matrix 
 computed outside the `mbl()` function. This can be done now with the new argument 
 `diss_method` of `mbl` which was previously named `"sm"` and it was in `mblControl()`.
 
 
-### `neigCleaning()` (now `search_neighbors()`)
+#### `neigCleaning()` (now `search_neighbors()`)
 
-- Function renamed to `search_neighbors`
-- Argument `cores` is deprecated, it was used to set the number of cores in some 
+* 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()`):
+#### `mblControl()` (renamed to `mbl_control()`):
 
-- `sm` argument is deprecated. Now the dissmilarity metric is an argument of the 
+* `sm` argument is deprecated. Now the dissmilarity metric is an argument of the 
 mbl function.
-- `scale` and `center` arguments have been moved to the `mbl()` function
-- Argument `range.pred.lim` renamed to `range_prediction_limits`
-- Argument `cores` is deprecated, it was used to set the number of cores in some 
+
+* `scale` and `center` arguments have been moved to the `mbl()` function.
+
+* 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 
+* `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)
+`resemble 1.3` (never released)
+===============
 
-* 11.04.2020 
+11.04.2020 
 
 The option 'movcor' for the argument sm of mblControl() is deprecated. The 
 'movcor' moving window correlations between spectra as dissimilarity measure. 
@@ -189,11 +254,11 @@ Now This option can be specified by using 'cor' as the method in the argument
 'sm' and passing a window size to the argument 'ws'of mblControl(). If 'ws' 
 is not specified, the standard correlation between spectra is computed.  
              
-* 27.02.2020 
+27.02.2020 
 
 The argument 'resampling' in mblControl() has been renamed to 'number'
              
-* 18.07.2019 
+18.07.2019 
 
 A bug in the scaling of the euclidean distances in fDiss was detected and fixed. 
 The distance ratios (between samples) were correctly calculated, but the final 
@@ -205,72 +270,84 @@ 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. 
 
-## `resemble 1.2.0001 (alma de coco)`
+`resemble 1.2.0001 (alma de coco)`
+===============
 
-* 13.09.2016 
+13.09.2016 
 
 A bug in the computation of the Mahalanobis distance in the PLS space was fixed. 
              
-* 06.09.2016 
+06.09.2016 
 
 Thanks to Matthieu Lesnoff who found a bug in the predict.orthoProjection 
 function (an error was thrown when PCA preditions were requested). This bug has 
 been fixed. 
              
-* 10.08.2016 
+10.08.2016 
 
 A bug in plot.mbl was fixed. It was not possible to plot mbl results when the 
 k.diss argument (threshold distances) was used in the mbl function.   
 
-* 10.08.2016 
+10.08.2016 
 
 Since the previous release, the "wapls1" regression (in the mbl function) 
 is actually compatible with valMethod = "loc_crossval" (in the mblControl). 
 In the previous documentation was wrongly stated otherwise. Now this has been 
 corrected in the documentation.
 
-* 09.08.2016 
+09.08.2016 
 
 the projection Matrix (projectionM) returned by plsProjection now only contains 
 the columns corresponding only to the number components retrieved
              
-## `resemble 1.2 (alma de coco)`
+`resemble 1.2 (alma de coco)`
+===============
+
+04.03.2016 
 
-* 04.03.2016 
 A patch was released for and extrange bug that prevented to run mbl 
 in parallel when the gpr method was used.
 
-* 19.01.2016 
+19.01.2016 
+
 Now it is possible to locally optimize the maximum and minimum pls factors in 
 wapls1 local regressions.
 
-* 09.12.2015 
+09.12.2015 
+
 Many thanks to Eva Ampe and Lorenzo Menichetti for their suggestions.
 
-* 08.12.2015 
+08.12.2015 
+
 A method for better estimates of RMSE values computed for the 'wapls1' method 
 has been implemented.
 
-* 08.12.2015 
+08.12.2015 
+
 The 'wapls2' method of the mbl function is no longer supported because of several 
 drawbacks computing reliable uncertainty estimates.
 
-* 18.11.2015 
+18.11.2015 
+
 Several functions are now based on C++ for faster computations.
 
-* 23.04.2014 
+23.04.2014 
+
 Added default variable names when they are missing and an error message when the 
 names of Xr do not match the names of Xu.
 
-* 23.04.2014 
+23.04.2014 
+
 plot.mbl draws now the circles around the actual centre function when the 
 spectra is not centred for mbl.
 
-* 20.03.2013 
+20.03.2013 
+
 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.
 
-## `resemble 1.1.1`
+`resemble 1.1.1`
+===============
 
-* 19.03.2013 Hello world! Initial release of the package
+19.03.2013 Hello world! Initial release of the package

From 5c5f566ea149afc1addf3cb0d762da52523a6914 Mon Sep 17 00:00:00 2001
From: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Date: Wed, 31 Aug 2022 20:08:38 +0200
Subject: [PATCH 17/17] Update README.md

---
 README.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index ea40219..590baf1 100644
--- a/README.md
+++ b/README.md
@@ -224,10 +224,9 @@ of soil properties using NIR spectroscopy and geographical information.
 compared several machine learning methods for predictive soil spectroscopy and 
 show that MBL `resemble` offers highly competive results.
 
-* 2020.01: [Sanderman et al., (2020)](https://acsess.onlinelibrary.wiley.com/doi/epdf/10.1002/saj2.20009) used `resemble` for the prediction of soil health indicatorsin the United States.
+* 2020.01: [Sanderman et al., (2020)](https://scholar.google.ch/scholar?cluster=8189603827145687468&hl=en&as_sdt=0,5&as_vis=1) used `resemble` for the prediction of soil health indicatorsin the United States.
 
-* 2019-03: Another paper using `resemble`... I published a [scientific paper](https://onlinelibrary.wiley.com/doi/10.1111/ejss.12752) were we used 
-memory-based learning (MBL) for digital soil mapping. Here we use MBL to remove 
+* 2019-03: I published a [scientific paper](https://scholar.google.com/scholar?cluster=1892507175331927677&hl=en&as_sdt=2005&sciodt=0,5&as_ylo=2022) were we used memory-based learning (MBL) for digital soil mapping. Here we use MBL to remove 
 local calibration outliers rather than using this approach to overcome the typical 
 complexity of large spectral datasets. (Ramirez‐Lopez, L., Wadoux, A. C.,
 Franceschini, M. H. D., Terra, F. S., Marques, K. P. P., Sayão, V. M., &