NEWS.md

resemble

resemble 2.2.2 (sky)

New features

• The argument spike in the mbl() function now accepts negative integers to avoid observations in the neighbrhoods.

Fixes

• A sanity check was added to cor_diss(). Correlation coefficients for observations with an standard deviation of 0 cannot be computed ([#38]#38).

• The pls_projection() did not work for more than one response variable and with the methods 'cumvar' or 'var' for the selection of the components. This has been fixed ([#37]#37).

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).

• 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