inst/changes.md
In resemble: Memory-Based Learning in Spectral Chemometrics

Changes implemented for version 2.0

search_neighbors() function
dissimilarity() function

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 wwas used to set the number of cores in some c++ internal functions via OpenMP in Rcpp. Multi-threading via OpenMP is still available, but the number of threads must be set in the R global enviroment (e.g. Sys.setenv("OMP_NUM_THREADS" = )). - 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. Multi-threading via OpenMP is still available, but the number of threads must be set in the R global enviroment (e.g. Sys.setenv("OMP_NUM_THREADS" = )).

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. Multi-threading via OpenMP is still available, but the number of threads must be set in the R global enviroment (e.g. Sys.setenv("OMP_NUM_THREADS" = )).

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()