resembleresemble 2.2.1 (Fix-Hodges)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
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.
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.
search_neighbors() function.
dissimilarity() function.
mbl is faster and a less memory-hungry.
New vignette.
unit tests have been introduced using the testthat package.
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).
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()"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 1.1.119.03.2013 Hello world! Initial release of the package