`resemble`

`resemble 2.2.2 (sky)`

- The argument
`spike`

in the`mbl()`

function now accepts negative integers to avoid observations in the neighbrhoods.

A sanity check was added to

`cor_diss()`

. Correlation coefficients for observations with an standard deviation of 0 cannot be computed ([#38]https://github.com/l-ramirez-lopez/resemble/issues/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]https://github.com/l-ramirez-lopez/resemble/issues/37).

`resemble 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`

.`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