Skip to content

Latest commit

 

History

History
279 lines (168 loc) · 7.06 KB

NEWS.md

File metadata and controls

279 lines (168 loc) · 7.06 KB
Raw

MsCoreUtils 1.17

MsCoreUtils 1.17.3

  • Use R_Calloc and R_Free instead of Calloc and Free in src/lowerConvexHull.c, respectively, to reflect changes in the R API and fullfil STRICT_R_HEADERS check.

MsCoreUtils 1.17.2

  • Fix typo in normalisation methods description.

MsCoreUtils 1.17.1

  • Fix common_path() to not return also the file name if the input parameter contains only identical character strings.

MsCoreUtils 1.15

MsCoreUtils 1.15.7

  • Add common_path() function.

MsCoreUtils 1.15.6

  • Bump version to force new package build on Bioconductor servers.

MsCoreUtils 1.15.5

  • Add function force_sorted() to adjust a numeric vector to ensure increasing/sorted values.

MsCoreUtils 1.15.4

  • Fix partial argument match (see issue #125).

MsCoreUtils 1.15.4

  • Fix documentation of ndotproduct.

MsCoreUtils 1.15.3

  • Add function breaks_ppm to create a sequence of numbers with increasing difference between elements (defined by parameter ppm).

MsCoreUtils 1.15.2

  • Porting baseline estimation function (see issue 119).

MsCoreUtils 1.15.1

  • Remove impute_mle2() since norm2 has been removed from CRAN (see issue 117).

MsCoreUtils 1.15.0

  • New Bioc devel version

MsCoreUtils 1.13

MsCoreUtils 1.13.1

  • Add functions entropy and nentropy.

MsCoreUtils 1.11

MsCoreUtils 1.11.6

  • Fix bug in impute_MinDet(MARGIN = 1) and add unit test.
  • Check that package is available and namespace is loaded adding stopifnot() when calling requireNamespace().

MsCoreUtils 1.11.5

  • Add function maxi to determine the maximal intensity value. This function returns NA_real_ instead of -Inf if all values are missing or if the length of the input parameter is 0.

MsCoreUtils 1.11.4

  • Check if parameter y is increasingly ordered in bin: issue #108.

MsCoreUtils 1.11.3

  • Add function sumi to sum intensity values with correct NA handling.

MsCoreUtils 1.11.2

MsCoreUtils 1.11.1

  • Add a MARGIN argument to (relevant) imputation functions to support (and make it explicit) along which dimensions (row or columns) imputation is performed.
  • New impute_mle2() function that uses norm2 (see issue #100).

MsCoreUtils 1.11.0

  • New Bioconductor 3.17 (devel) release

MsCoreUtils 1.10

MsCoreUtils 1.10.0

  • New Bioconductor 3.16 (stable) release

MsCoreUtils 1.9

MsCoreUtils 1.9.2

  • feat: imputation is compatible with HDF5Matrix objects
  • feat: normalization is compatible with HDF5Matrix objects
  • feat: matrix aggregation is compatible with HDF5Matrix objects
  • fix+feat: aggregate_by_matrix now correctly handles missing data and implements 'na.rm'
  • Fix rla/rowRla man page.

MsCoreUtils 1.9.1

  • Random forest imputation (using missForest) is now available (`method = "RF")

MsCoreUtils 1.9.0

  • New Bioc devel version

MsCoreUtils 1.7

MsCoreUtils 1.7.5

  • Function bin gains parameter returnMids to choose whether or not bin mid-points should be returned in the result list.

MsCoreUtils 1.7.4

  • Fix ppm to always return a positive value (issue #94).

MsCoreUtils 1.7.3

  • Add citation.

MsCoreUtils 1.7.2

  • Use Matrix::colSums() by default to handle sparce 'Matrix' and 'matrix' adjacency matrices.

MsCoreUtils 1.7.1

  • New aggregate_by_matrix() that uses an adjacency matrix to aggregate quantitative features.
  • Set colnames to the outputs of aggregate_by_matrix() and aggregate_by_vector() to make sure that these are always set and not reply on the underlying function.

MsCoreUtils 1.7.0

  • New Bioc devel version

MsCoreUtils 1.5

Changes in 1.5.1

  • Add which.first and which.last.

Changes in 1.5.0

  • New Bioc devel version

MsCoreUtils 1.3

Changes in 1.3.3

  • Add join_gnps and gnps to allow calculation of GNPS spectra similarity scores.

Changes in 1.3.2

  • Add rt2numeric(), rt2character() and formatRt().
  • New impute_fun() function for user-provide imputation function.

Changes in 1.3.1

  • Add Josep Badia Aparicio as a contributor

Changes in 1.3.0

  • New Bioc devel version

MsCoreUtils 1.1

Changes in 1.1.7

  • Rewrite c("left", "right", "inner", "outer") join in C <2020-10-06 Tue>.

Changes in 1.1.6

  • Rewrite closest in C <2020-09-24 Thu>.
  • Fix #65 and #66.

Changes in 1.1.5

  • Add ... to functions to join and compare peaks; see also #131.

Changes in 1.1.4

  • Change references to Feature to QFeatures <2020-07-14 Tue>
  • Ensure closest accept just argument tolerance of length 1 or length(x); see also #61, PR #62 <2020-08-07 Thu>.
  • The tolerance argument in closest should now be of length 1 or of length(x) (was length(table) before) <2020-08-20 Thu>.

Changes in 1.1.3

  • For an empty table closest and common return a vector of length x with NA or FALSE, respectively (instead of 1 and TRUE). Fixes #55 <2020-06-18 Thu>.
  • closest and common ignore NA in table <2020-06-19 Fri>.
  • Fix rbindFill for single data.frame or DataFrame as input <2020-06-23 Tue>.

Changes in 1.1.2

  • New colCounts() aggregation function <2020-05-27 Wed>.

Changes in 1.1.1

  • Add some popular distance/similarity metrices: ndotproduct neuclidean navdist nspectraangle; see also PR #33.

  • Add deprecation note to dotproduct <2020-05-22 Fri>.

Changes in 1.1.0

  • Bioconductor devel version (Bioc 3.12)

MsCoreUtils 1.0

Changes in 1.0.0.

  • Bioconductor release version (Bioc 3.11)

MsCoreUtils 0.99

MsCoreUtils 0.99.3

  • Trigger build.

MsCoreUtils 0.99.2

  • Provide more comprehensive description.
  • Add vignette.

MsCoreUtils 0.99.1

  • Additional functions, and using Author@R to specify (unique) RforMassSpectrometry Package Maintainer.

MsCoreUtils 0.99.0

  • First release of MsCoreUtils with core function to get extreme values, grouping/matching, noise/smoothing, similarity measurements, various helper function, and function to process (impute and normalise) quantitative features.