Changes in version 2024-10-11 (2024-10-11)               

  - make duplicates' helpers supporting combo assays as well

               Changes in version 2024-10-07 (2024-10-07)               

  - refactor the logic for dealing with duplicates in assay data

               Changes in version 2024-10-03 (2024-10-03)               

  - fixed issue in average_biological_replicated (fit_type)

               Changes in version 2024-09-16 (2024-09-16)               

  - add functions set_unique_cl_names_dt and set_unique_drug_names_dt

               Changes in version 2024-09-04 (2024-09-04)               

  - remove hack with checkDimnames

               Changes in version 2024-08-30 (2024-08-30)               

  - remove GDS fit_source from gDRviz

               Changes in version 2024-08-28 (2024-08-28)               

  - extend the logic of get_additional_variables to support other
    sources of fitting metrics

               Changes in version 2024-08-14 (2024-08-14)               

  - extend the logic of average_biological_replicates_dt to calculate
    standard deviation

               Changes in version 2024-08-06 (2024-08-06)               

  - add functions for setting unique identifiers in the colData and
    rowData of SE

               Changes in version 2024-07-30 (2024-07-30)               

  - refactor average_biological_replicates_dt and
    get_additional_variables to support unprettified identifiers

               Changes in version 2024-07-17 (2024-07-17)               

  - update define_matrix_grid_positions

               Changes in version 2024-07-12 (2024-07-12)               

  - move get_combo_col_settings and get_iso_colors to gDRplots package

               Changes in version 2024-07-08 (2024-07-08)               

  - add residual sum of square and p-value to Metrics assay

               Changes in version 2024-07-03 (2024-07-03)               

  - add vignette section about prettifying logic

               Changes in version 2024-06-24 (2024-06-24)               

  - fixed issue in vignette

               Changes in version 2024-05-27 (2024-05-27)               

  - synchronize Bioconductor and GitHub versioning

               Changes in version 2024-05-22 (2024-05-22)               

  - fix check notes

  - move convert_se_assay_to_custom_dt, capVals and
    get_settings_from_json from gDRcomponents package

               Changes in version 2024-05-17 (2024-05-17)               

  - simplify logic of supported experiments

               Changes in version 2024-05-16 (2024-05-16)               

  - move define_matrix_grid_positions and round_concentration functions
    from gDRcore package

               Changes in version 2024-05-08 (2024-05-08)               

  - fix typo

               Changes in version 2024-04-30 (2024-04-30)               

  - move validator functions from gDRcomponents to gDRutils

               Changes in version 2024-04-15 (2024-04-15)               

  - add get_testdata_combo and get_testdata_codilution

               Changes in version 2024-03-07 (2024-03-07)               

  - clean up the package

  - simplify keywords

               Changes in version 2024-02-28 (2024-02-28)               

  - add fit_source to header list

               Changes in version 2024-02-26 (2024-02-26)               

  - improve pkgdown site
      - improved references
      - valid NEWS.md

               Changes in version 2024-02-22 (2024-02-22)               

  - restore tooltips in table

               Changes in version 2024-02-14 (2024-02-14)               

  - make documentation compatible with pkdgdown

               Changes in version 2024-01-30 (2024-01-30)               

  - rename matrix into combination

               Changes in version 2024-01-22 (2024-01-22)               

  - add new description fields

               Changes in version 2023-12-01 (2023-12-01)               

  - fix bug with refining rowData
  - extend the list of headers

               Changes in version 2023-11-22 (2023-11-22)               

  - sync master with devel branch
  - update schema to support NA in reference division time
  - add minor fix in code styling
  - add new function gemoetric_mean
  - transform values into numeric in predict_efficacy_from_conc function
  - add "Treatment" as template identifier

               Changes in version 2023-10-24 (2023-10-24)               

  - release Bioc 3.18

  - prerelease Bioc 3.18

               Changes in version 2023-10-18 (2023-10-18)               

  - adjust NEWS to Bioc format

               Changes in version 2023-10-09 (2023-10-09)               

  - add support for flattening averaged assays

               Changes in version 2023-09-22 (2023-09-22)               

  - fix bug in the case of conc=0 for evaluating efficacy

               Changes in version 2023-09-19 (2023-09-19)               

  - add wide_structure param to convert_mae_assay_to_dt

               Changes in version 2023-09-08 (2023-09-08)               

  - updated experimentalist description in schema

               Changes in version 2023-09-05 (2023-09-05)               

  - add Replicate as a new identifier

  - improve the logic of standardize_MAE to keep SE-specific metadata
    and be able to revert standardization

               Changes in version 2023-08-01 (2023-08-01)               

  - keep unchanged names in DataFrame

  - tidy code

               Changes in version 2023-06-27 (2023-06-27)               

  - add assert for missing rownames

               Changes in version 2023-06-22 (2023-06-22)               

  - replaced RDS with qs

               Changes in version 2023-06-20 (2023-06-20)               

  - fix check in R 4.3

               Changes in version 2023-06-12 (2023-06-12)               

  - switch from merge to [[

  - replace order with data.table::setorder
  - add support for custom identifiers in merge_SE

               Changes in version 2023-06-07 (2023-06-07)               

  - switch from aggregate to data.table

               Changes in version 2023-06-06 (2023-06-06)               

  - replaced reshape2 functions by functions from data.table

               Changes in version 2023-05-22 (2023-05-22)               

  - format the vignette with BiocStyle

  - fix related with data.table
  - remove .get_treated_conditions and .get_untreated_conditions

               Changes in version 2023-05-18 (2023-05-18)               

  - add support for merging combination-data assays

               Changes in version 2023-05-12 (2023-05-12)               

  - update after unifying normalization types

  - fix lintr

               Changes in version 2023-05-09 (2023-05-09)               

  - removed cotreatment entry from EXPERIMENT_GROUPS

  - fix bug in convert_mae_assay_to_dt

               Changes in version 2023-05-08 (2023-05-08)               

  - refactor code with single ampersand in if statements

               Changes in version 2023-04-28 (2023-04-28)               

  - change order of untreated tags

               Changes in version 2023-04-24 (2023-04-24)               

  - changed data.frame to data.table

               Changes in version 2023-04-20 (2023-04-20)               

  - switch to OSI license

  - clean-up vignette

               Changes in version 2023-04-18 (2023-04-18)               

  - extend the logic of apply_bumpy_function

               Changes in version 2023-04-17 (2023-04-17)               

  - add R 4.2 as a dependency

               Changes in version 2023-04-14 (2023-04-14)               

  - fix examples

               Changes in version 2023-04-13 (2023-04-13)               

  - make linter happy

               Changes in version 2023-04-12 (2023-04-12)               

  - add license

               Changes in version 2023-04-07 (2023-04-07)               

  - update maintainer

               Changes in version 2023-03-28 (2023-03-28)               

  - downgrade version to make it Bioconductor compatible

               Changes in version 2023-03-13 (2023-03-13)               

  - tidy code

               Changes in version 2023-03-09 (2023-03-09)               

  - better handling of corner cases for the single-agent fitting

               Changes in version 2023-03-08 (2023-03-08)               

  - add support for splitting normalization data types

  - restore necessary functions

               Changes in version 2023-03-01 (2023-03-01)               

  - add examples of identifiers

  - remove obsolete code

               Changes in version 2023-02-22 (2023-02-22)               

  - tidy code

               Changes in version 2023-02-10 (2023-02-10)               

  - add tests for convert_se_ref_assay_to_dt

               Changes in version 2023-01-10 (2023-01-10)               

  - add helpers for colData/rowData refinement

               Changes in version 2022-12-22 (2022-12-22)               

  - fix warnings in unit tests

               Changes in version 2022-12-20 (2022-12-20)               

  - R CMD check returns 0 errors ✓ | 0 warnings ✓ | 0 notes ✓

               Changes in version 2022-12-15 (2022-12-15)               

  - default apply_bumpy_function parallelize to TRUE

               Changes in version 2022-12-08 (2022-12-08)               

  - add apply_bumpy_function support

               Changes in version 2022-12-07 (2022-12-07)               

  - add co-dilution to single-agent group

               Changes in version 2022-11-30 (2022-11-30)               

  - bugfix in validate_SE

               Changes in version 2022-10-18 (2022-10-18)               

  - add update_env_idfs_from_mae function

               Changes in version 2022-10-04 (2022-10-04)               

  - add helper for dealing with idfs' synonyms

               Changes in version 2022-09-21 (2022-09-21)               

  - promote or demote fields in a BumpyMatrix object and perform
    summarization on assays.

               Changes in version 2022-08-11 (2022-08-11)               

  - major improvements in JSON validation/conversion logic
      - provide info about JSON schemes via env variables
      - convert and validate MAE summary next to the SE experiments

               Changes in version 2022-07-25 (2022-07-25)               

  - move json validation/conversion logic from gDRelastic

               Changes in version 2022-07-11 (2022-07-11)               

  - standardize MAE using default gDR identifiers

               Changes in version 2022-06-29 (2022-06-29)               

  - remove adding integer identifiers at the end of colnames/rownames

               Changes in version 2022-06-02 (2022-06-02)               

  - release 1.3.0

               Changes in version 2022-05-27 (2022-05-27)               

  - correct recognition of empty SE

               Changes in version 2022-05-25 (2022-05-25)               

  - remove redundant validation of rownames in SE

               Changes in version 2022-05-03 (2022-05-03)               

  - update prettify function
  - fix hardcoded identifiers in validated_SE

               Changes in version 2022-04-29 (2022-04-29)               

  - avoid using grep for getting cotreatment identifiers

               Changes in version 2022-04-26 (2022-04-26)               

  - switched from unnamed to named vector of experiment groups for
    single-agent
  - fix the logic in validating single-agent experiments

               Changes in version 2022-04-13 (2022-04-13)               

  - set r2 value to NA for invalid and 0 for constant fits

               Changes in version 2022-04-08 (2022-04-08)               

  - added identifier descriptions

  - fix wrong order of elements in rownames in SE

               Changes in version 2022-04-07 (2022-04-07)               

  - add cap_ic50 function

               Changes in version 2022-03-31 (2022-03-31)               

  - extend possible Barcode identifiers

               Changes in version 2022-03-30 (2022-03-30)               

  - fix hardcoded identifiers in validate SE

               Changes in version 2022-03-28 (2022-03-28)               

  - add a space between two-word cotreatment identifiers

               Changes in version 2022-03-24 (2022-03-24)               

  - remove all R CMD check warnings

               Changes in version 2022-03-22 (2022-03-22)               

  - change prettify functions to not substitute metadata

               Changes in version 2022-03-21 (2022-03-21)               

  - add helper function for MAE/experiments

               Changes in version 2022-03-19 (2022-03-19)               

  - move constant fit warning

               Changes in version 2022-03-18 (2022-03-18)               

  - add .calculate_complement

               Changes in version 2022-03-16 (2022-03-16)               

  - move duplication warning

               Changes in version 2022-03-14 (2022-03-14)               

  - add support for identifier validation

               Changes in version 2022-03-03 (2022-03-03)               

  - add getter and setter for experiment_raw_data

               Changes in version 2022-02-16 (2022-02-16)               

  - refactor identifier drugname to drug_name

               Changes in version 2022-02-10 (2022-02-10)               

  - add MAEpply function

               Changes in version 2022-02-01 (2022-02-01)               

  - update documentation

               Changes in version 2022-01-31 (2022-01-31)               

  - support SE- init for different BioC versions

               Changes in version 2022-01-25 (2022-01-25)               

  - standardize/improve CI

  - switch unit tests from SE to MAE from gDRtestData

               Changes in version 2022-01-07 (2022-01-07)               

  - update assert in validate_MAE

  - update SE-related functions of gDRutils to support MAE

               Changes in version 2021-12-21 (2021-12-21)               

  - move combo-related functions from gDRviz
  - add unit tests for combo-related functions

               Changes in version 2021-11-04 (2021-11-04)               

  - do not create a nested list of identifiers during merging SE

               Changes in version 2021-11-01 (2021-11-01)               

  - fix issued with new SummarizedExperiment

               Changes in version 2021-10-22 (2021-10-22)               

  - refactor: generalize prediction help functions for fits

               Changes in version 2021-09-27 (2021-09-27)               

  - update validate_SE as per combos

               Changes in version 2021-09-22 (2021-09-22)               

  - feat: use 'GRvalue' and 'RelativeViability' as normalization_types
    in 'fit_curves'

               Changes in version 2021-09-15 (2021-09-15)               

  - fix bug with getting_SE_identifiers for untreated_tag

               Changes in version 2021-09-13 (2021-09-13)               

  - fix obsolete arguments in reset_env_identifiers

               Changes in version 2021-09-07 (2021-09-07)               

  - fix bug with getting identifiers for untreated_tag

               Changes in version 2021-08-26 (2021-08-26)               

  - move NA logic for elements of BumpyMatrix with no data to fit_curve

               Changes in version 2021-08-25 (2021-08-25)               

  - remove additional ordering line in df_to_bm_assay.R

               Changes in version 2021-08-19 (2021-08-19)               

  - update list of available identifiers - 2nd and 3rd drug, data_source
  - update the logic for get_identifier and .get_id
  - add prettified_identifier-

               Changes in version 2021-08-13 (2021-08-13)               

  - fix bug with wrong order of rows and cols in df_to_bm_assay

               Changes in version 2021-07-06 (2021-07-06)               

  - remove hard version equality for pkg deps

               Changes in version 2021-06-29 (2021-06-29)               

  - add barcode as identifiers and store identifiers within
    split_SE_components

               Changes in version 2021-06-25 (2021-06-25)               

  - update the logic for CI/CD - repos fetching is now handled with
    technical user

               Changes in version 2021-06-21 (2021-06-21)               

  - refactor logisticFit with error handling

               Changes in version 2021-06-18 (2021-06-18)               

  - add concentration and template as additional identifiers

  - remove deprecated functions
  - switch from getMetadata to split_SE_components
  - refactor df_to_bm_assay

               Changes in version 2021-06-02 (2021-06-02)               

  - upgrade validate_SE by checking if rowData and colData do not have
    empty strings
  - isolate flatten function

  - release 1.0.0

  - fix bug with merging flatten assays

               Changes in version 2021-05-24 (2021-05-24)               

  - refactor validate_SE function

               Changes in version 2021-05-18 (2021-05-18)               

  - add merge_SE function

  - fix typo in SE validator function

  - add SE validator function

               Changes in version 2021-05-13 (2021-05-13)               

  - refactor prettify_flat_metrics function

               Changes in version 2021-04-30 (2021-04-30)               

  - remove Metrics_rownames during flattening data.frame/data.table

               Changes in version 2021-04-29 (2021-04-29)               

  - add prettify_flat_metrics function

  - bugfix flattening data.tables

  - bugfix data.table merge in convert_se_assay_ref_to_dt

               Changes in version 2021-04-27 (2021-04-27)               

  - add support for flattening data.tables

               Changes in version 2021-04-21 (2021-04-21)               

  - switch from processing_metadata to .internal

               Changes in version 2021-04-20 (2021-04-20)               

  - add support for getting and setting processing info metadata

               Changes in version 2021-04-19 (2021-04-19)               

  - sort BumpyMatrix created from dt

               Changes in version 2021-04-14 (2021-04-14)               

  - revert metric arguments in 'convert_se_assay_to_dt'

               Changes in version 2021-04-09 (2021-04-09)               

  - add support for getting and setting fit parameter metadata

               Changes in version 2021-04-07 (2021-04-07)               

  - standardize metric header names

  - add more options for returned data - with 'Metrics' assay in the
    case of convert_se_assay_to_dt
  - add 'convert_se_ref_assay_to_dt' function

               Changes in version 2021-03-30 (2021-03-30)               

  - add support for getting and setting metadata on the
    SummarizedExperiment object

  - add support for getting and setting metadata on the
    SummarizedExperiment object
  - add numeric type assertions and tests for logistic_4parameters

               Changes in version 2021-03-23 (2021-03-23)               

  - remove positional naming dependence on assay_to_dt for -
    merge_metrics = TRUE argument

               Changes in version 2021-03-16 (2021-03-16)               

  - minor refactor to assay_to_dt
  - deprecated support for assay_to_dt- include_controls = TRUE argument
    - not backwards compatible

               Changes in version 2021-03-09 (2021-03-09)               

  - update .estimate_xc50 and add tests

               Changes in version 2021-03-04 (2021-03-04)               

  - fix bug with wrong class for S3 methods in convert_assay_data_to_dt
  - update the documentation

               Changes in version 2021-03-02 (2021-03-02)               

  - fix bug with missing class in assert for matrix

               Changes in version 2021-02-10 (2021-02-10)               

  - modify fit_curves to take in flexible curve_type- s
  - clean-up assay_to_dt

               Changes in version 2021-02-04 (2021-02-04)               

  - added linter

               Changes in version 2021-02-03 (2021-02-03)               

  - move assay_to_dt from gDR to gDRutils
  - refactor assay_to_dt to support two assay types
      - list of DFrame- s
      - BumpyMatrix objects
  - move .get_treated_conditions and .get_untreated_conditions from gDR
    to gDRutils

               Changes in version 2021-01-26 (2021-01-26)               

  - allow for DFrame as input

  - 's/BumpyMatrix::splitToBumpyMatrix/BumpyMatrix::splitAsBumpyMatrix/'

               Changes in version 2021-01-20 (2021-01-20)               

  - refactor RVGRfits and rename to fit_curves
  - make logisticFit function independent of curve_type

               Changes in version 2021-01-19 (2021-01-19)               

  - move df_to_assay.R from gDRcore to gDRutils
  - move df_to_bm_assay.R from gDRcore to gDRutils
  - update identifiers_list.R

               Changes in version 2020-12-14 (2020-12-14)               

  - refactor get_identifiers and get_headers to be settable and cached

  - totally, finally, and unscrupulously remove dplyr package from
    gDRutils
  - replace IC by RV

               Changes in version 2020-10-12 (2020-10-12)               

  - add CI

               Changes in version 2020-10-09 (2020-10-09)               

  - fix assay_to_df

  - update namespaces

               Changes in version 2020-10-05 (2020-10-05)               

  - minor refactor

               Changes in version 2020-09-14 (2020-09-14)               

  - add small fixes for assays with empty DataFrame

               Changes in version 2020-09-02 (2020-09-02)               

  - update logic as per new db model

               Changes in version 2020-08-07 (2020-08-07)               

  - update variable names as per new db model

               Changes in version 2020-07-02 (2020-07-02)               

  - import pipes from magrittr

               Changes in version 2020-06-10 (2020-06-10)               

  - including the masked field to be able to remove the masked data from
    averages