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Changelog

Source: NEWS.md

gDRutils 1.5.2 - 2024-11-05

  • add get_env_var helper

gDRutils 1.5.1 - 2024-11-05

  • synchronize Bioconductor and GitHub versioning

gDRutils 1.3.17 - 2024-10-24

  • make average_biological_replicates_dt more restrictive - fewer columns to check for duplicates

gDRutils 1.3.16 - 2024-10-11

  • make duplicates’ helpers supporting combo assays as well

gDRutils 1.3.15 - 2024-10-07

  • refactor the logic for dealing with duplicates in assay data

gDRutils 1.3.14 - 2024-10-03

  • fixed issue in average_biological_replicated (fit_type)

gDRutils 1.3.13 - 2024-09-16

  • add functions set_unique_cl_names_dt and set_unique_drug_names_dt

gDRutils 1.3.12 - 2024-09-04

  • remove hack with checkDimnames

gDRutils 1.3.11 - 2024-08-30

  • remove GDS fit_source from gDRviz

gDRutils 1.3.10 - 2024-08-28

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

gDRutils 1.3.9 - 2024-08-14

  • extend the logic of average_biological_replicates_dt to calculate standard deviation

gDRutils 1.3.8 - 2024-08-06

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

gDRutils 1.3.7 - 2024-07-30

  • refactor average_biological_replicates_dt and get_additional_variables to support unprettified identifiers

gDRutils 1.3.6 - 2024-07-17

  • update define_matrix_grid_positions

gDRutils 1.3.5 - 2024-07-12

  • move get_combo_col_settings and get_iso_colors to gDRplots package

gDRutils 1.3.4 - 2024-07-08

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

gDRutils 1.3.3 - 2024-07-03

  • add vignette section about prettifying logic

gDRutils 1.3.2 - 2024-06-24

  • fixed issue in vignette

gDRutils 1.3.1 - 2024-05-27

  • synchronize Bioconductor and GitHub versioning

gDRutils 1.1.17 - 2024-05-22

  • fix check notes

gDRutils 1.1.16 - 2024-05-22

  • move convert_se_assay_to_custom_dt, capVals and get_settings_from_json from gDRcomponents package

gDRutils 1.1.15 - 2024-05-17

  • simplify logic of supported experiments

gDRutils 1.1.14 - 2024-05-16

  • move define_matrix_grid_positions and round_concentration functions from gDRcore package

gDRutils 1.1.13 - 2024-05-08

  • fix typo

gDRutils 1.1.12 - 2024-04-30

  • move validator functions from gDRcomponents to gDRutils

gDRutils 1.1.11 - 2024-04-15

  • add get_testdata_combo and get_testdata_codilution

gDRutils 1.1.10 - 2024-03-07

  • clean up the package

gDRutils 1.1.9 - 2024-03-07

  • simplify keywords

gDRutils 1.1.8 - 2024-02-28

  • add fit_source to header list

gDRutils 1.1.7 - 2024-02-26

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

gDRutils 1.1.6 - 2024-02-22

  • restore tooltips in table

gDRutils 1.1.5 - 2024-02-14

  • make documentation compatible with pkdgdown

gDRutils 1.1.4 - 2024-01-30

  • rename matrix into combination

gDRutils 1.1.3 - 2024-01-22

  • add new description fields

gDRutils 1.1.2 - 2023-12-01

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

gDRutils 1.1.1 - 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

gDRutils 1.1.0 - 2023-10-24

  • release Bioc 3.18

gDRutils 1.0.0 - 2023-10-24

  • prerelease Bioc 3.18

gDRutils 0.99.34 - 2023-10-18

  • adjust NEWS to Bioc format

gDRutils 0.99.33 - 2023-10-09

  • add support for flattening averaged assays

gDRutils 0.99.32 - 2023-09-22

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

gDRutils 0.99.31 - 2023-09-19

  • add wide_structure param to convert_mae_assay_to_dt

gDRutils 0.99.30 - 2023-09-08

  • updated experimentalist description in schema

gDRutils 0.99.29 - 2023-09-05

  • add Replicate as a new identifier

gDRutils 0.99.28 - 2023-09-05

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

gDRutils 0.99.27 - 2023-08-01

  • keep unchanged names in DataFrame

gDRutils 0.99.26 - 2023-08-01

  • tidy code

gDRutils 0.99.25 - 2023-06-27

  • add assert for missing rownames

gDRutils 0.99.24 - 2023-06-22

  • replaced RDS with qs

gDRutils 0.99.23 - 2023-06-20

  • fix check in R 4.3

gDRutils 0.99.22 - 2023-06-12

  • switch from merge to [[

gDRutils 0.99.21 - 2023-06-12

gDRutils 0.99.20 - 2023-06-07

  • switch from aggregate to data.table

gDRutils 0.99.19 - 2023-06-06

  • replaced reshape2 functions by functions from data.table

gDRutils 0.99.18 - 2023-05-22

  • format the vignette with BiocStyle

gDRutils 0.99.17 - 2023-05-22

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

gDRutils 0.99.16 - 2023-05-18

  • add support for merging combination-data assays

gDRutils 0.99.15 - 2023-05-12

  • update after unifying normalization types

gDRutils 0.99.14 - 2023-05-12

  • fix lintr

gDRutils 0.99.13 - 2023-05-09

  • removed cotreatment entry from EXPERIMENT_GROUPS

gDRutils 0.99.12 - 2023-05-09

  • fix bug in convert_mae_assay_to_dt

gDRutils 0.99.11 - 2023-05-08

  • refactor code with single ampersand in if statements

gDRutils 0.99.10 - 2023-04-28

  • change order of untreated tags

gDRutils 0.99.9 - 2023-04-24

  • changed data.frame to data.table

gDRutils 0.99.8 - 2023-04-20

  • switch to OSI license

gDRutils 0.99.7 - 2023-04-20

  • clean-up vignette

gDRutils 0.99.6 - 2023-04-18

  • extend the logic of apply_bumpy_function

gDRutils 0.99.5 - 2023-04-17

  • add R 4.2 as a dependency

gDRutils 0.99.4 - 2023-04-14

  • fix examples

gDRutils 0.99.3 - 2023-04-13

  • make linter happy

gDRutils 0.99.2 - 2023-04-12

  • add license

gDRutils 0.99.1 - 2023-04-07

  • update maintainer

gDRutils 0.99.0 - 2023-03-28

  • downgrade version to make it Bioconductor compatible

gDRutils 0.1.3.22 - 2023-03-13

  • tidy code

gDRutils 0.1.3.21 - 2023-03-09

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

gDRutils 0.1.3.20 - 2023-03-08

  • add support for splitting normalization data types

gDRutils 0.1.3.19 - 2023-03-08

  • restore necessary functions

gDRutils 0.1.3.18 - 2023-03-01

  • add examples of identifiers

gDRutils 0.1.3.17 - 2023-03-01

  • remove obsolete code

gDRutils 0.1.3.16 - 2023-02-22

  • tidy code

gDRutils 0.1.3.15 - 2023-02-10

  • add tests for convert_se_ref_assay_to_dt

gDRutils 0.1.3.14 - 2023-01-10

  • add helpers for colData/rowData refinement

gDRutils 0.1.3.13 - 2022-12-22

  • fix warnings in unit tests

gDRutils 0.1.3.12 - 2022-12-20

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

gDRutils 0.1.3.11 - 2022-12-15

  • default apply_bumpy_function parallelize to TRUE

gDRutils 0.1.3.10 - 2022-12-08

  • add apply_bumpy_function support

gDRutils 0.1.3.9 - 2022-12-07

  • add co-dilution to single-agent group

gDRutils 0.1.3.8 - 2022-11-30

  • bugfix in validate_SE

gDRutils 0.1.3.7 - 2022-10-18

  • add update_env_idfs_from_mae function

gDRutils 0.1.3.6 - 2022-10-04

  • add helper for dealing with idfs’ synonyms

gDRutils 0.1.3.5 - 2022-09-21

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

gDRutils 0.1.3.4 - 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

gDRutils 0.1.3.3 - 2022-07-25

  • move json validation/conversion logic from gDRelastic

gDRutils 0.1.3.2 - 2022-07-11

  • standardize MAE using default gDR identifiers

gDRutils 0.1.3.1 - 2022-06-29

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

gDRutils 0.1.3.0 - 2022-06-02

  • release 1.3.0

gDRutils 0.1.0.48 - 2022-05-27

  • correct recognition of empty SE

gDRutils 0.1.0.47 - 2022-05-25

  • remove redundant validation of rownames in SE

gDRutils 0.1.0.46 - 2022-05-03

  • update prettify function
  • fix hardcoded identifiers in validated_SE

gDRutils 0.1.0.45 - 2022-04-29

  • avoid using grep for getting cotreatment identifiers

gDRutils 0.1.0.44 - 2022-04-26

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

gDRutils 0.1.0.43 - 2022-04-13

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

gDRutils 0.1.0.42 - 2022-04-08

  • added identifier descriptions

gDRutils 0.1.0.41 - 2022-04-08

  • fix wrong order of elements in rownames in SE

gDRutils 0.1.0.40 - 2022-04-07

  • add cap_ic50 function

gDRutils 0.1.0.39 - 2022-03-31

  • extend possible Barcode identifiers

gDRutils 0.1.0.38 - 2022-03-30

  • fix hardcoded identifiers in validate SE

gDRutils 0.1.0.37 - 2022-03-28

  • add a space between two-word cotreatment identifiers

gDRutils 0.1.0.36 - 2022-03-24

  • remove all R CMD check warnings

gDRutils 0.1.0.35 - 2022-03-22

  • change prettify functions to not substitute metadata

gDRutils 0.1.0.34 - 2022-03-21

  • add helper function for MAE/experiments

gDRutils 0.1.0.33 - 2022-03-19

  • move constant fit warning

gDRutils 0.1.0.32 - 2022-03-18

  • add .calculate_complement

gDRutils 0.1.0.31 - 2022-03-16

  • move duplication warning

gDRutils 0.1.0.30 - 2022-03-14

  • add support for identifier validation

gDRutils 0.1.0.29 - 2022-03-03

  • add getter and setter for experiment_raw_data

gDRutils 0.1.0.28 - 2022-02-16

  • refactor identifier drugname to drug_name

gDRutils 0.1.0.27 - 2022-02-10

  • add MAEpply function

gDRutils 0.1.0.26 - 2022-02-01

  • update documentation

gDRutils 0.1.0.25 - 2022-01-31

  • support SE- init for different BioC versions

gDRutils 0.1.0.24 - 2022-01-25

  • standardize/improve CI

gDRutils 0.1.0.23 - 2022-01-25

  • switch unit tests from SE to MAE from gDRtestData

gDRutils 0.1.0.22 - 2022-01-07

  • update assert in validate_MAE

gDRutils 0.1.0.21 - 2022-01-07

  • update SE-related functions of gDRutils to support MAE

gDRutils 0.1.0.20 - 2021-12-21

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

gDRutils 0.1.0.19 - 2021-11-04

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

gDRutils 0.1.0.18 - 2021-11-01

  • fix issued with new SummarizedExperiment

gDRutils 0.1.0.17 - 2021-10-22

  • refactor: generalize prediction help functions for fits

gDRutils 0.1.0.16 - 2021-09-27

  • update validate_SE as per combos

gDRutils 0.1.0.15 - 2021-09-22

  • feat: use ‘GRvalue’ and ‘RelativeViability’ as normalization_types in ‘fit_curves’

gDRutils 0.1.0.14 - 2021-09-15

  • fix bug with getting_SE_identifiers for untreated_tag

gDRutils 0.1.0.13 - 2021-09-13

  • fix obsolete arguments in reset_env_identifiers

gDRutils 0.1.0.12 - 2021-09-07

  • fix bug with getting identifiers for untreated_tag

gDRutils 0.1.0.11 - 2021-08-26

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

gDRutils 0.1.0.10 - 2021-08-25

  • remove additional ordering line in df_to_bm_assay.R

gDRutils 0.1.0.9 - 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-

gDRutils 0.1.0.8 - 2021-08-13

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

gDRutils 0.1.0.7 - 2021-07-06

  • remove hard version equality for pkg deps

gDRutils 0.1.0.6 - 2021-06-29

  • add barcode as identifiers and store identifiers within split_SE_components

gDRutils 0.1.0.5 - 2021-06-25

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

gDRutils 0.1.0.4 - 2021-06-18

  • add concentration and template as additional identifiers

gDRutils 0.1.0.3 - 2021-06-21

  • refactor logisticFit with error handling

gDRutils 0.1.0.2 - 2021-06-18

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

gDRutils 0.1.0.1 - 2021-06-02

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

gDRutils 0.1.0.0 - 2021-06-02

  • release 1.0.0

gDRutils 0.0.0.49 - 2021-06-02

  • fix bug with merging flatten assays

gDRutils 0.0.0.48 - 2021-05-24

  • refactor validate_SE function

gDRutils 0.0.0.47 - 2021-05-18

  • add merge_SE function

gDRutils 0.0.0.46 - 2021-05-18

  • fix typo in SE validator function

gDRutils 0.0.0.45 - 2021-05-18

  • add SE validator function

gDRutils 0.0.0.44 - 2021-05-13

  • refactor prettify_flat_metrics function

gDRutils 0.0.0.43 - 2021-04-30

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

gDRutils 0.0.0.42 - 2021-04-29

  • add prettify_flat_metrics function

gDRutils 0.0.0.41 - 2021-04-29

  • bugfix flattening data.tables

gDRutils 0.0.0.40 - 2021-04-29

  • bugfix data.table merge in convert_se_assay_ref_to_dt

gDRutils 0.0.0.39 - 2021-04-27

  • add support for flattening data.tables

gDRutils 0.0.0.38 - 2021-04-21

  • switch from processing_metadata to .internal

gDRutils 0.0.0.37 - 2021-04-20

  • add support for getting and setting processing info metadata

gDRutils 0.0.0.36 - 2021-04-19

  • sort BumpyMatrix created from dt

gDRutils 0.0.0.35 - 2021-04-14

  • revert metric arguments in ‘convert_se_assay_to_dt’

gDRutils 0.0.0.34 - 2021-04-09

  • add support for getting and setting fit parameter metadata

gDRutils 0.0.0.33 - 2021-04-07

  • standardize metric header names

gDRutils 0.0.0.32 - 2021-04-07

  • 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

gDRutils 0.0.0.31 - 2021-03-30

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

gDRutils 0.0.0.30 - 2021-03-30

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

gDRutils 0.0.0.29 - 2021-03-23

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

gDRutils 0.0.0.28 - 2021-03-16

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

gDRutils 0.0.0.27 - 2021-03-09

  • update .estimate_xc50 and add tests

gDRutils 0.0.0.26 - 2021-03-04

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

gDRutils 0.0.0.25 - 2021-03-02

  • fix bug with missing class in assert for matrix

gDRutils 0.0.0.24 - 2021-02-10

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

gDRutils 0.0.0.23 - 2021-02-04

  • added linter

gDRutils 0.0.0.22 - 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

gDRutils 0.0.0.21 - 2021-01-26

  • allow for DFrame as input

gDRutils 0.0.0.20 - 2021-01-26

  • ‘s/BumpyMatrix::splitToBumpyMatrix/BumpyMatrix::splitAsBumpyMatrix/’

gDRutils 0.0.0.19 - 2021-01-20

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

gDRutils 0.0.0.18 - 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

gDRutils 0.0.0.15 - 2020-12-14

  • refactor get_identifiers and get_headers to be settable and cached

gDRutils 0.0.0.14 - 2020-12-14

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

gDRutils 0.0.0.13 - 2020-10-12

  • add CI

gDRutils 0.0.0.12 - 2020-10-09

  • fix assay_to_df

gDRutils 0.0.0.11 - 2020-10-09

  • update namespaces

gDRutils 0.0.0.10 - 2020-10-05

  • minor refactor

gDRutils 0.0.0.9 - 2020-09-14

  • add small fixes for assays with empty DataFrame

gDRutils 0.0.0.8 - 2020-09-02

  • update logic as per new db model

gDRutils 0.0.0.7 - 2020-08-07

  • update variable names as per new db model

gDRutils 0.0.0.6 - 2020-07-02

  • import pipes from magrittr

gDRutils 0.0.0.4 - 2020-06-10

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