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Changelog

Source: NEWS.md

CausalGPS 0.5.0 (2024-06-19)

Added

  • estimate_gps now accepts formula for generating GPS object.
  • estimate_gps now has functions for generic plot, print, and summary functions.
  • trim_it function.

Removed

  • preprocess_data function.
  • trim_gps function.

CausalGPS 0.4.2 (2024-04-13)

CRAN release: 2024-04-13

Added

  • heads-up message about changes in the software design that will be implemented in CausalGPS version 0.5.x.

CausalGPS 0.4.1 (2023-09-29)

CRAN release: 2023-09-29

Added

  • Extra step to check consistency of delta_n with exposure range.
  • Software paper examples were added.

Changed

  • Plotting pseudo population includes object details. Set include_details = TRUE.
    *generate_pseudo_pop does not take Y as an input.

CausalGPS 0.4.0 (2023-05-25)

CRAN release: 2023-05-25

Changed

  • Docker image supports R 4.2.3
  • generate_syn_data supports vectorized_y to accelerate data generation.
  • matching_fun –> dist_measure
  • matching_l1 –> matching_fn
  • estimate_semipmetric_erf now takes the gam models optional arguments.
  • estimate_pmetric_erf now takes the gnm models optional arguments.
  • trim_quantiles –> exposure_trim_qtls
  • generate_pseudo_pop function accepts gps_obj as an optional input.
  • internal_use is not part of parameters for estimate_gps function.
  • estimate_gps function only returns id, w, and computed gps as part of dataset.
  • Now the design and analysis phases are explicitly separated.
  • gps_model –> gps_density. Now it takes, normal and kernel options instead of parametric and non-parametric options.

Added

  • estimate_npmetric_erf supports both locpol and KernSmooth approaches.
  • There is gps_trim_qtls input parameter to trim data samples based on gps values.
  • Now users can also collect the original data in the pseudo population object.

Fixed

  • A bug with swapping transformed covairates with original one.

CausalGPS 0.3.1 (2023-05-15)

CRAN release: 2023-05-16

Changed

  • Some of unit tests have less accuracy to overcome the bug with stats::density function.

CausalGPS 0.3.0 (2023-02-15)

CRAN release: 2023-02-15

Changed

  • Unit tests support new wCorr release (#193).
  • Only optimized compilation is supported. In the previous versions, this approach is known as optimzied_compile == TRUE.

Added

  • The earth package is part of suggested packages.

CausalGPS 0.2.9 (2022-12-16)

CRAN release: 2022-12-16

Fixed

  • fixed a bug based on covariate balance threshold (#178, @naeemkh).
  • estimate_npmetric_erf assigns user-defined log file.

Changed

  • The process now prints the progress message based on the selected thresholds.
  • In estimate_npmetric_erf:
    • matched_Y –> m_Y
    • matched_w –> m_w
    • matched_cw –> counter_weight
  • In estimate_npmetric_erf function, the matched_cw input is now mandatory.
  • Internal kernel smoothing now uses locpol::locpol function.
  • The entire data set is trimmed based on trimming quantiles.
  • earth and ranger are not installed automatically. They can be installed manually if needed.
  • sysdata.rda is modified to reflect transition from counter and ipw to counter_weight
  • counter_weight is used as a counter or weight, in matching or weighting approaches. counter and ipw are dropped.
  • sl_lib becomes a required argument.
  • The package has been transferred into NSAPH-Software Github account.
  • Summary function of gpsm_pspop S3 object returns details of the adjusting process.

Added

  • Now Kolmogorov-Smirnov(KS) statistics are provided for the computed pseudo population.
  • effect size for the generated pseudo population is computed and reported.
  • Binary search approach is used when scale = 1.
  • pseodo_pop also includes covariate column names.
  • compute_closest_wgps_helper_no_sc is added to take care of the mostly used special case (scale = 1).

Removed

  • Dropped importing KernSmooth and tidyr packages.
  • pred_model argument dropped. The package only predicts using SuperLearner.

CausalGPS 0.2.8 (2022-06-22)

CRAN release: 2022-06-22

Fixed

  • Message for not implemented methods changed to reduce misunderstanding.
  • Empty counter will raise error in estimating non-parametric response function.

Changed

  • matching_l1 returns frequency table instead of entire vector.
  • Vectorized population compilation and used data.table for multi-thread assignment.
  • Removed nested parallelism in compiling pseudo population, which results in close control on memory.
  • estimate_npmetric_erf also returns optimal h and risk values.

Added

  • estimate_gps returns the optimal hyperparameters.
  • estimate_gps returns S3 object.
  • Internal xgboost approach support verbose parameter.
  • Pseudo-population object now report the parameters that are used for the best covariate balance.

CausalGPS 0.2.7 (2022-02-04)

CRAN release: 2022-02-07

Fixed

  • Naming covariate balance scores.

Changed

  • Restarting adaptive approach to keep trying up to maximum attempt.

Added

  • Synthetic data (synthetic_us_2010)
  • Check on not defined covariate balance (absolute_corr_fun, absolute_weighted_corr_fun)
  • Covariate balance threshold type: mean, median, maximal.
  • Improved test coverage.
  • Singularity definition file.

CausalGPS 0.2.6 (2021-09-06)

CRAN release: 2021-09-06

Added

  • added the status of optimized compile to generate_pseudo_pop function output.
  • compute_closest_wgps accepts the number of user-defined threads.

Changed

  • Vignette file names.
  • The trim condition from > and < into >= and <=.
  • Removed seed input from generate_syn_data function. In R package, setting seed value inside function is not recommended. Users can set the seed before using the function.
  • OpenMP uses user defined number of cores.

Fixed

  • Initial covariate balance for weighted approach. The counter column was not preallocated correctly.
  • Counter value for compiling. The initial value was set to one, which, however, zero is the correct one.
  • Private variable issue with OpenMP.
  • Fixed OpenMP option on macOS checks.

Removed

CausalGPS 0.2.5 (2021-07-23)

CRAN release: 2021-07-23

Changed

  • User needs to activate the logger

Fixed

  • CRAN package URLs are in canonical forms.

CausalGPS 0.2.4 (2021-07-11)

Added

  • OpenMP for Rcpp code
  • optimized_compile
  • log_system_info()
  • Frequently asked questions
  • logo

Changed

  • estimate_gps.Rmd
  • estimate_semi_erf -> estimate_semipmetric_erf
  • estimate_erf -> estimate_npmetric_erf
  • estimate_hr -> estimate_pmetric_erf
  • gen_pseudo_pop -> generate_pseudo_pop
  • gen_syn_data -> generate_syn_data
  • estimate_erf accepts counter as an input
  • estimate_erf can use multiple cores
  • generating_pseudo_population.Rmd
  • estimate_erf function description
  • estimate_hr function description
  • estimate_semi_erf function description
  • compute_risk function description and return value
  • outcome_models.Rmd
  • generate_synthetic_data.Rmd

Fixed

  • Rcpp parLapply worker processors arguments

Removed

  • running_appr

CausalGPS 0.2.3 (2021-05-12)

Fixed

  • Fixed documentations

CausalGPS 0.2.2 (2021-05-12)

Added

  • estimate_semi_erf
  • estimate_hr

Changed

  • Package name: GPSmatching –> CausalGPS