SEQTaRget 1.4.1

• Strip row-level vectors from fastglm objects to reduce weight.statistics memory usage and use a new internal function to print the coefficient table.
• Strip row-level vectors from outcome models before storing in @outcome.model
• Fix clean_fastglm to strip row-level vectors from nested multinomial weight models
• No longer store survival.curve ggplot object; regenerate on demand via km_curve()
• Removed several local() wrappers and made several code optimizations.
• Improved documentation of the datasets in the package.
• Implement check for perfect separation when fitting logistic regression models.
• Fixed a bug in and make some improvements to internal.weights().
• Removed three unused slots in SEQopts().
• Add alt text to figures in vignettes.
• Fixed SEQuential() time.col validation detecting and repairing non-zero-indexed time.
• Add validation for eligible.col values
• Add Paul Madley-Dowd as a co-author
• Add check for overlapping time_varying.cols and fixed.cols
• Add bounds validation for numeric and integer options in SEQopts()
• Add check for duplicate id/time combinations in input data
• Add check that treat.level values exist in the treatment column
• Add validation for excused.cols flags
• Add validation for followup.min/max ordering
• Add binary check for outcome.col in non-hazard analyses
• Add treat.level length validation for multinomial and non-multinomial analyses
• Add binary validation for cense.eligible and weight.eligible_cols
• Remove additional eligibility rows if not needed
• Amend defaults for followup.min and weight.lower from -Inf to 0
• Fix bootstrapping for risk difference and risk ratio estimates to use paired per-iteration estimates
• Optimizations to use less RAM
• Fix duplicate scale_color_manual warning and plot.subtitle label bug in internal.plot()
• Run doseresponse and ITT vignette chunks on GitHub Actions
• Fix km_curve() returning list instead of ggplot for non-subgroup case
• Fix km_curve() subtitle condition
• Fix risk.comparison() CIs being NA with competing events
• Move selection.random before expansion to reduce peak memory usage
• Replace cbind() with := in expansion chain to avoid intermediate copy
• Replace merge() with data.table native join in expansion data_list combine step
• Replace rbind weight construction with copy+in-place to reduce peak memory
• Drop wt and tmp columns immediately after weight is computed in all code paths
• Remove redundant setDF calls in fast_model_matrix
• Free WDT before bootstrap loop when data.return is FALSE
• Use match(TRUE, ...) instead of which(...)[1] to find first switch/event per group
• Replace sapply loop with single matrix multiply in multinomial prediction
• Vectorise survival curve predictions into a single inline.pred call per treatment level
• Free result list after extraction in internal_survival.R to reduce peak memory during bootstrap
• Free analytic list after subgroup loop in SEQuential.R to reduce peak memory during survival curve computation
• Avoid copy() in data_all construction and free data list in internal_survival.R to reduce peak memory during bootstrap
• Filter to followup==0 before adding trialID in internal.survival to avoid copying entire expanded dataset
• Trim base_DT to only prediction-needed columns before replication in internal.survival to reduce peak memory
• Remove unnecessary copy(weight) for model.data in internal.weights since it is never modified in-place
• Free baseDT after bootstrap loop in internal.survival to reduce peak memory during survival curve computation
• Fix multinomial.summary: replace vcov() with fastglm $se field and add missing Coefficient column to prevent rbind mismatch
• Add test_coverage.R with tests targeting uncovered code paths to increase coverage
• Remove some no longer used variables and dead code
• Further memory reduction optimizations

v1.4.1

• Strip row-level vectors from fastglm objects to reduce weight.statistics memory usage and use a new internal function to print the coefficient table.
• Strip row-level vectors from outcome models before storing in @outcome.model
• Fix clean_fastglm to strip row-level vectors from nested multinomial weight models
• No longer store survival.curve ggplot object; regenerate on demand via km_curve()

v1.4.0

• Removed several local() wrappers and made several code optimizations.
• Improved documentation of the datasets in the package.
• Implement check for perfect separation when fitting logistic regression models.
• Fixed a bug in and make some improvements to internal.weights().
• Removed three unused slots in SEQopts().
• Add alt text to figures in vignettes.
• Fixed SEQuential() time.col validation detecting and repairing non-zero-indexed time.
• Add validation for eligible.col values
• Add Paul Madley-Dowd as a co-author
• Add check for overlapping time_varying.cols and fixed.cols
• Add bounds validation for numeric and integer options in SEQopts()
• Add check for duplicate id/time combinations in input data
• Add check that treat.level values exist in the treatment column
• Add validation for excused.cols flags
• Add validation for followup.min/max ordering
• Add binary check for outcome.col in non-hazard analyses
• Add treat.level length validation for multinomial and non-multinomial analyses
• Add binary validation for cense.eligible and weight.eligible_cols
• Remove additional eligibility rows if not needed
• Amend defaults for followup.min and weight.lower from -Inf to 0
• Fix bootstrapping for risk difference and risk ratio estimates to use paired per-iteration estimates
• Optimizations to use less RAM
• Fix duplicate scale_color_manual warning and plot.subtitle label bug in internal.plot()
• Run doseresponse and ITT vignette chunks on GitHub Actions
• Fix km_curve() returning list instead of ggplot for non-subgroup case
• Fix km_curve() subtitle condition
• Fix risk.comparison() CIs being NA with competing events
• Move selection.random before expansion to reduce peak memory usage
• Replace cbind() with := in expansion chain to avoid intermediate copy
• Replace merge() with data.table native join in expansion data_list combine step
• Replace rbind weight construction with copy+in-place to reduce peak memory
• Drop wt and tmp columns immediately after weight is computed in all code paths
• Remove redundant setDF calls in fast_model_matrix
• Free WDT before bootstrap loop when data.return is FALSE
• Use match(TRUE, ...) instead of which(...)[1] to find first switch/event per group
• Replace sapply loop with single matrix multiply in multinomial prediction
• Vectorise survival curve predictions into a single inline.pred call per treatment level
• Free result list after extraction in internal_survival.R to reduce peak memory during bootstrap
• Free analytic list after subgroup loop in SEQuential.R to reduce peak memory during survival curve computation
• Avoid copy() in data_all construction and free data list in internal_survival.R to reduce peak memory during bootstrap
• Filter to followup==0 before adding trialID in internal.survival to avoid copying entire expanded dataset
• Trim base_DT to only prediction-needed columns before replication in internal.survival to reduce peak memory
• Remove unnecessary copy(weight) for model.data in internal.weights since it is never modified in-place
• Free baseDT after bootstrap loop in internal.survival to reduce peak memory during survival curve computation
• Fix multinomial.summary: replace vcov() with fastglm $se field and add missing Coefficient column to prevent rbind mismatch
• Add test_coverage.R with tests targeting uncovered code paths to increase coverage
• Remove some no longer used variables and dead code
• Further memory reduction optimizations

SEQTaRget 1.3.6

• Added a set.seed() call in internal.hazard() to make main estimate reproducible. And also implement fix to ensure the bootstrapping, including both standard error and percentiles, is deterministic given the seed.

SEQTaRget 1.3.6

• Added a set.seed() call in internal.hazard() to make main estimate reproducible. And also implement fix to ensure the bootstrapping, including both standard error and percentiles, is deterministic given the seed.

SEQTaRget 1.3.5

• The hazard_ratio() function now correctly desscribes the estimate as "Hazard ratio"
• The bootstrapping now collects the log hazard ratio instead of the hazard ratio because the log hazard ratio has better normality properties.
• The covariates() function now returns more nicely formatted output (with spaces around ~ and + symbols in the model formulae)

SEQTaRget 1.3.5 pre-release

• The hazard_ratio() function now correctly desscribes the estimate as "Hazard ratio"
• The bootstrapping now collects the log hazard ratio instead of the hazard ratio because the log hazard ratio has better normality properties.
• The covariates() function now returns more nicely formatted output (with spaces around ~ and + symbols in the model formulae)

SEQTaRget 1.3.4

Implemented some code optimizations:

• Replace a table() call with data.table's .N
• Remove all gc() calls
• Use a keyed index in bootstrapping
• Remove some uses of copy()

SEQTaRget 1.3.4 pre-release

• Implemented some code optimizations
  • Replace a table() call with data.table's .N
  • Remove all gc() calls
  • Use a keyed index in bootstrapping
  • Remove some uses of copy()

SEQTaRget 1.3.3

• Found and fixed a bug which caused excused switches to be overwritten.
• Fix excusing override (#115)
• Added visit option (#116)