Changelog

Source: NEWS.md

cellreportR 0.2.0

Rescopes the package from a single-plate assay helper to a full screening pipeline. The unit of replication is now a first-class notion throughout: acquisitions are resolved into units, cells are standardized against the control condition of their own batch, and every effect is reported at both unit and cell level so the difference between the two is visible rather than assumed. Existing 0.1.0 functions are unchanged and continue to work.

Ingest

• cr_read_export() and cr_read_exports() read one, or a whole recursive tree of, segmented single-cell exports (.csv / .xlsx), keeping source_file and source_path on every row. Base names repeat across plates, so the path – not the file name – identifies an acquisition.
• cr_column_map() declares a tolerant vendor-header contract: absent names are skipped silently rather than raising, and headers that embed unit glyphs are matched by prefix. A strict renamer was what previously forced a second, near-duplicate ingest path to exist.
• cr_path_spec() and cr_parse_paths() recover design facts that live in the directory tree rather than inside the files, and cr_filename_grammar() states the token grammar a file name must match. An unmatched name is an error, never a default: absence of a token is itself meaningful, so one typo would otherwise reclassify a treated unit as a control and pull it into its own batch’s denominator.
• cr_marker_rules() and cr_extract_markers() turn parenthetical name markers into typed flags. A half-acquisition marker on a file and the same word on a directory mean different things and are kept apart; unrecognised markers are captured verbatim rather than guessed at.

Units and balancing

• cr_merge_rules(), cr_assign_units() and cr_unit_map() resolve files into analysis units. A second-half acquisition merges into its unit, a re-acquisition merges into its plain sibling, and a look-alike suffix that denotes a physically different unit does not merge. The map reports which units were assembled from more than one file.
• cr_centroid_overlap() is the evidence test behind that last rule: two files that share essentially no object centroids are not the same unit.
• cr_exclude_small() drops objects below a quantile of the pooled area distribution – a data-derived threshold, with the realised absolute value recorded in the quality-control log.
• cr_balance_cells() caps each unit’s cell contribution under an explicit seed, so a unit acquired in two halves cannot weight the shared control denominator twice. Order matters: exclusion first, then balancing, or the threshold is computed on a differently weighted pool.

Batch standardization

• cr_batch_key(), cr_batch_reference() and cr_standardize_batch() standardize every cell against the control condition of its own batch, where a batch is a combination of design columns rather than a single variable. Both centres are retained deliberately: the fold change keeps the mean denominator while the gate compares medians, because the signal is right-skewed and mixing the two makes the gate quietly stricter than the rule it states.

Quality control

• cr_qc_gate() implements the biological gate – a treated unit must exceed the control of its own batch – and reports which verdicts depend on the centre chosen instead of hiding the choice.
• cr_qc_gate_impact() re-estimates every affected contrast with and without each excluded unit, so “one unit changes the verdict” carries a number. This matters most when the excluded unit sits in the reference arm.
• cr_apply_gate() and cr_qc_report() apply the gate and record what it removed.

Effect sizes

• cr_effect_grid() computes the mean shift, Cohen’s d, Hedges’ g and Cliff’s delta with analytic confidence intervals across the whole compound-by-contrast grid, at unit or at cell level.
• cr_compare_levels() contrasts the two levels directly. Cell-level intervals are typically several-fold narrower on the same data; that is pseudo-replication, not precision, and is why the unit level carries the interpretation.
• Multiplicity adjustments are reported alongside the unadjusted p-value, never in place of it: effect sizes with intervals are the reportable quantity for an exploratory screen.
• cr_blocked_effect() refits each contrast within block, since units on one plate share a preparation, a session and a single control denominator.
• cr_unit_variability() reports unit-to-unit spread and fold range. This is explicitly not within-unit technical repeatability, which this class of design cannot estimate at all.

Sample size

• cr_conservative_effect(), cr_power() and cr_power_grid() solve the two-sample design twice: once for the observed estimate and once for the confidence bound nearer the null, returning NA where the interval spans the null. The conservative figure is the reportable one – powering a screen’s top hit on its own point estimate is circular, because that candidate is largest only by virtue of having been selected for being largest.

Visualization

• cr_plot_screen(), cr_plot_forest(), cr_plot_sample_size(), cr_plot_specificity() and cr_plot_qc_gate() cover the screen figure set, with row order and interval statements computed from the data rather than typed.
• cr_theme(), cr_palette(), cr_shapes() and cr_scale_group() own the design contract once: a colour-vision-safe palette, no red/green pair ever carrying meaning, redundant shape encoding wherever hue encodes a grouping, and duplicate-aesthetic guides suppressed so a composite emits one legend.
• cr_save_plot() writes raster and vector output from one call.

Tables and generated numbers

• cr_tables(), cr_table_disposition(), cr_table_qc() and cr_export_tables() emit reported counts and supplementary tables from the analysis objects. The one hand-maintained table in earlier work was where a point estimate from one run got spliced beside an interval from another.
• cr_macros(), cr_macros_from(), cr_macro_name(), cr_format_number() and cr_enumerate() write every quoted number into a single generated include file, so a stale number becomes impossible rather than a proofreading miss. Enumerations are computed too, since those sentences were hardcoded once and were wrong.
• cr_render_report() renders the parameterised report template.

Infrastructure

• Added inst/CITATION, a .lintr configuration, and a lint workflow alongside R-CMD-check, pkgdown and test-coverage.
• The pkgdown reference index is grouped by pipeline stage.
• Coverage reporting is informational and no longer fails continuous integration when an optional dependency or a browser is unavailable on a runner.

cellreportR 0.1.0

First release. End-to-end analysis and reporting for cell culture microscopy assays, picking up where segmentation leaves off.

Import

• cr_read_cells(), cr_read_design(), cr_read_cellprofiler(), cr_read_qupath(), cr_read_segmantr(), cr_build_experiment() and cr_validate_experiment() build and check the experiment container.

Quality control

• cr_qc_filter(), cr_qc_doublets(), cr_qc_intensity(), cr_qc_manual() and cr_qc_summary() apply threshold filters and summarise what they removed.

Normalization

• cr_normalize(), cr_background_subtract() and cr_correct_batch().

Quantification

• cr_summarize_wells(), cr_fold_change() and cr_compute_metrics().

Statistical analysis

• cr_test(), cr_test_all(), cr_effect_size() and cr_power_analysis() provide tests at cell or replicate level with effect sizes.

Discriminability

• cr_logistic(), cr_roc(), cr_auc() and cr_confusion_matrix().

Dose-response

• cr_dose_response() (4PL / 3PL / linear) and cr_ic50().

Visualization

• Thirteen cr_plot_* functions covering plate layouts, distributions, scatter plots, fold-change and effect-size forest plots, ROC curves, dose-response, quality-control dashboards, spatial plots, heatmaps and time courses.

Reporting

• cr_report(), cr_export_results() and cr_export_plots().

Interactive front-end

• cr_run_app() launches a guided multi-tab application covering import, quality control, normalization, analysis, dose-response fitting, visualisation and report export.

Helpers

• cr_example_experiment(), cr_example_design(), cr_example_files(), cr_well_to_rowcol(), cr_rowcol_to_well(), cr_channels(), cr_n_cells(), cr_filter_cells() and cr_merge_experiments().