rcicr

Reproducibility impact

• **batchGenerateCI() and batchGenerateCI2IFC() now group a tibble correctly.** Called on a tibble with more than one group in by, rcicr 1.1.0 through 1.4.1 returned a single classification image instead of one per group. That image was built from alternating trials of different groups and named after the first group. A data.frame, or a tibble with one group, was never affected, and its results do not change. (#336) You were affected if the list these functions returned had one element although your data held several participants or conditions; data read with readr or processed with dplyr is a tibble. Recompute those CIs with this version, or with an older one after as.data.frame(). No stimuli need regenerating or responses recollecting. Of the affected versions, only 1.3.0 and 1.4.1 were released on CRAN; the others were GitHub releases. The 1.1.0 entry below saying these functions accept tibble columns held only for a single group.
• **The default InfoVal reference now needs the stimulus seed saved in the file.** Without a response_seed, the reference replays that seed. A file without one (made with generateStimuli2IFC(seed = NULL), or with the seed field removed) now stops with an error before anything is simulated. The error gives the call that stores a reproducible reference, generateReferenceDistribution2IFC(rdata, response_seed = <n>), which later computeInfoVal2IFC() calls reuse, and, for a file that cannot be written, computeInfoVal2IFC(..., response_seed = <n>). Files with a seed are unaffected. Such a file used to reseed from the clock, so its reference could not be reproduced. generateReferenceDistribution2IFC() and computeInfoVal2IFC(force_gen_ref_dist = TRUE) returned a different one on every call. The first automatic computeInfoVal2IFC() stored one that later calls reused, so the InfoVal was stable on that copy of the file and different on any other. This happened on every version back to 1.0.1 for files made with seed = NULL, and on 1.4.0 and 1.4.1 for files without the field; earlier versions stopped on those. A reference already stored by 1.4.0 or later is still used, with a message that it cannot be regenerated from the file. An older stored reference, which rcicr rebuilds, now stops like any other. Replacing either with a seeded reference makes the InfoVal reproducible; it will differ from the one reported before. (#334)

Bug fixes

• **Saving a reference distribution no longer risks the stimulus .Rdata file.** computeInfoVal2IFC() and generateReferenceDistribution2IFC() store the reference in that file, and a save that was interrupted (Esc, an error, R killed or crashing) could leave it unloadable, losing the only record of the stimuli. The file is now backed up beside itself for the duration of the save, as <file>.rcicr-backup, and restored automatically if the save fails. It keeps its owner, group and permissions. (#333) If R is killed during the save, the backup remains, and any function that reads the damaged file says so. If the file still loads, the next save stops and asks you to delete the backup, since rcicr does not delete a file it cannot prove it made. If the file no longer loads, check that the backup holds this experiment (the error shows how), restore it with file.copy("<file>.rcicr-backup", "<file>", overwrite = TRUE, copy.mode = FALSE), check that the file loads again, and only then delete the backup. Leftover <file>.rcicr-staging-* files are incomplete copies and can be deleted. Limits: a writable file in a read-only directory (Unix), and a file name over 228 bytes, are saved as before, without a backup, with a warning. On Windows, a writable file in a folder that refuses new files now stops with an error instead of being saved, as does any save where the backup cannot be made, such as on a full disk. On Windows the backup has its folder's permissions rather than being private to you. Power loss and operating-system crashes are not covered, and two R sessions saving the same file at once remain unsafe.
• **generateCI() stops when some, but not all, participants IDs are NA.** It used to return a CI in which every pixel was NA, with only min/max warnings, and write it as a solid black PNG; every version since 1.0.1 did this. The error names the trials without an ID. Give them one, or remove them from stimuli, responses and participants alike. An all-NA participants still means no grouping, and no valid result changes. (#337)
• **generateStimuli2IFC() never overwrites a stimulus .Rdata file.** Its file name records the minute, so two calls into one folder with the same label and seed in the same minute used to write one file, and the first set's PNGs lost the only record of their noise parameters. The name is now reserved before anything is generated, and the call stops, having written nothing, if that file exists or if another call into the same folder with the same seed, started in the same minute, is still running. The error says to use a different label or stimulus_path, or to delete the file if the set is being regenerated on purpose. The time in the name is now the start of the call rather than its end. (#338)
• **An img_size the noise scales cannot tile now gets an error that says so.** The finest of nscales scales tiles the image with 2^(nscales - 1) patches per side, so img_size must be divisible by that. generateNoisePattern(), and through it generateStimuli2IFC() and simulateNoiseIntensities(), used to fail with "number of items to replace is not a multiple of replacement length". The error now names the constraint, the nearest valid sizes and the largest nscales that fits. Every size that worked still works. (#339)