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Glossary
- Amplitude: The estimated height of an oscillation, defined as half the peak-to-trough distance of a fitted rhythmic waveform, reflects the strength or robustness of the rhythmic signal.
- ARSER: A periodicity-detection algorithm combining autoregressive spectral estimation with harmonic regression, well-suited for identifying both sinusoidal and non-sinusoidal rhythmic profiles.
- False Discovery Rate (FDR): A statistical method to correct for multiple testing in large datasets. It controls the proportion of false positives among significant features. In this analysis, FDR values (adjusted via Benjamini-Hochberg) were calculated for all MetaCycle outputs to rigorously filter for significant rhythmicity in host, parasite, and vector datasets.
- Intraerythrocytic Developmental Cycle (IDC): The asexual replication cycle of Plasmodium parasites within host erythrocytes progresses through the Ring, Trophozoite, and Schizont stages. The duration and synchrony of the IDC are species-dependent, typically approximating multiples of 24 hours.
- JTK_CYCLE: A non-parametric, rank-based algorithm that identifies rhythmicity by matching ordered data to idealized cosine reference curves, providing robustness to noise and outliers in high-dimensional datasets.
- Lomb–Scargle (LS): A spectral method designed to detect periodicity in unevenly or irregularly sampled time-series data by estimating power across a frequency spectrum.
- Meta2d: A MetaCycle function that integrates rhythmicity statistics from JTK_CYCLE, Lomb–Scargle, and ARSER to generate unified estimates of period, phase, amplitude, and significance.
- MetaCycle: An R package for systematic periodicity analysis that incorporates ARSER, JTK_CYCLE, and Lomb–Scargle methods to provide robust detection of rhythmic patterns across large time-series datasets.
- Rhythmic Antimalarial Drug Interactions: Drug targets or interacting proteins in Plasmodium that display rhythmic expression at the transcript level, influencing the timing and efficacy of antimalarial therapies.
- Rhythmic Virulence Factors: Recurring, time-dependent changes in gene, protein, or metabolite levels that follow circadian, infradian, or ultradian patterns in Plasmodium, host, or vector systems.
- Molecular Rhythmicity: Recurring, time-dependent changes in gene, protein, or metabolite levels that follow circadian, infradian, or ultradian patterns in Plasmodium, host, or vector systems.
- Period: The time required for a rhythmic variable to complete one full oscillatory cycle.
- Phase (Acrophase): The timing of the peak of a rhythmic signal within its cycle is used to define the relative position of oscillatory events.