The risks of using the chi-square periodogram to estimate the period of biological rhythms.
The risks of using the chi-square periodogram to estimate the period of biological rhythms.
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DOI：
10.1371/journal.pcbi.1008567
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发表时间：
2021-01
影响因子：
4.3
通讯作者：
Hughey JJ
中科院分区：
文献类型：
--
作者：
Tackenberg MC;Hughey JJ
卡方周期图（CSP），40多年前开发的，仍然是最流行的方法来估计昼夜节律（约24小时）的周期之一。以前的工作表明，CSP有时比其他方法更不准确，但对原因和条件的理解仍然不完整。使用模拟的节奏的时间过程中，我们发现，CSP是倾向于低估的方式，取决于真实的周期和时间过程的长度的周期。这种低估偏差在短时间内最为严重（例如，3天），但在更长的模拟时间过程中也是可见的（例如，12天）和小鼠轮跑和离体生物发光的实验时间过程中。我们将偏倚的来源追溯到周期图中的不连续性，这些不连续性与CSP用于计算给定测试周期的观测方差的时间点数量有关。通过修改计算以避免不连续性，我们开发了一个新的版本，贪婪CSP，显示出减少的偏差和提高的准确性。尽管如此，即使是贪婪的CSP在我们模拟的时间过程中也往往不如另一种方法，即Lomb-Scargle周期图准确。因此，尽管我们的研究描述了对经典方法的重大改进，但它也表明用户在估计生物节律周期时通常应避免CSP。卡方周期图是估算周期长度的常用方法，周期长度是自然界中发现的日常生物节律的最重要特性之一。在这项研究中，我们确定了卡方周期图中不准确性的主要来源，并使用广泛的模拟和实验观察到的生物节律来量化不准确性。虽然我们修改的卡方周期图计算，以提高其准确性，我们也表明，修订后的版本仍然是准确性低于替代方法，Lomb-Scargle周期图。因此，我们的工作为如何更好地估计生物节律的周期提供了证据。
The chi-square periodogram (CSP), developed over 40 years ago, continues to be one of the most popular methods to estimate the period of circadian (circa 24-h) rhythms. Previous work has indicated the CSP is sometimes less accurate than other methods, but understanding of why and under what conditions remains incomplete. Using simulated rhythmic time-courses, we found that the CSP is prone to underestimating the period in a manner that depends on the true period and the length of the time-course. This underestimation bias is most severe in short time-courses (e.g., 3 days), but is also visible in longer simulated time-courses (e.g., 12 days) and in experimental time-courses of mouse wheel-running and ex vivo bioluminescence. We traced the source of the bias to discontinuities in the periodogram that are related to the number of time-points the CSP uses to calculate the observed variance for a given test period. By revising the calculation to avoid discontinuities, we developed a new version, the greedy CSP, that shows reduced bias and improved accuracy. Nonetheless, even the greedy CSP tended to be less accurate on our simulated time-courses than an alternative method, namely the Lomb-Scargle periodogram. Thus, although our study describes a major improvement to a classic method, it also suggests that users should generally avoid the CSP when estimating the period of biological rhythms. The chi-square periodogram is a popular method for estimating period length, one of the most important properties of the daily biological rhythms found throughout nature. In this study, we identify a major source of inaccuracy in the chi-square periodogram, and quantify the inaccuracy using a broad array of simulated and experimentally observed biological rhythms. Although we revise the chi-square periodogram calculation to improve its accuracy, we also show that the revised version is still less accurate than an alternative method, the Lomb-Scargle periodogram. Our work thus provides evidence on how to obtain better estimates of the period of biological rhythms.
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DOI：
10.1016/j.cub.2017.02.037
发表时间：
2017-04-03
期刊：
Current biology : CB
影响因子：
--
作者：
Tso CF;Simon T;Greenlaw AC;Puri T;Mieda M;Herzog ED
通讯作者：
Herzog ED
DOI：
10.1073/pnas.1511351113
发表时间：
2016-03-29
影响因子：
11.1
作者：
Smyllie, Nicola J.;Chesham, Johanna E.;Hastings, Michael H.
通讯作者：
Hastings, Michael H.
影响因子：
6.8
作者：
Wehr, Thomas A.
通讯作者：
Wehr, Thomas A.
影响因子：
3.5
作者：
Leise, Tanya L.
通讯作者：
Leise, Tanya L.
影响因子：
3.7
作者：
Buijink MR;Almog A;Wit CB;Roethler O;Olde Engberink AH;Meijer JH;Garlaschelli D;Rohling JH;Michel S
通讯作者：
Michel S