trimData

trimData() allows users to define start date, start time and number of days for analysing data sets.

Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007>, and Stoleru method: Stoleru et al. (2004) <doi:10.1038/nature02926>. Rose plots and circular analysis are based on methods from - Batschelet (1981) <ISBN:0120810506> and Zar (2010) <ISBN:0321656865>.

Lakshman Abhilash

phase

Analyse Biological Time-Series Data

trimData function

<dl><dt>data</dt>
<dd>Input data file. This must be DAM scanned monitor files, saved in 1-min intervals starting at time 00:00.</dd>
<dt>start.date</dt>
<dd>Define starting date for analysis. Date inputs must be in this form: "DD Mon YY"; August 6, 2020 must be input as "6 Aug 20". Any other form will result in computation errors.</dd>
<dt>start.time</dt>
<dd>Define start time for analysis. Times must be input in the 24-h format and in the following form: "HH:MM"; 10 AM must be "10:00" and 10 PM must be "22:00".</dd>
<dt>n.days</dt>
<dd>Number of days to analyse.</dd>
<dt>bin</dt>
<dd>Intervals in which data are sampled (in minutes). This defaults to 1.</dd>
<dt>t.cycle</dt>
<dd>Define the period of the environmental cycle or a single day in hours. This defaults to 24.</dd></dl>

Arguments

Trim data for downstream analyses — trimData

<dl>

<dt>data</dt>
<dd>Input data file. This must be DAM scanned monitor files, saved in 1-min intervals starting at time 00:00.</dd>


<dt>start.date</dt>
<dd>Define starting date for analysis. Date inputs must be in this form: "DD Mon YY"; August 6, 2020 must be input as "6 Aug 20". Any other form will result in computation errors.</dd>


<dt>start.time</dt>
<dd>Define start time for analysis. Times must be input in the 24-h format and in the following form: "HH:MM"; 10 AM must be "10:00" and 10 PM must be "22:00".</dd>


<dt>n.days</dt>
<dd>Number of days to analyse.</dd>


<dt>bin</dt>
<dd>Intervals in which data are sampled (in minutes). This defaults to 1.</dd>


<dt>t.cycle</dt>
<dd>Define the period of the environmental cycle or a single day in hours. This defaults to 24.</dd>

</dl>

trimData: Trim data for downstream analyses

Description

Usage

Value

Arguments

Examples