Step 4: Vignettes
Vignettes are examples of how to run the package. Running these vignettes is important to be sure CATkit is properly installed.
--You can find help on valid input data formats in the Running Cat pages.
--Instructions for running these vignettes, along with the call, input files, and expected result files, are available here. (If you have already downloaded files from Installation page, you may already have these files.)
--Detailed information on parameterizing and running CATkit can be found here.
Vignette 0: Performs a multiple-component cosinor analysis, composed of 3 cosines of periods 24, 12 and 8 hours. A model with multiple cosines is used because it may fit the data better than a single cosine model.
data: Clgi001.dat
output: clgi001.datnoTaper--06Apr17--11-37-55Vignette0Cos .rtf
clgi001.datnoTaper--06Apr17--11-37-55Vignette0Cos.dat
clgi001.datnoTaper--06Apr17--11-37-55Vignette0Cos .pdf
Vignette 1: Artificially generated test data contains two pure frequencies: 48-hrs and 24-hrs. The call to CAT performs a sweep of frequencies, a spectrum analysis, to identify where there are periodic rhythms present in a time series.
data: Signal10-20.txt
output: Signal10-20.txtnoTaper--06Apr17--15-36-47Vignette1Cos.pdf;
Signal10-20.txtnoTaper--06Apr17--15-36-47Vignette1Cos.rtf;
Signal10-20.txtnoTaper--06Apr17--15-36-47Vignette1Cos.dat.
Vignette 2: Using systolic blood pressure data from the first month of a newborn's life, a progressive analysis is performed across spans of data, and for a spectrum of frequencies at each span.
data: FWedited.txt
output: FWedited.txtnoTaper--06Apr17--13-16-29Vignette2Cos.pdf;
FWedited.txtnoTaper--06Apr17--13-16-29Vignette2Cos.rtf;
FWedited.txtnoTaper--06Apr17--13-16-29Vignette2Cos.dat
Vignette 3: Performs smoothing, actogram, autocorrelation and crosscorrelation on two sets of murine activity data, comparing phase difference.
data: good-6d-2m-part.txt
activity stress c57--stress copy2-part.txt
output: activity stress c57--stress copy2-part.txt--16Sep,2017--150911output.pdf
With gratitude to the Alessandro Bartolomucci lab for sharing murine activity data for use in this vignette.
Vignette 4: Using lipid and behavioral data collected every 6 hours over a day, performs a Population Mean Cosinor on parameters resulting from cosinor analysis. The resulting MESOR, Amplitude and Acrophase renders it possible to make inferences concerning a population rhythm.
data: cos02x03.csv
output: cos02x03.csv—[date]—[time]V8,G5,10PMC.rtf
Vignette 5: Using lipid and behavioral data collected every 6 hours over a day, performs a Population Mean Cosinor Parameter Test on parameters resulting from PMC, testing for equivalency of rhythm parameters (MESOR, Amplitude, Phi, (Amp,Phi)).
data: cos02x03.csv
output: cos02x03.csv—[date]—[time]V8,G5,10ParamTest.rtf
--You can find help on valid input data formats in the Running Cat pages.
--Instructions for running these vignettes, along with the call, input files, and expected result files, are available here. (If you have already downloaded files from Installation page, you may already have these files.)
--Detailed information on parameterizing and running CATkit can be found here.
Vignette 0: Performs a multiple-component cosinor analysis, composed of 3 cosines of periods 24, 12 and 8 hours. A model with multiple cosines is used because it may fit the data better than a single cosine model.
data: Clgi001.dat
output: clgi001.datnoTaper--06Apr17--11-37-55Vignette0Cos .rtf
clgi001.datnoTaper--06Apr17--11-37-55Vignette0Cos.dat
clgi001.datnoTaper--06Apr17--11-37-55Vignette0Cos .pdf
Vignette 1: Artificially generated test data contains two pure frequencies: 48-hrs and 24-hrs. The call to CAT performs a sweep of frequencies, a spectrum analysis, to identify where there are periodic rhythms present in a time series.
data: Signal10-20.txt
output: Signal10-20.txtnoTaper--06Apr17--15-36-47Vignette1Cos.pdf;
Signal10-20.txtnoTaper--06Apr17--15-36-47Vignette1Cos.rtf;
Signal10-20.txtnoTaper--06Apr17--15-36-47Vignette1Cos.dat.
Vignette 2: Using systolic blood pressure data from the first month of a newborn's life, a progressive analysis is performed across spans of data, and for a spectrum of frequencies at each span.
data: FWedited.txt
output: FWedited.txtnoTaper--06Apr17--13-16-29Vignette2Cos.pdf;
FWedited.txtnoTaper--06Apr17--13-16-29Vignette2Cos.rtf;
FWedited.txtnoTaper--06Apr17--13-16-29Vignette2Cos.dat
Vignette 3: Performs smoothing, actogram, autocorrelation and crosscorrelation on two sets of murine activity data, comparing phase difference.
data: good-6d-2m-part.txt
activity stress c57--stress copy2-part.txt
output: activity stress c57--stress copy2-part.txt--16Sep,2017--150911output.pdf
With gratitude to the Alessandro Bartolomucci lab for sharing murine activity data for use in this vignette.
Vignette 4: Using lipid and behavioral data collected every 6 hours over a day, performs a Population Mean Cosinor on parameters resulting from cosinor analysis. The resulting MESOR, Amplitude and Acrophase renders it possible to make inferences concerning a population rhythm.
data: cos02x03.csv
output: cos02x03.csv—[date]—[time]V8,G5,10PMC.rtf
Vignette 5: Using lipid and behavioral data collected every 6 hours over a day, performs a Population Mean Cosinor Parameter Test on parameters resulting from PMC, testing for equivalency of rhythm parameters (MESOR, Amplitude, Phi, (Amp,Phi)).
data: cos02x03.csv
output: cos02x03.csv—[date]—[time]V8,G5,10ParamTest.rtf