Step 3: Installing CAT
Select Quick Start instructions, in the left column, if you are comfortable with minimal guidance. For more detailed instructions, follow instructions in the right column. Information on functions CAT performs can be fund in Analysis Techniques. Further details on parameterization are given under Running CAT.
If you have already installed CATkit and simply want to update it, download the latest CATkit_x.x.tar.gz. Do not unpack it. (To uninstall a previous version, click the X at the far right of the CATkit package name in the RStudio "Packages" tab.)
Note for Mac users: To avoid unpacking the tar.gz on download, right click (2-finger click) on filename and "Download Linked File As...". Or you can turn off unpacking in Safari: http://apple.stackexchange.com/questions/961/how-to-stop-safari-from-unzipping-files-after-download
Select Quick Start instructions, in the left column, if you are comfortable with minimal guidance. For more detailed instructions, follow instructions in the right column. Information on functions CAT performs can be fund in Analysis Techniques. Further details on parameterization are given under Running CAT.
If you have already installed CATkit and simply want to update it, download the latest CATkit_x.x.tar.gz. Do not unpack it. (To uninstall a previous version, click the X at the far right of the CATkit package name in the RStudio "Packages" tab.)
Note for Mac users: To avoid unpacking the tar.gz on download, right click (2-finger click) on filename and "Download Linked File As...". Or you can turn off unpacking in Safari: http://apple.stackexchange.com/questions/961/how-to-stop-safari-from-unzipping-files-after-download
CAT: Quick Start InstallationThese instructions assume you have R and RStudio installed. Detailed instructions are found to the right.
Installing packages: These packages should be added before installing CAT, if they are not already there: stats utils MASS graphics rtf png season signal grDevices magic assertr CombMSC Hmisc To check for these, open RStudio. In the lower right window, click on the Packages tab, search for each package. If the package is found, it is already installed. If not found, you can install it by clicking on Install Packages, and typing in the name of each package to be installed, one at a time, or all together. Copy and paste the above package names into the Packages field. The top field, Install From, should say CRAN. (If you are asked which server to load from, pick one that is recommended, or nearby). You can normally accept all the defaults, and click the Install button. After installing these, check the box beside the name of each of the above in the Packages tab. This will load them for use. Installing CAT 1. Download CATkit_3.3.8.tar.gz. Do not unzip, simply save. 2. Install as a package into RStudio. In RStudio, in the right hand window, go to the Packages tab, click on Install Packages. Select Package Archive File in the Install From drop down. Browse to CATkitx.xx.tar.gz as the Package Archive. Click the Install button 3. Check the box beside CATkit package name in the Packages tab. You may get warnings if your version of R is older, but this is usually not a problem. Step 4: Running Vignettes
After installation, you can run some tests to see sample outputs Download installing_CAT.zip and unzip to a known location. In the "Installing CAT" folder, follow instructions on page 2 of "Installing CAT from tar.pdf ". Compare your output file to those included in the download. If your output matches the sample file, you'll know the package is working correctly. Input File Formats Input formats must meet the requirements described here. Examples can be found in the installing_CAT.zip download file, in the folder "Sample Formats". See also sample input files in the vignettes folders found in that download, or on the Data Formats web page. The data, date/time or factors column(s) can be in any column. See Running Cat, Running CAT Cosinor, Running CAT PMC, or Running CAT PMCtest for parameterization of a header. CAT and CAT Cosinor use the same data file format. Date and Time can be in any column, in any of three formats: 1) numeric (in number of hours from starting time); 2) a one column date/time character string in any format, as specified by the timeFormat parameter 3) a two column format consisting of Date in the first column, and Time in the second, as specified by the timeFormat parameter: c(3,6). The timeFormat parameter uses R time formatting, e.g., "%Y-%m-%d %H:%M:%S". See R function strptime for time formatting details. Format 1: SampleSines.txt (comma delimited) Format 2: FWedited.txt (comma delimited) Format 3: good-6d-2m-part.txt (tab delimited) CAT PMC and CAT PMCtest have a different file format than CAT and CAT Cosinor. There are four required column headers, one optional VarID column, and any number of GrpID columns: PR, MESOR, Amp, Phi (case insensitive), variable, factor1, factor2..... Format 1: cos02x03.csv (comma delimited) |
CAT: Detailed Installation InstructionsDownload this zip file, unzip, and read instructions in Installing CAT folder.
The download "installing_cat_x.zip" includes the following:
Installing Packages v1.3.pdf Installing CAT from tar.pdf Four Vignette folders, and Vignette.r script to run them Sample Data folder Read Me.rtf
With gratitude to the Alessandro Bartolomucci lab for sharing murine activity data for use in these vignettes. CAT: CATkit packageThis is the CATkit R package. Download and place in an accessible location. Do not unzip! (Instructions for installing this are in the document you downloaded above: "Installing CAT from tar.pdf").
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