{"id":341,"date":"2017-05-05T19:22:09","date_gmt":"2017-05-05T19:22:09","guid":{"rendered":"http:\/\/sites.warnercnr.colostate.edu\/gwhite\/?page_id=341"},"modified":"2017-05-05T19:22:09","modified_gmt":"2017-05-05T19:22:09","slug":"set-preferences","status":"publish","type":"page","link":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/set-preferences\/","title":{"rendered":"Set Preferences"},"content":{"rendered":"

Contents<\/a> – Index<\/a><\/span><\/p>\n

\n

Set Preferences<\/b><\/span><\/p>\n

Various options to set preferences for Program MARK are available from the File | Preferences menu choice.\u00a0\u00a0<\/span><\/p>\n

Display BIC instead of AICc in Results Browser<\/b><\/span><\/p>\n

This option uses the BIC<\/a> (or QBIC<\/a>) model selection method instead of AICc<\/a> (or QAICc<\/a>) in the Results Browser<\/a>.\u00a0 Model weights<\/a> and model likelihood<\/a> are also computed using BIC instead of AICc.<\/span><\/p>\n

Display QAICc Weights in Results Browser<\/b><\/span><\/p>\n

This option is to display the QAICc weight in the Results Browser<\/a> Window.\u00a0 If this option is checked, the Results Browser window will display a column labeled AICc Weight<\/a> (or QAICc Weight<\/a> if c-hat<\/a> > 1).\u00a0 If this option is not checked, then the model weight column will not be displayed.<\/span><\/p>\n

If you change this option while the Results Browser window is open, you will have to close the window (click the X box at the upper right corner), and then reopen the Results Browser from the Browser menu option.<\/span><\/p>\n

Display Model Likelihood Column in Results Browser<\/b><\/span><\/p>\n

This option is to display the model likelihood for each of the models in the Results Browser<\/a> Window.\u00a0 The model likelihood is the ratio of the\u00a0 <\/span>AICc Weight<\/a><\/span> (or <\/span>QAICc Weight<\/a><\/span> if <\/span>c-hat<\/a><\/span> > 1) of the model divided by the weight of the minimum AICc model.<\/span><\/p>\n

If you change this option while the Results Browser window is open, you will have to close the window (click the X box at the upper right corner), and then reopen the Results Browser from the Browser menu option.<\/span><\/p>\n

Display -2log(L) in Results Browser<\/b><\/span><\/p>\n

<\/b>This option adds a column to the Results Browser<\/a> where the -2log(Likelihood) value is reported.<\/span><\/p>\n

Display Time Stamp in Results Browser<\/b><\/span><\/p>\n

This option adds a column to the Results Browser<\/a> where a time stamp<\/a> for the model is reported.\u00a0 The time stamp consists of YY:MM:DD:HH:MM:SS, i.e., the last 2 digits of the year, month, day, hour, minute, and seconds when the job was run.<\/span><\/p>\n

Name first column of design matrix Beta0 instead of Beta1<\/b><\/span><\/p>\n

The purpose of this option is to allow the first column of the design matrix<\/a> to be numbered zero instead of 1.<\/span><\/p>\n

Make first row of a time effect the reference row<\/b><\/span><\/p>\n

The purpose of this option is to make the first row of a time effect in the design matrix<\/a> the reference row, rather than the previous default of the last row of the time effect corresponding to the intercept.\u00a0 This option affects the <\/span>Full Design Matrix<\/a><\/span> and <\/span>Pre-defined Models<\/a><\/span> that use a design matrix.<\/span><\/p>\n

No page separators in the numerical estimation file<\/b><\/span><\/p>\n

This option makes the numerical estimation file one continuous list of output, with no page separators.\u00a0 That is, there are no page headings or numbers that break up the output for printing.<\/span><\/p>\n

Show Tip of the Day when starting the program<\/b><\/span><\/p>\n

This option causes MARK to display a “Tip of the Day” when the program is started.\u00a0 At this point, not enough Tips are available to make you want to use the option.<\/span><\/p>\n

Show message when model is retrieved<\/b><\/span><\/p>\n

This purpose of this option is to display a message when model is retrieved from the Results Browser window.\u00a0 This option is useful for novices because retrieval of models that do not have a design matrix don’t show any response on the screen.\u00a0 That is, the PIMs are changed, but none of this is obvious to the user if no PIM windows are open.\u00a0 Hence, novice users like to see a message that tells them a model was retrieved.\u00a0 If the model has a design matrix, then a design matrix window is opened, so a obvious response is noticed.\u00a0 Once a user becomes familar with the operation of the program, the lack of a message is a benefit.<\/span><\/p>\n

Turn off color for non-zero values of the desing matrix to show patterns<\/b><\/span><\/p>\n

The Design Matrix<\/a> defaults to using background colors<\/a> to make non-zero values stand out.\u00a0 This coloring of the design matrix can be time consuming, particularly for large matrices.\u00a0 Hence, to turn this option off, click this option.<\/span><\/p>\n

Set number of characters in a design matrix cell<\/b><\/span><\/p>\n

The Design Matrix<\/a> has only a limited number of characters in each cell.\u00a0 The maximum can be increased, with details in <\/span>design matrix cell size<\/a><\/span>.\u00a0 Large values for this variable can significantly slow down the processing of large design matrices.<\/span><\/p>\n

Turn off warning of using identity design matrix if no design matrix window is open<\/b><\/span><\/p>\n

If the Design Matrix<\/a> Window is not open, you will be asked whether you want to use an identity<\/a> design matrix.\u00a0 This option turns off this warning.<\/span><\/p>\n

Do not save deleted models for later undeleting<\/b><\/span><\/p>\n

Program MARK normally saves models that are deleted from the Results Browser<\/a>.\u00a0\u00a0 However, for large data sets with complicated models, saving the model can cause memory problems that cause MARK to abort.\u00a0 This option turns off the saving of models when they are deleted from the Results Browser.<\/span><\/p>\n

Use non-interactive model averaging parameter specification window<\/b><\/span><\/p>\n

For data types that have a large number of PIMs, or when the number of occasions is large and the PIMs will not display completely on the screen, the specification of parameters for model averaging becomes problematic.\u00a0 This option allows parameters to be specified for model averaging in a dialog window that is not as interactive as the default, but works for large problems.<\/span><\/p>\n

Add 1 to K when computing QAICc with c-hat > 1<\/b><\/span><\/p>\n

Some people feel that every model should have one additional parameter included if a value of c is estimated for the set of models.\u00a0 This option automatically adds 1 to K<\/i>, the number of parameters estimated, for each model.\u00a0 However, the effect on model selection results is typically extremely small, and can result in errors in the value of K<\/i>.\u00a0 Thus, I do not generally recommend this option.<\/span><\/p>\n

Do not ask user about exiting MARK when RED Exit Box Clicked<\/b><\/span><\/p>\n

Experienced users find it annoying to continually be asked to verify something that they want to do.\u00a0 This option turns off the request to be sure you want to exit out of MARK.<\/span><\/p>\n

Use Excel 2007 for spreadsheet output<\/b><\/span><\/p>\n

When Microsoft released Excel 2007, there were some incompatibilites that showed up.\u00a0 So, if you are having trouble with dumping values into Excel from MARK, either check or uncheck this option to see if these procedures now work.<\/span><\/p>\n

Number of Integration Nodes<\/b><\/span><\/p>\n

Specify the number of integration nodes for Gaussian-Hermite quadrature.that is used for the <\/span>individual heterogeneity models<\/a><\/span>.\u00a0 The minium allowed is 15, maximum 505, with the recommended default of 101.<\/span><\/p>\n

Number of Threads<\/b><\/span><\/p>\n

Specify the <\/span>number of threads<\/a><\/span> to use for numerical processing.<\/span><\/p>\n

Editor Location<\/b><\/span><\/p>\n

The default text editor in MARK to list text output in is NotePad.\u00a0 If you prefer a different editor, you can specify the location in this box.\u00a0 The Browse push box allows you to find the location of your favorite editor and place this location in the text box.<\/span><\/p>\n

Set design matrix colors<\/b><\/span><\/p>\n

This option\u00a0 allows the user to change the colors of the text and background of cells in the design matrix<\/a>.\u00a0 That is, 3 types of cells are distinguished in the design matrix: those containing zeros, those containing ones, and those containing other values.\u00a0 This option allows you to change these colors to suit your individual tastes.\u00a0 See Design Matrix Colors<\/a> for more information.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

Contents – Index Set Preferences Various options to set preferences for Program MARK are available from the File | Preferences menu choice.\u00a0\u00a0 Display BIC instead of AICc in Results Browser This option uses the BIC (or QBIC) model selection method …<\/p>\n

Set Preferences<\/span> Read More »<\/a><\/p>\n","protected":false},"author":117,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-341","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/341","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/users\/117"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/comments?post=341"}],"version-history":[{"count":1,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/341\/revisions"}],"predecessor-version":[{"id":342,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/341\/revisions\/342"}],"wp:attachment":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/media?parent=341"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}