{"id":178,"date":"2017-04-18T02:28:32","date_gmt":"2017-04-18T02:28:32","guid":{"rendered":"http:\/\/sites.warnercnr.colostate.edu\/gwhite\/?page_id=178"},"modified":"2017-04-18T02:45:42","modified_gmt":"2017-04-18T02:45:42","slug":"overview","status":"publish","type":"page","link":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/overview\/","title":{"rendered":"Overview"},"content":{"rendered":"

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

\n

Overview<\/b><\/span><\/p>\n

Motivation<\/u>\u00a0<\/span><\/p>\n

The motivation for developing Program MARK was to bring a common interface to the estimation of survival from marked animals.\u00a0 Marked animals can be re-encountered as either alive or dead, in a variety of experimental frameworks.\u00a0 Prior to MARK, no program combined the estimation of survival from both live and dead re-encounters.<\/span><\/p>\n

Capabilities<\/u><\/span><\/p>\n

Program MARK provides survival estimates from marked animals when they are re-encountered at a later time.\u00a0 The time intervals between re-encounters do not have to be equal.\u00a0 If not specified by the user, these time intervals are assumed to be 1.\u00a0 More than one group of animals can be modeled, e.g., treatment and control animals.\u00a0 The re-encounters can be from dead recoveries (e.g., the animal is harvested), from live recaptures (e.g. the animal is re-trapped), or from radio-tracking.\u00a0 See Model Structure<\/a> for more detail.<\/span><\/p>\n

The basic input to Program MARK is the encounter history for each animal.\u00a0 The user can use a summarized form of the encounter histories when multiple animals have the same history.\u00a0 See Encounter Histories File<\/a> for more details of how encounter histories are formatted for use by MARK.<\/span><\/p>\n

In addition to providing the survival estimates, these estimates can be developed as part of a model.\u00a0 That is, an underlying model is built that predicts the survival estimates.\u00a0 Parameters can be constrained to be the same across re-encounter occasions, or by age, or by group, using the parameter index matrix, or PIM.\u00a0 See Parameter Matrices<\/a> for more detail.\u00a0 A set of common models for screening data initially are provided, with time effects, group effects, time*group effects, and a null model of none of the above provided for each parameter, with all possible combinations across all parameters.\u00a0 See Pre-Defined Models<\/a> for more details.<\/span><\/p>\n

The model can include covariates, specific to the individual animal or to the re-encounter occasion.\u00a0 Examples are the weight of the animal at the time of marking, or the average temperature over the survival interval.\u00a0 See Design Matrix<\/a> for more detail.\u00a0 Besides the logit link function, other link functions<\/a> include the log-log, complementary log-log, sin, log, and identity.<\/span><\/p>\n

Program MARK computes the estimates of model parameters via numerical maximum likelihood techniques.\u00a0 The FORTRAN program that does this computation also determines numerically the number of parameters that are identifiable in the model, and reports its guess of one parameter that is not identifiable.\u00a0 The number of estimable parameters is used to compute the QAICc<\/a> for the model.<\/span><\/p>\n

Outputs for various models that the user has built are stored in a database, known as the Results Database<\/a>.\u00a0 The input data are also stored in this database, making it a complete description of the model building process.\u00a0 The database is viewed in a Results Browser<\/a> window.<\/span><\/p>\n

Summaries available from the Results Browser<\/a> window include viewing and printing model output (estimates,\u00a0 standard errors, and goodness-of-fit tests), deviance residuals from the model (including graphics and point and click capability to view the encounter history responsible for a particular residual), likelihood ratio and ANODEV between models, and adjustments for over dispersion.<\/span><\/p>\n

Windows Interface<\/u><\/span><\/p>\n

These capabilities are implemented in a Microsoft Windows style interface.\u00a0 Thus, most PC users are familiar with the operation of such programs, and find navigation reasonably easy.\u00a0 Windows can be closed by clicking\u00a0 on the window’s close button, and generally manipulated using standard Window’s conventions.\u00a0 Context-sensitive help screens are available with Help click buttons and the F1 key.\u00a0 The Shift-F1 key can also be used to investigate the function of a particular control or menu item.\u00a0 Help screens include hypertext links to other help screens, with the intent to provide all the necessary program documentation on-line with Help screens.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

Contents – Index Overview Motivation\u00a0 The motivation for developing Program MARK was to bring a common interface to the estimation of survival from marked animals.\u00a0 Marked animals can be re-encountered as either alive or dead, in a variety of experimental …<\/p>\n

Overview<\/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-178","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/178","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=178"}],"version-history":[{"count":11,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/178\/revisions"}],"predecessor-version":[{"id":212,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/178\/revisions\/212"}],"wp:attachment":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/media?parent=178"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}