{"id":251,"date":"2017-04-18T03:26:29","date_gmt":"2017-04-18T03:26:29","guid":{"rendered":"http:\/\/sites.warnercnr.colostate.edu\/gwhite\/?page_id=251"},"modified":"2017-04-18T03:26:29","modified_gmt":"2017-04-18T03:26:29","slug":"nest-survival","status":"publish","type":"page","link":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/nest-survival\/","title":{"rendered":"Nest Survival"},"content":{"rendered":"

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

\n

Nest Survival<\/b><\/span> <\/p>\n

The nest survival data type is a slightly different model than the Known Fate<\/a> data type included in MARK.\u00a0 The input data in the encounter histories file is specified with the Nest Survival Group=1 statement.\u00a0 Following this command are the data on the nests for this group.\u00a0 For each nest record, 5 values must be given.\u00a0 First is the day the nest(s) was\/were found, labelled time i<\/i>.\u00a0 Next is the last day the nest(s) was\/were known to be present, labelled time j<\/i>, which for successful nests should be the day the nest hatched.\u00a0 Then comes the last day that a nest(s) was checked or should have hatched, labelled time k<\/i>, which for successful nests should be the day the nest hatched.\u00a0 However, for successful nests, all the information about survival is contained in times i<\/i> and j<\/i>.\u00a0 Time k<\/i> is only used for unsuccessful nests to bracket the interval when the nest was destroyed.\u00a0 The fourth variable is the fate of the nest(s): 0 means successful, and 1 means destroyed or unsuccessful.\u00a0 The last (fifth) value is the number (frequency) of nests that had this history.Individual covariates<\/a> are allowed after these 5 required variables.\u00a0 The following is an example input file for nest success data with 2 groups and 63 occasions, where one individual covariate (age of nest at time the nest was found) is included:<\/span><\/p>\n

Nest survival group=1;<\/span>
\n\/*GGOO, 1995-076*\/\u00a0 53 59 63 1\u00a0 1\u00a0 4;<\/span>
\n\/*OGDD, 1995-047*\/\u00a0 18 36 36 0\u00a0 1 11;<\/span>
\n\/*WGDD, 1995-003*\/\u00a0 1 20 20 0\u00a0 1 15;<\/span>
\n\/*OGDD, 1995-027*\/\u00a0 14 26 26 0\u00a0 1 17;<\/span>
\n\/*OGDY, 1995-032*\/\u00a0 14 24 24 0\u00a0 1 19;<\/span>
\n\/*OGYW, 1995-051*\/\u00a0 23 30 30 0\u00a0 1 22;<\/span>
\n\/*WGYY, 1995-054*\/\u00a0 25 31 31 0\u00a0 1 23;<\/span>
\n\/*WGOO, 1995-068*\/\u00a0 39 40 40 0\u00a0 1 28;<\/span>
\n\/*WGOB, 1995-069*\/\u00a0 39 40 40 0\u00a0 1 28;<\/span>
\n\/*YGDY, 1995-049*\/\u00a0\u00a0 22 23 23 0\u00a0 1 29;<\/span>
\nNest survival group=2;<\/span>
\n\/*WGYB, 1995-014*\/\u00a0 11 37 37 0\u00a0 1\u00a0 3;<\/span>
\n\/*GGDD, 1995-018*\/\u00a0 12 38 38 0\u00a0 1\u00a0 3;<\/span>
\n\/*OGOO, 1995-055*\/\u00a0 26 49 49 0\u00a0 1\u00a0 4;<\/span>
\n\/*YGDB, 1995-007*\/\u00a0\u00a0 10 34 34 0\u00a0 1\u00a0 5;<\/span>
\n\/*WGYG, 1995-044*\/\u00a0 17 37 37 0\u00a0 1\u00a0 9;<\/span>
\n\/*OGDG, 1995-004*\/\u00a0 6 25 25 0\u00a0 1 10;<\/span>
\n\/*WGYD, 1995-045*\/\u00a0 17 34 34 0\u00a0 1 12;<\/span>
\n\/*WGOG, 1995-062*\/\u00a0 30 30 36 1\u00a0 1 12;<\/span>
\n\/*WGDB, 1995-020*\/\u00a0 13 25 25 0\u00a0 1 17;<\/span>
\n\/*YGBB, 1995-074*\/\u00a0\u00a0 44 55 55 0\u00a0 1 18;<\/span>
\n\/*WGGW, 1995-078*\/\u00a0 58 58 61 1\u00a0 1 18;<\/span>
\n\/*YGDD, 1995-038*\/\u00a0\u00a0 16 26 26 0\u00a0 1 19;<\/span>
\n\/*YGWY, 1995-072*\/\u00a0 43 46 46 0\u00a0 1 26;<\/span><\/p>\n

The first nest for group 1 was found on day i<\/i> = 53, checked and found still present on day j<\/i> = 59, and found destroyed on day k<\/i> = 63.\u00a0 The last variable (an individual covariate) in this example is the age of the nest at the time it was first found — 4 days old for the first nest.\u00a0 The second nest for group 1 was found on day i<\/i> = 18, and found to successfully hatched on day j<\/i> = 36.\u00a0 The age of this nest was 11 days when it was found on day 18.<\/span><\/p>\n

The number of occasions for the nest survival model is the total number of days that nests are checked, with the first nest checked on day 1.\u00a0 Thus, if the last day a nest is checked is 70, then the number of occasions would be 70.<\/span><\/p>\n

For successful nests, i.e., fate=0, the last time seen alive (j<\/i>) and the last time (k<\/i>) should always be the same and equal to the day the nest hatched.\u00a0 For unsuccessful nests, fate>0, j<\/i> < k.<\/i>\u00a0 In MARK, the cell probability is modeled as the product of the survival rates from time i<\/i> to time j<\/i>-1.\u00a0 For successful nests, time k<\/i> is ignored.\u00a0 For situations where the date of hatch is not known exactly, none of the times should exceed the potential hatch date, because the nest should not be considered at risk of failure when it has already hatched.\u00a0 For unsuccessful nests, the cell probability for the nest is taken as the product of the survival rates from time i<\/i> to time j<\/i>-1, times 1 minus the product of survival from j<\/i> to k<\/i>-1.<\/span><\/p>\n

The following series of examples for 5 occasions will clarify how to code nest survival data with the triplet i<\/i>, j<\/i>, and k<\/i>.<\/span><\/p>\n

i<\/i> = 1\u00a0\u00a0 j<\/i> = 3\u00a0 k<\/i> = 5\u00a0\u00a0 fate = 1\u00a0\u00a0 gives 1010100001, with cell probability S(1)S(2)[1 – S(3)S(4)].<\/span><\/p>\n

i<\/i> = 1\u00a0\u00a0 j<\/i> = 3\u00a0 k<\/i> = 3\u00a0\u00a0 fate = 0\u00a0\u00a0 gives 1010100000, with cell probability S(1)S(2).<\/span><\/p>\n

i<\/i> = 1\u00a0\u00a0 j<\/i> = 3\u00a0 k<\/i> = 3\u00a0\u00a0 fate = 1\u00a0\u00a0 is invalid because the nest was observed both present and destroyed on day 3.<\/span><\/p>\n

i<\/i> = 1\u00a0\u00a0 j<\/i> = 1\u00a0 k<\/i> = 3\u00a0\u00a0 fate = 1\u00a0\u00a0 is gives 1000010000, with cell probability 1 – S(1)S(2).<\/span><\/p>\n

i<\/i> = 1\u00a0\u00a0 j<\/i> = 1\u00a0 k<\/i> = 3\u00a0\u00a0 fate = 0\u00a0\u00a0 is invalid because the nest was observed present only on day i<\/i> = 1.\u00a0 If the nest was still present on day 3, then j<\/i> should have been coded as j<\/i> = 3.<\/span><\/p>\n

i<\/i> = 1\u00a0\u00a0 j<\/i> = 3\u00a0 k<\/i> = 5\u00a0\u00a0 fate = 0\u00a0 is partially invalid because the nest was observed for the interval 1 to 5, when the nest was successful, but the coding shown will only use the data from 1 to 3, giving 1000100000, with cell probability S(1)S(2).\u00a0 For fate = 0, j<\/i> = k<\/i>.<\/span><\/p>\n

i<\/i> = 3\u00a0\u00a0 j<\/i> = 3\u00a0 k<\/i> = 3\u00a0\u00a0 fate = 0 or 1 is invalid because the nest was not observed over an interval for either fate.<\/span><\/p>\n

The key difference between Known Fate and Nest Survival data types is that with nest survival data, we don’t know exactly what day the nest was destroyed for cases where the nest was unsuccessful.\u00a0 Thus, consider the cell probability for the first nest described above.\u00a0 The cell probability would look like:<\/span>
\nS(53) S(54) S(55) S(56) S(57) S(58) [1 – S(59) S(60) S(61) S(62)] .<\/span>
\nThe first portion of the expression models the survival of the nest from day i<\/i> = 53 to day j<\/i> = 59.\u00a0 The second portion of the expression, in brackets, models the failure of the nest during the interval from day j<\/i> = 59 to day k<\/i> = 63.\u00a0 That is, had the nest been successful during this interval, the probability would have been\u00a0 S(59) S(60) S(61) S(62).\u00a0 Because the nest was destroyed at some time during that interval, this quantity is substracted from 1.\u00a0 The encounter history for this example would consist of 52 pairs of ’00’, followed by the following string with blanks inserted to delimit occasions denoted on the second line:<\/span>
\n10 00 00 00 00 00 10 00 00 01\u00a0<\/span>
\n53 54 55 56 57 58 59 60 61 62<\/span><\/p>\n

Effective Sample Size<\/b><\/span><\/p>\n

The effective sample size for AICc<\/a> is computed somewhat differently for the nest survival model than other models in MARK.\u00a0 Typically, each binomial trial in a model provides one degree of freedom.\u00a0 For the nest survival model, each day that the nest is known to survive contributes 1 degree of freedom because each day is a binomial trial where the result is known.\u00a0 However, the interval in which a nest fails only contributes 1 degree of freedom also, because the exact day of failure is not known, but only that the nest failed during the interval.\u00a0 Thus, a record like<\/span><\/p>\n

\/*YGBB, 1995-074*\/\u00a0\u00a0 44 55 55 0\u00a0 1 18;<\/span><\/p>\n

contributes 10 degrees of freedom, because there are 10 binomial trials where the nest was known to succeed.\u00a0 However, the following record only contributes a single degree of freedom, because the nest failed somewhere in the interval 58-61.<\/span><\/p>\n

\/*WGGW, 1995-078*\/\u00a0 58 58 61 1\u00a0 1 18;<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

Contents – Index Nest Survival  The nest survival data type is a slightly different model than the Known Fate data type included in MARK.\u00a0 The input data in the encounter histories file is specified with the Nest Survival Group=1 statement.\u00a0 …<\/p>\n

Nest Survival<\/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-251","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/251","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=251"}],"version-history":[{"count":1,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/251\/revisions"}],"predecessor-version":[{"id":252,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/251\/revisions\/252"}],"wp:attachment":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/media?parent=251"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}