{"id":280,"date":"2017-04-18T03:43:30","date_gmt":"2017-04-18T03:43:30","guid":{"rendered":"http:\/\/sites.warnercnr.colostate.edu\/gwhite\/?page_id=280"},"modified":"2017-04-18T03:43:30","modified_gmt":"2017-04-18T03:43:30","slug":"occupancy-estimation-multiple-states-single-season","status":"publish","type":"page","link":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/occupancy-estimation-multiple-states-single-season\/","title":{"rendered":"Occupancy Estimation Multiple States Single Season"},"content":{"rendered":"

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

\n

Occupancy Estimation Multiple States Single Season<\/b><\/span><\/p>\n

Estimation of occupancy rates<\/a> generally assume that a site or plot is occupied or not occupied.\u00a0 This model extends this concept to not occupied, and 2 levels of occupancy.\u00a0 For example, a plot may be occupied by a pair of adults that either reproduce, or do not reproduce.\u00a0 Given that the occupancy states are hierarchial, a “1” is coded for the lower level of occupancy (e.g., adults, but no young), and a “2” is coded for the higher level of occupancy (adults plus young).\u00a0 Nichols et al. (2007)<\/a> developed this model with an example of California spotted owls (Strix occidentalis occidentalis<\/i>) where sites were occupied by 1 or more adults, and or occupied by both adults and young.\u00a0 I will use their example to explain the 5 parameters of this model.<\/span><\/p>\n

The real parameters<\/a> of this model are:<\/span><\/p>\n

psi1(i<\/i>) = probability that a site i<\/i> is occupied regardless of reproductive state, Pr(true state = 1 or 2);<\/span><\/p>\n

psi2(i<\/i>) = probability that young occurred, given that the site i<\/i> is occupied, Pr(true state = 2 | true state = 1 or 2);<\/span><\/p>\n

p<\/i>1(i, t<\/i>) = probability that occupancy is detected for site i<\/i>, period t<\/i>, given that true state = 1, Pr(detection | true state = 1);<\/span><\/p>\n

p<\/i>2(i, t<\/i>) = probability that occupancy is detected for site i<\/i>, period t<\/i>, given that true state = 2, Pr(detection | true state = 2);<\/span><\/p>\n

delta(i, t<\/i>) = probability that evidence of successful reproduction is found, given detection of occupancy at site i<\/i>, period t<\/i>, with successful reproduction, Pr(classified state 2|true state = 2).<\/span><\/p>\n

Thus, psi1 and psi2 are single parameters relating to a site, whereas p<\/i>1, p<\/i>2, and delta are time-specific parameters, and thus the number of values in the PIM<\/a> for each of these parameters equals the number of occasions.<\/span><\/p>\n

The product psi1*psi2 is the unconditional probability that a site is occupied by successful breeders, and is provided as a derived parameter<\/a> in MARK.<\/span><\/p>\n

The encounter histories file<\/a> for this data type consists of only the L columns, and the example from Nichols et al. (2007) is shown here.<\/span><\/p>\n

\/* occasions=5, groups=1 *\/<\/span>
\n1.221\u00a0 1;\u00a0\u00a0<\/span>
\n011..\u00a0 1;\u00a0\u00a0<\/span>
\n1.1..\u00a0 2;\u00a0\u00a0<\/span>
\n.1212\u00a0 1;\u00a0\u00a0<\/span>
\n1111.\u00a0 1;\u00a0\u00a0<\/span>
\n1022.\u00a0 1;\u00a0\u00a0<\/span>
\n111.1\u00a0 1;\u00a0\u00a0<\/span>
\n0.20.\u00a0 1;\u00a0\u00a0<\/span>
\n11100\u00a0 1;\u00a0\u00a0<\/span>
\n.11..\u00a0 1;\u00a0\u00a0<\/span>
\n.011.\u00a0 1;\u00a0\u00a0<\/span>
\n0110.\u00a0 1;\u00a0\u00a0<\/span>
\n11111\u00a0 3;\u00a0\u00a0<\/span>
\n.0.11\u00a0 1;\u00a0\u00a0<\/span>
\n1100.\u00a0 1;\u00a0\u00a0<\/span>
\n101..\u00a0 1;\u00a0\u00a0<\/span>
\n…0.\u00a0 2;\u00a0\u00a0<\/span>
\n.111.\u00a0 2;\u00a0\u00a0<\/span>
\n0.0.0\u00a0 1;\u00a0\u00a0<\/span>
\n0.210\u00a0 1;\u00a0\u00a0<\/span>
\n01110\u00a0 1;\u00a0\u00a0<\/span>
\n0.0.1\u00a0 1;\u00a0\u00a0<\/span>
\n…1.\u00a0 2;\u00a0\u00a0<\/span>
\n0….\u00a0 3;\u00a0\u00a0<\/span>
\n1.2..\u00a0 3;\u00a0\u00a0<\/span>
\n.1101\u00a0 1;\u00a0\u00a0<\/span>
\n.12..\u00a0 2;\u00a0\u00a0<\/span>
\n1122.\u00a0 3;\u00a0\u00a0<\/span>
\n0120.\u00a0 1;\u00a0\u00a0<\/span>
\n.1111\u00a0 1;\u00a0\u00a0<\/span>
\n11202\u00a0 1;\u00a0\u00a0<\/span>
\n11220\u00a0 1;\u00a0\u00a0<\/span>
\n10110\u00a0 1;\u00a0\u00a0<\/span>
\n.10..\u00a0 1;\u00a0\u00a0<\/span>
\n1.200\u00a0 1;\u00a0\u00a0<\/span>
\n00…\u00a0 1;\u00a0\u00a0<\/span>
\n0122.\u00a0 2;\u00a0\u00a0<\/span>
\n0.11.\u00a0 1;\u00a0\u00a0<\/span>
\n0.100\u00a0 1;<\/span>
\n0..11\u00a0 1;<\/span>
\n\u00a0\u00a0<\/span>
\nNotice that “.” are used to indicate that a site was not surveyed on a particular occasion, and “0”, “1” and “2” indicate the level of occupancy detected.<\/span><\/p>\n

To accommodate this data type’s use of “2”, the other occupancy models<\/a>, including the Royle\/Nichols occupancy models<\/a>, treat the “2” encounter code as a “1”, and do not distinguish between them as does this data type.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

Contents – Index Occupancy Estimation Multiple States Single Season Estimation of occupancy rates generally assume that a site or plot is occupied or not occupied.\u00a0 This model extends this concept to not occupied, and 2 levels of occupancy.\u00a0 For example, …<\/p>\n

Occupancy Estimation Multiple States Single Season<\/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-280","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/280","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=280"}],"version-history":[{"count":1,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/280\/revisions"}],"predecessor-version":[{"id":281,"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/pages\/280\/revisions\/281"}],"wp:attachment":[{"href":"https:\/\/sites.warnercnr.colostate.edu\/gwhite\/wp-json\/wp\/v2\/media?parent=280"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}