# Calculate psi (transition probabilities between sites in two phases of the annual cycle) Provides simple maximum-likelihood point estimate of transition probabilities that does not include measures of uncertainty. Incorporates detection heterogeneity where appropriate (band/ring return data), but not location uncertainty. Shared primarily for testing; use of `estTransition` is recommended instead. ```r calcTransition( banded = NULL, reencountered = NULL, counts = NULL, originAssignment = NULL, targetAssignment = NULL, originNames = NULL, targetNames = NULL, method = "SANN" ) calcPsi( banded = NULL, reencountered = NULL, counts = NULL, originAssignment = NULL, targetAssignment = NULL, originNames = NULL, targetNames = NULL, method = "SANN" ) ``` ## Arguments - `banded`: For band return data, a vector of the number of released animals from each origin site (including those never reencountered in a target region) - `reencountered`: For band return data, a matrix with B rows and W columns. Number of animals reencountered on each target site by origin site they came from - `counts`: Migration data without target-region detection heterogeneity (i.e., anything but band return data) can be entered one of two ways: either here or with `originAssignment` and `targetAssignment`. If here, a matrix with B rows and W columns with counts of animals observed in each combination of origin and target site - `originAssignment`: Assignment of animals (not including band return data) to origin season sites. A vector of integers (1-B) with length number of animals tracked. Note that these data can either be entered using this argument and `targetAssignment` or using `counts`, but not both - `targetAssignment`: Assignment of animals (not including band return data) to target season sites. A vector of integers (1-W) with length number of animals tracked. Note that these data can either be entered using this argument and `originAssignment` or using `counts`, but not both - `originNames`: Optional, but recommended to keep track. Vector of names for the origin sites. If not provided, the function will either try to get these from another input or provide default names (capital letters) - `targetNames`: Optional, but recommended to keep track. Vector of names for the target sites. If not provided, the function will either try to get these from another input or provide default names (numbers) - `method`: See `optim`. "SANN" is slow but reasonably accurate. "Nelder-Mead" is fast but not accurate here. "BFGS" is also fast but not very stable here ## Returns `calcTransition` returns a list with the element(s): - **`psi`**: Matrix with point estimate of transition probabilities - **`r`**: Vector containing point estimate of reencounter probabilities at each target site. Not included unless data includes band reencounters ## Examples ```r nOriginSites <- 4 nTargetSites <- 4 originNames <- LETTERS[1:nOriginSites] targetNames <- 1:nTargetSites psiTrue <- array(c(0.1, 0.2, 0.3, 0.4, 0.2, 0.3, 0.4, 0.1, 0.3, 0.4, 0.1, 0.2, 0.4, 0.1, 0.2, 0.3), c(nOriginSites, nTargetSites), dimnames = list(originNames, targetNames)) rowSums(psiTrue) rTrue <- c(0.5, 0.05, 0.3, 0.6) banded1 <- c(500, 1000, 2000, 3000) reencountered1 <- simCMRData(psiTrue, banded1, rTrue)$reencountered psi_r_calc_sloppy <- calcTransition(banded = banded1, reencountered = reencountered1, originNames = originNames, targetNames = targetNames, method = "BFGS") psi_r_calc_sloppy psi_r_calc <- calcTransition(banded = banded1, reencountered = reencountered1, originNames = originNames, targetNames = targetNames, method = "SANN") psi_r_calc psi_r_mcmc <- estTransition(banded = banded1, reencountered = reencountered1, originNames = originNames, targetNames = targetNames, method = "MCMC", nSamples = 45000, nBurnin = 5000, #reduced for example speed nThin = 1, verbose = 0) print(psi_r_mcmc) psi_r_boot <- estTransition(banded = banded1, reencountered = reencountered1, originNames = originNames, targetNames = targetNames, method = "bootstrap", nSamples = 200) #reduced for example speed print(psi_r_boot) ``` ## See Also `estTransition`, `optim`

calcTransition function