Calculate the mean number of steps to first passage

cond_passage(samc, origin, dest) # S4 method for samc,missing,location cond_passage(samc, dest) # S4 method for samc,location,location cond_passage(samc, origin, dest)

samc | A |
---|---|

origin | A positive integer or character name representing transient state
\(\mathit{i}\). Corresponds to row \(\mathit{i}\) of matrix \(\mathbf{P}\)
in the |

dest | A positive integer or character name representing transient state
\(\mathit{j}\). Corresponds to column \(\mathit{j}\) of matrix \(\mathbf{P}\)
in the |

See Details

\(\tilde{t}=\tilde{B}_j^{-1}\tilde{F}\tilde{B}_j{\cdot}1\)

**cond_passage(samc, dest)**The result is a vector where each element corresponds to a cell in the landscape, and can be mapped back to the landscape using the

`map`

function. Element*i*is the mean number of steps before absorption starting from location*i*conditional on absorption into*j*Note that mathematically, the formula actually does not return a value for when

*i*is equal to*j*. This leads to a situation where the resultant vector is actually one element short and the index for some of the elements may be shifted. The**cond_passage()**function fills inserts a`0`

value for vector indices corresponding to*i == j*. This corrects the final result so that vector indices work as expected, and allows the vector to be properly used in the`map`

function.**cond_passage(samc, origin, dest)**The result is a numeric value representing the mean number of steps before absorption starting from a given origin conditional on absorption into

*j*.As described above, mathematically the formula does not return a result for when the

`origin`

and`dest`

inputs are equal, so the function simply returns a`0`

in this case.

**WARNING**: This function is not compatible when used with data where there
are states with total absorption present. When present, states representing
total absorption leads to unsolvable linear equations. The only exception to this
is when there is a single total absorption state that corresponds to input to
the `dest`

parameter. In this case, the total absorption is effectively
ignored when the linear equations are solved.

**WARNING**: This function will crash when used with data representing
a disconnected graph. This includes, for example, isolated pixels or islands
in raster data. This is a result of the transition matrix for disconnected
graphs leading to some equations being unsolvable. Different options
are being explored for how to best identify these situations in data and
handle them accordingly.

Any relevant performance information about this function can be found in the
performance vignette: `vignette("performance", package = "samc")`

# "Load" the data. In this case we are using data built into the package. # In practice, users will likely load raster data using the raster() function # from the raster package. res_data <- samc::ex_res_data abs_data <- samc::ex_abs_data occ_data <- samc::ex_occ_data # Make sure our data meets the basic input requirements of the package using # the check() function. check(res_data, abs_data)#> [1] TRUE#> [1] TRUE# Setup the details for our transition function tr <- list(fun = function(x) 1/mean(x), # Function for calculating transition probabilities dir = 8, # Directions of the transitions. Either 4 or 8. sym = TRUE) # Is the function symmetric? # Create a `samc-class` object with the resistance and absorption data using # the samc() function. We use the recipricol of the arithmetic mean for # calculating the transition matrix. Note, the input data here are matrices, # not RasterLayers. samc_obj <- samc(res_data, abs_data, tr_args = tr) # Convert the occupancy data to probability of occurrence occ_prob_data <- occ_data / sum(occ_data, na.rm = TRUE) # Calculate short- and long-term metrics using the analytical functions short_mort <- mortality(samc_obj, occ_prob_data, time = 50) short_dist <- distribution(samc_obj, origin = 3, time = 50) long_disp <- dispersal(samc_obj, occ_prob_data)#> #> Cached diagonal not found. #> Performing setup. This can take several minutes... Complete. #> Calculating matrix inverse diagonal... #> Complete #> Diagonal has been cached. Continuing with metric calculation...visit <- visitation(samc_obj, dest = 4) surv <- survival(samc_obj) # Use the map() function to turn vector results into RasterLayer objects. short_mort_map <- map(samc_obj, short_mort) short_dist_map <- map(samc_obj, short_dist) long_disp_map <- map(samc_obj, long_disp) visit_map <- map(samc_obj, visit) surv_map <- map(samc_obj, surv)