context("Survival")

for(test in testlist) {
  # Create the samc object
  samc_obj <- test$samc

  # Extract Q
  Q <- samc_obj$q_matrix
  Q <- as.matrix(Q)

  # Create an indentity matrix
  I <- diag(nrow(Q))

  # Fundamental matrix
  F_mat <- solve(I - Q)

  # Prepare the occupancy data
  occ_ras <- raster::raster(test$init)
  pv <- as.vector(occ_ras)
  pv <- pv[is.finite(pv)]


  # Run the tests
  test_that("Testing survival(samc)", {

    r1 <- survival(samc_obj)

    v1 <- numeric(nrow(Q))
    v1[] <- 1

    r2 <- F_mat %*% v1

    # Verify equality
    expect_equal(as.vector(r1), as.vector(r2))
  })

  test_that("Testing survival(samc, init)", {
    # Calculate psi*z using survival(samc, init)
    r1 <- survival(samc_obj, test$init)

    v1 <- numeric(nrow(Q))
    v1[] <- 1

    r2 <- pv %*% F_mat %*% v1

    # Verify equality
    expect_equal(as.vector(r1), as.vector(r2))
  })
}