tests/testthat/helper-matrices.R

In jonesor/Rage: Life History Metrics from Matrix Population Models

# regular matrices
mat_u <- rbind(
  c(0.1, 0, 0, 0),
  c(0.5, 0.2, 0.1, 0),
  c(0, 0.3, 0.3, 0.1),
  c(0, 0, 0.5, 0.6)
)

mat_f <- rbind(
  c(0, 0, 1.1, 1.6),
  c(0, 0, 0.8, 0.4),
  c(0, 0, 0, 0),
  c(0, 0, 0, 0)
)

mat_c <- rbind(
  c(0, 0, 0.4, 0.4),
  c(0, 0, 0.1, 0.6),
  c(0, 0, 0, 0),
  c(0, 0, 0, 0)
)


# matrices with na
mat_u_na <- rbind(
  c(0.1, 0, 0, 0),
  c(0.5, 0.2, 0.1, 0),
  c(0, 0.3, NA, 0.1),
  c(0, 0, 0.5, 0.6)
)

mat_f_na <- rbind(
  c(0, 0, 1.1, 1.6),
  c(NA, 0, 0.8, 0.4),
  c(0, 0, 0, 0),
  c(0, 0, 0, 0)
)

mat_c_na <- rbind(
  c(0, 0, 0.4, 0.4),
  c(0, 0, 0.1, 0.6),
  c(0, 0, 0, 0),
  c(0, NA, 0, 0)
)

# zero matrices
mat_u_zero <- matrix(0, nrow = 4, ncol = 4)
mat_f_zero <- matrix(0, nrow = 4, ncol = 4)
mat_c_zero <- matrix(0, nrow = 4, ncol = 4)

# singular matU
mat_u_singular <- rbind(
  c(0.1, 0, 0, 0),
  c(0.5, 0.2, 0, 0),
  c(0, 0.3, 0.5, 0.4),
  c(0, 0, 0.5, 0.6)
)

# survivalIssue matU
mat_u_survissue <- rbind(
  c(0.1, 0, 0, 0),
  c(0.5, 0.2, 0.1, 0),
  c(0, 0.3, 0.3, 0.1),
  c(0, 0, 0.7, 0.6)
)


# inter-reproductive stage
mat_u_inter <- rbind(
  c(0.1, 0, 0, 0, 0),
  c(0.5, 0.2, 0.1, 0, 0),
  c(0, 0.3, 0.3, 0.1, 0),
  c(0, 0, 0.4, 0.4, 0.1),
  c(0, 0, 0, 0.1, 0.4)
)

mat_f_inter <- rbind(
  c(0, 1.1, 0, 1.6, 0),
  c(0, 0.8, 0, 0.4, 0),
  c(0, 0, 0, 0, 0),
  c(0, 0, 0, 0, 0),
  c(0, 0, 0, 0, 0)
)


# age-based mpm
mat_u_age <- rbind(
  c(0, 0, 0, 0),
  c(0.8, 0, 0, 0),
  c(0, 0.7, 0, 0),
  c(0, 0, 0.6, 0)
)

mat_f_age <- rbind(
  c(0, 0, 1.1, 1.6),
  c(0, 0, 0, 0),
  c(0, 0, 0, 0),
  c(0, 0, 0, 0)
)


# non-square
mat_u_notsq <- rbind(
  c(0.1, 0, 0, 0),
  c(0.5, 0.2, 0.1, 0),
  c(0, 0.3, 0.3, 0.1),
  c(0, 0, 0.5, 0.6),
  c(0, 0, 0, 0.1)
)

mat_f_notsq <- rbind(
  c(0, 0, 1.1, 1.6),
  c(0, 0, 0.8, 0.4),
  c(0, 0, 0, 0),
  c(0, 0, 0, 0),
  c(0, 0, 0, 0)
)


# all stages reproductive
mat_u_allrep <- rbind(
  c(0.1, 0.0),
  c(0.4, 0.5)
)

mat_f_allrep <- rbind(
  c(0.7, 1.6),
  c(0, 0)
)

# matrices with properly named life stages
mat_u_named <- `dimnames<-`(mat_u, list(
  c("sm", "md", "lg", "xl"),
  c("sm", "md", "lg", "xl")
))

mat_f_named <- `dimnames<-`(mat_f, list(
  c("sm", "md", "lg", "xl"),
  c("sm", "md", "lg", "xl")
))

# matrices with improperly named life stages
mat_u_named_mismatch <- `colnames<-`(mat_u_named, rev(colnames(mat_u_named)))

mat_u_named_partial <- `rownames<-`(mat_u_named, NULL)