t_index_calculation: Calculates time-dependent index when nodes weights or...

In riverconn: Fragmentation and Connectivity Indices for Riverscapes

Calculates time-dependent index when nodes weights or barriers passability are changing

Description

Calculates time-dependent index when nodes weights or barriers passability are changing

Usage

t_index_calculation(
  graph = graph,
  ...,
  barriers_metadata,
  id_barrier = "id_barrier",
  year = "year",
  pass_u = "pass_u",
  pass_d = "pass_d",
  weights_metadata,
  weight = "length",
  nodes_id = "name",
  parallel = TRUE,
  ncores
)

Arguments

graph	an object of class igraph. Can be both directed or undirected.
...	other arguments passed to the function index_calculation
barriers_metadata	data.frame that must contain a column having the same name as the 'id_barrier' attribute of the graph, and two columns with the corresponding upstream and downstream improved passabilities (see pass_u and pass_d), and a column with the year passability was changed. This data frame can be obtained from easily-formatted data with the function t_passability_sequencer.
id_barrier	graph edges attribute used to label barriers. Default is "id_barrier". It should be present in the 'barriers metadata' input as well.
year	field of the 'barriers metadata' where temporal information on the changes in passability is stored.
pass_u	field of the 'barriers metadata' where temporal-dependent upstream passability is stored.
pass_d	field of the 'barriers metadata' where temporal-dependent downstream passability is stored.
weights_metadata	data.frame that must contain a column having the same name as the 'nodes_id' attribute of the graph, a column with he corresponding weight information (see 'weight' parameter), and a column with the year weight was changed. This data frame can be obtained from easily-formatted data with the function t_weight_sequencer.
weight	param weight graph vertex attribute used to assign weights to the reaches (nodes). Default is "length".
nodes_id	graph vertex attribute used to uniquely label reaches (nodes). Default is "name".
parallel	logical value to flag if parallel option is to be used.
ncores	define how many cores are used in parallel processing. Active only when parallel = TRUE

Value

a data.frame with a 'year' field and related connectivity index. If index_type = "reach", the data.frame is organized by 'year' and 'name'.

References

Baldan, D., Cunillera-Montcusí, D., Funk, A., & Hein, T. (2022). Introducing ‘riverconn’: an R package to assess river connectivity indices. Environmental Modelling & Software, 156, 105470.

Examples

library(igraph)
g <- igraph::graph_from_literal(1-+2, 2-+4, 3-+2, 4-+6, 6-+5)
E(g)$id_barrier <- c(NA, NA, "1", NA, NA)
E(g)$type <- ifelse(is.na(E(g)$id_barrier), "joint", "dam")
V(g)$length <- c(1, 1, 2, 3, 4,5)
V(g)$Id <- V(g)$name
E(g)$pass_u <- E(g)$pass_d <- ifelse(!is.na(E(g)$id_barrier),0.1,NA)
barriers_data <- data.frame("id_barrier" = c("1"),
   "year_c" = 2000, "pass_c_u" = 0.1, "pass_c_d" = 0.4)
seq_ops <- c("c")
barriers_metadata <- t_passability_sequencer(barriers_data, seq_ops)
weights_dataframe <- data.frame("name" = seq(1,6) %>% as.character,
    "length_1999" = c(1, 1, 2, 3, 4,5))
weights_metadata <- t_weights_sequencer(weights_dataframe, weight = "length")
t_index <- t_index_calculation(g, barriers_metadata = barriers_metadata,
 weights_metadata = weights_metadata, weight = "length", parallel = FALSE, B_ij_flag = FALSE)

riverconn documentation built on May 31, 2023, 8:02 p.m.