Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

Value

The result of calling rhs(lhs).

Helper function for clustering methods

Description

Helper function for clustering methods

Helper function for calculate distance

Add group names to hclust labels.

Add colors to dendrogram

Usage

cluster(x, c_method, d_method)

distance(x, d_method)

cls_add_group(cls, df, indiv, group, pad = TRUE)

cls_color(cls, df, indiv, group)

Arguments

Value

cluster() returns result of clustering. $clustering_method: c_method $distance_method: d_method

distance() returns distance matrix.

    Inputing cls return a color vector, 
            inputing dend return a dend with color.

Examples

library(dplyr)
df <- 
  tibble::tibble(
  stand = paste0("ST_", c("A", "A", "A", "B", "B", "C", "C", "C", "C")),
species = paste0("sp_", c("a", "e", "d", "e", "b", "e", "d", "b", "a")),
  abundance = c(3, 3, 1, 9, 5, 4, 3, 3, 1))
cls <- 
  df2table(df) %>%
  cluster(c_method = "average", d_method = "bray")
library(ggdendro)
# show standard cluster
ggdendro::ggdendrogram(cls)

# show cluster with group
data(dune, package = "vegan")
data(dune.env, package = "vegan")
cls <- 
  cluster(dune, c_method = "average", d_method = "bray")
df <- tibble::rownames_to_column(dune.env, "stand")
cls <- cls_add_group(cls, df, indiv = "stand", group = "Use")
ggdendro::ggdendrogram(cls)

Calculating diversity

Description

Calculating diversity

Usage

d(x)

h(x, base = exp(1))

Arguments

Value

A numeric vector.

Convert data.frame and table to each other.

Description

Convert data.frame and table to each other.

Usage

df2table(df, st = "stand", sp = "species", ab = "abundance")

table2df(tbl, st = "stand", sp = "species", ab = "abundance")

dist2df(dist)

Arguments

Value

df2table() return table, 
table2df() return data.frame,
dist2df() return data.frame.

Examples

tibble::tibble(
   st = paste0("st_", rep(1:2, times = 2)), 
   sp = paste0("sp_", rep(1:2, each = 2)), 
   ab = runif(4)) %>%
  dplyr::bind_rows(., .) %>%
  print() %>%
  df2table("st", "sp", "ab")

Draw layer construction plot

Description

Draw layer construction plot

Add mid point and bin width of layer heights.

Compute mid point of layer heights.

Compute bin width of layer heights.

Usage

draw_layer_construction(
  df,
  stand = "stand",
  height = "height",
  cover = "cover",
  group = "",
  ...
)

add_mid_p_bin_w(df, height = "height")

mid_point(x)

bin_width(x)

Arguments

Value

draw_layer_construction() returns gg object, add_mid_p_bin_w() returns dataframe including mid_point and bin_width columns. mid_point() and bin_width() return a numeric vector.

Examples

library(dplyr)
n <- 10
height_max <- 20
ly_list    <- c("B", "S", "K")
st_list    <- LETTERS[1]
sp_list    <- letters[1:9]
st_group   <- NULL
sp_group   <- rep(letters[24:26], 3)
cover_list <- 2^(0:4)
df <- gen_example(n = n, use_layer = TRUE,
                  height_max = height_max, ly_list = ly_list,
                  st_list  = st_list,  sp_list  = sp_list,
                  st_group = st_group, sp_group = sp_group,
                  cover_list = cover_list)

# select stand and summarise by sp_group
df %>%
  dplyr::group_by(height, sp_group) %>%
  dplyr::summarise(cover = sum(cover), .groups = "drop") %>%
  draw_layer_construction(group = "sp_group", colour = "white")

Generate vegetation example

Description

Stand, species, and cover are basic. Layer, height, st_group, are sp_group optional.

Usage

gen_example(
  n = 300,
  use_layer = TRUE,
  height_max = 20,
  ly_list = "",
  st_list = LETTERS[1:9],
  sp_list = letters[1:9],
  st_group = NULL,
  sp_group = NULL,
  cover_list = 2^(0:6)
)

Arguments

Value

A dataframe with columns: stand, layer, species, cover, st_group and sp_group.

Examples

n <- 300
height_max <- 20
ly_list    <- c("B1", "B2", "S1", "S2", "K")
st_list    <- LETTERS[1:9]
sp_list    <- letters[1:9]
st_group   <- rep(LETTERS[24:26], 3)
sp_group   <- rep(letters[24:26], 3)
cover_list <- 2^(0:6)
gen_example(n = n, use_layer = TRUE,
            height_max = height_max, ly_list = ly_list, 
            st_list  = st_list,  sp_list  = sp_list,
            st_group = st_group, sp_group = sp_group,
            cover_list = cover_list)

Helper function for Indicator Species Analysis

Description

Calculating diversity indices such as species richness (s), Shannon's H' (h), Simpson' D (d), Simpson's inverse D (i).

Usage

ind_val(
  df,
  stand = NULL,
  species = NULL,
  abundance = NULL,
  group = NULL,
  row_data = FALSE
)

Arguments

Value

A data.frame.

Examples

library(dplyr)
library(tibble)
data(dune, package = "vegan")
data(dune.env, package = "vegan")
df <- 
  dune %>%
  table2df(st = "stand", sp = "species", ab = "cover") %>%
  dplyr::left_join(tibble::rownames_to_column(dune.env, "stand"))
ind_val(df, abundance = "cover", group = "Moisture")

Check cols one-to-one, or one-to-multi in data.frame

Description

Check cols one-to-one, or one-to-multi in data.frame

Usage

is_one2multi(df, col_1, col_2)

is_one2one(df, col_1, col_2)

is_multi2multi(df, col_1, col_2)

cols_one2multi(df, col, inculde_self = TRUE)

select_one2multi(df, col, inculde_self = TRUE)

unique_length(df, col_1, col_2)

Arguments

Value

is_one2multi(), is_one2one(), is_multi2multi() return a logical. cols_one2multi() returns strings of colnames that has one2multi relation to input col. unique_length() returns a list.

Examples

df <- tibble::tibble(
  x     = rep(letters[1:6], each = 1),
  x_grp = rep(letters[1:3], each = 2),
  y     = rep(LETTERS[1:3], each = 2),
  y_grp = rep(LETTERS[1:3], each = 2),
  z      = rep(LETTERS[1:3], each = 2),
  z_grp  = rep(LETTERS[1:3], times = 2))

unique_length(df, "x", "x_grp")

is_one2one(df, "x", "x_grp")
is_one2one(df, "y", "y_grp")
is_one2one(df, "z", "z_grp")

Helper function for ordination methods

Description

Helper function for ordination methods

Usage

ordination(tbl, o_method, d_method = NULL, ...)

ord_plot(ord, score = "st_scores", x = 1, y = 2)

ord_add_group(ord, score = "st_scores", df, indiv, group)

ord_extract_score(ord, score = "st_scores", row_name = NULL)

Arguments

Value

ordination() returns result of ordination. $st_scores: scores for stand. $sp_scores: scores for species. $eig_val: eigen value for stand. $results_raw: results of original ordination function. $ordination_method: o_method. $distance_method: d_method. ord_plot() returns ggplot2 object. ord_extract_score() extracts stand or species scores from ordination result. ord_add_group() adds group data.frame into ordination scores.

Examples

library(ggplot2)
library(vegan)
data(dune)
data(dune.env)

df <- 
  table2df(dune) %>%
  dplyr::left_join(tibble::rownames_to_column(dune.env, "stand"))
sp_dammy <- 
 tibble::tibble("species" = colnames(dune), 
                "dammy_1" = stringr::str_sub(colnames(dune), 1, 1),
                "dammy_6" = stringr::str_sub(colnames(dune), 6, 6))
df <- dplyr::left_join(df, sp_dammy)

ord_dca <- ordination(dune, o_method = "dca")
ord_pca <- 
  df %>%
  df2table() %>%
  ordination(o_method = "pca")

ord_dca_st <- 
  ord_extract_score(ord_dca, score = "st_scores")
ord_pca_sp <- 
  ord_add_group(ord_pca, 
  score = "sp_scores", df, indiv = "species", group = "dammy_1")

Pad a string to the longest width of the strings.

Description

Pad a string to the longest width of the strings.

Usage

pad2longest(string, side = "right", pad = " ")

Arguments

Value

    Strings.

Examples

x <- c("a", "ab", "abc")
pad2longest(x, side = "right", pad = " ")

Read data from BiSS (Biodiversity Investigation Support System) to data frame.

Description

BiSS data is formatted as JSON.

Usage

read_biss(txt, join = TRUE)

Arguments

Value

A data frame.

Examples

library(dplyr)
# path <- "set file path"
path <- "https://raw.githubusercontent.com/matutosi/biodiv/main/man/example.json"
read_biss(path)

Helper function for calculating diversity

Description

Calculating diversity indices such as species richness (s), Shannon's H' (h), Simpson' D (d), Simpson's inverse D (i).

Usage

shdi(df, stand = NULL, species = NULL, abundance = NULL)

Arguments

Value

A data.frame. Including species richness (s), Shannon's H' (h), Simpson' D (d), Simpson's inverse D (i).

Examples

data(dune, package = "vegan")
df <- table2df(dune)
shdi(df)