crop_area {quadcleanR}

Crop quadrats based on area

Description

Using the location of annotated points within quadrats and the size of the quadrat, crop quadrat data to a smaller area, while maintaining the spatial relationships between points. Useful for making different sized quadrat data comparable.

Usage

crop_area(
  data,
  row,
  column,
  id,
  dim,
  obs_rm = FALSE,
  obs_range,
  res = FALSE,
  res_dim_x,
  res_dim_y
)

Arguments

data

A data frame containing annotations, in long format, such that all observations are contained in one column.

row

The column name in data which contains the row locations of the annotated points.

column

The column name in data which contains the column location of the annotated points.

id

The column name in data which contains the quadrat ID for the annotated points.

dim

A vector with length of 2, containing the proportion of the row and columns to crop. First element will be the proportion of the rows and the second will be the proportion of the columns.

obs_rm

If obs_rm = FALSE, no quadrats will be removed from the returned data set. If obs_rm = TRUE, quadrats will be removed from the returned data set based on the number of annotated observations in the cropped area as specified by obs_range.

obs_range

A vector with length of 2, specifying the min and max accepted number of annotated observations to retain in the data set.

res

If res = TRUE if the dimensions of each quadrat are known. These must be the same units as the row and column locations. If dimensions are not known, specify res = FALSE, and the function will estimate the max dimensions based off the max row and column location for the annotated points.

res_dim_x

The column name in data which contains the max column dimension for each quadrat.

res_dim_y

The column name in data which contains the max row dimension for each quadrat.

Value

A data frame in of quadrat annotations with a subset of annotated points.

Examples

#Creating the data file
tags <- c("Clad", "Sinu", "Sarco", "Loph")

site <- c(rep("Site1", times = 100),
         rep("Site2", times = 100),
         rep("Site3", times = 100),
         rep("Site4", times = 100))
row <- c(sample(x = c(1:2000), size = 100, replace = TRUE),
        sample(x = c(1:2000), size = 100, replace = TRUE),
        sample(x = c(1:2000), size = 100, replace = TRUE),
        sample(x = c(1:2000), size = 100, replace = TRUE))
column <- c(sample(x = c(1:2000), size = 100, replace = TRUE),
           sample(x = c(1:2000), size = 100, replace = TRUE),
           sample(x = c(1:2000), size = 100, replace = TRUE),
           sample(x = c(1:2000), size = 100, replace = TRUE))
label <- c(sample(x = tags, size = 100, replace = TRUE),
          sample(x = tags, size = 100, replace = TRUE),
          sample(x = tags, size = 100, replace = TRUE),
          sample(x = tags, size = 100, replace = TRUE))
coral_annotations <- data.frame(site, row, column, label)

crop_area_coral <- crop_area(data = coral_annotations, row = "row",
                            column = "column", id = "site", dim = c(0.5, 0.5))

coral_annotations$col_dim <- 2000
coral_annotations$row_dim <- 2000

crop_area_coral_2 <- crop_area(data = coral_annotations, row = "row",
                              column = "column", id = "site", dim = c(0.5, 0.5),
                              res = TRUE, res_dim_x = "col_dim", res_dim_y = "row_dim")