Sum columns containing unusable observations and remove rows that contain more than the specified cutoff number of unusable points. Helpful if there are annotations that were unidentifiable and you want to remove them from the total usable observations, and you can remove quadrats with too many unusable observations.
Arguments
- data
A data frame with each row representing a sampling unit (ex. a quadrat or photo).
- unusable
A vector of column names containing unusable observations.
- max
If
max = FALSE, no threshold will be examined. Ifmax = TRUE, a threshold cutoff needs to be provided where rows containing more than thecutoffwill be removed from the data frame.- cutoff
The threshold number where rows containing more unusable observations than the
cutoffwill be removed from the data frame.- above_cutoff
If
above_cutoff = TRUE, the data frame returned will be the rows containing more unusable observations than the cutoff. Ifabove_cutoff = FALSEthe data frame returned will be the rows containing equal to or less unusable observations than the cutoff.- rm_unusable
If
rm_unusable = TRUE, the columns named in the unusable vector will be removed from the data frame. These columns will not be removed ifrm_unusable = FALSE, though duplicate data will remain.
Examples
#create data set for example
Sites <- as.factor(c("One", "One", "Two", "Two", "Three", "Three"))
Transect <- as.factor(c("1-Shallow", "2-Shallow", "1-Shallow", "2-Shallow",
"1-Shallow", "2-Shallow"))
Acropora.sp <- c(1, 2, 3, 4, 5, 6)
Gardineroseris.sp <- c(6, 1, 2, 3, 4, 5)
Psammocora.sp <- c(5, 6, 1, 2, 3, 4)
Leptastrea.sp <- c(4, 5, 6, 1, 2, 3)
Blurry <- c(3, 4, 5, 6, 1, 2)
Unk <- c(2, 3, 4, 5, 6, 1)
coral_cover <- data.frame(Sites, Transect, Acropora.sp, Gardineroseris.sp,
Psammocora.sp, Leptastrea.sp, Blurry, Unk)
usable_obs(coral_cover, c("Blurry", "Unk"))
#> Sites Transect Acropora.sp Gardineroseris.sp Psammocora.sp Leptastrea.sp
#> 1 One 1-Shallow 1 6 5 4
#> 2 One 2-Shallow 2 1 6 5
#> 3 Two 1-Shallow 3 2 1 6
#> 4 Two 2-Shallow 4 3 2 1
#> 5 Three 1-Shallow 5 4 3 2
#> 6 Three 2-Shallow 6 5 4 3
#> unusable
#> 1 5
#> 2 7
#> 3 9
#> 4 11
#> 5 7
#> 6 3
usable_obs(coral_cover, c("Blurry", "Unk"), above_cutoff = TRUE)
#> Warning: no max specified
#> Sites Transect Acropora.sp Gardineroseris.sp Psammocora.sp Leptastrea.sp
#> 1 One 1-Shallow 1 6 5 4
#> 2 One 2-Shallow 2 1 6 5
#> 3 Two 1-Shallow 3 2 1 6
#> 4 Two 2-Shallow 4 3 2 1
#> 5 Three 1-Shallow 5 4 3 2
#> 6 Three 2-Shallow 6 5 4 3
#> unusable
#> 1 5
#> 2 7
#> 3 9
#> 4 11
#> 5 7
#> 6 3
usable_obs(coral_cover, c("Blurry", "Unk"), rm_unusable = FALSE)
#> Warning: duplication exists in the data frame
#> Sites Transect Acropora.sp Gardineroseris.sp Psammocora.sp Leptastrea.sp
#> 1 One 1-Shallow 1 6 5 4
#> 2 One 2-Shallow 2 1 6 5
#> 3 Two 1-Shallow 3 2 1 6
#> 4 Two 2-Shallow 4 3 2 1
#> 5 Three 1-Shallow 5 4 3 2
#> 6 Three 2-Shallow 6 5 4 3
#> Blurry Unk unusable
#> 1 3 2 5
#> 2 4 3 7
#> 3 5 4 9
#> 4 6 5 11
#> 5 1 6 7
#> 6 2 1 3
usable_obs(coral_cover, c("Blurry", "Unk"), max = TRUE, cutoff = 8)
#> Sites Transect Acropora.sp Gardineroseris.sp Psammocora.sp Leptastrea.sp
#> 1 One 1-Shallow 1 6 5 4
#> 2 One 2-Shallow 2 1 6 5
#> 3 Three 1-Shallow 5 4 3 2
#> 4 Three 2-Shallow 6 5 4 3
#> unusable
#> 1 5
#> 2 7
#> 3 7
#> 4 3
usable_obs(coral_cover, c("Blurry", "Unk"), max = TRUE, cutoff = 8, above_cutoff = TRUE)
#> Sites Transect Acropora.sp Gardineroseris.sp Psammocora.sp Leptastrea.sp
#> 1 Two 1-Shallow 3 2 1 6
#> 2 Two 2-Shallow 4 3 2 1
#> unusable
#> 1 9
#> 2 11