lencat: Constructs length class/category variable.

In FSA: Simple Fisheries Stock Assessment Methods

Constructs length class/category variable.

Description

Constructs a vector that contains the length class or category to which an individual belongs. Optionally, that vector can be appended to the original data frame.

Usage

lencat(x, ...)

## Default S3 method:
lencat(
  x,
  w = 1,
  startcat = NULL,
  breaks = NULL,
  right = FALSE,
  use.names = FALSE,
  as.fact = use.names,
  droplevels = drop.levels,
  drop.levels = FALSE,
  ...
)

## S3 method for class 'formula'
lencat(
  x,
  data,
  w = 1,
  startcat = NULL,
  breaks = NULL,
  right = FALSE,
  use.names = FALSE,
  as.fact = use.names,
  droplevels = drop.levels,
  drop.levels = FALSE,
  vname = NULL,
  ...
)

Arguments

x	A numeric vector that contains the length measurements or a formula of the form ~x where “x” generically represents a variable in data that contains length measurements. This formula can only contain one variable.
...	Not implemented.
w	A single numeric that indicates the width of length categories to create. Ignored if breaks is not NULL.
startcat	A single numeric that indicates the beginning of the first length category. Only used with w. See details for how this is handled when NULL.
breaks	A numeric vector of lower values for the break points of the length categories.
right	A logical that indicates if the intervals should be closed on the right (and open on the left) or vice versa.
use.names	A logical that indicates whether the names for the values in breaks should be used for the levels in the new variable. Will throw a warning and then use default levels if TRUE but names(breaks) is NULL.
as.fact	A logical that indicates that the new variable should be returned as a factor (=TRUE) or not (=FALSE; default).
droplevels, drop.levels	A logical that indicates that the new variable should retain all levels indicated in breaks (=FALSE; default) or not. Ignored if as.fact=FALSE.
data	A data.frame that minimally contains the length measurements given in the variable in the formula.
vname	A string that contains the name for the new length class variable.

Details

If breaks is non-NULL, then w and startcat will be ignored. The vector of values in breaks should begin with a value smaller than the minimum observed value and end with a value larger than the maximum observed value. If the lowest break value is larger than the minimum observed value, then an error will occur. If the largest break value is smaller than the maximum observed value, then an additional break value larger than the maximum observed value will be added to breaks (and a warning will be sent). The values in breaks do not have to be equally spaced.

If breaks=NULL (the default), then the value in w is used to create equally spaced categories. If startcat=NULL (the default), then the length categories will begin with the first value less than the minimum observed value “rounded” by w. For example, if the minimum observed value is 67, then the first length category will be 65 if w=5, 60 if w=10, 50 if w=25, and 50 if w=50. The length categories will continue from this starting value by values of w until a value greater than the largest observed value in x. The length categories are left-inclusive and right-exclusive by default (i.e., right=FALSE).

The start of the length categories may also be set with startcat. The number in the startcat argument should be less than the smallest value in x. Additionally, the number of decimals in startcat should not be more than the number of decimals in w (e.g., startcat=0.4 and w=1 will result in an error).

One may want to convert apparent numeric values to factor values if some of the length categories are missing (e.g., if factor values are used, for example, then tables of the length category values will have values for all length categories; i.e., it will have zeros for the length categories that are missing). The numeric values can be converted to factors by including as.fact. See the “real data” example.

The observed values in x should be rounded to the appropriate number of decimals to avoid misplacement of individuals into incorrect length categories due to issues with machine-precision (see discussion in all.equal.)

Value

If the formula version of the function is used, then a data.frame is returned with the a new variable, named as in vname (defaults to LCat), appended to the original data.frame. If the default version of the function is used, then a single vector is returned. The returned values will be numeric unless breaks is named and use.names=TRUE or if as.fact=TRUE.

IFAR Chapter

2-Data Manipulation.

Author(s)

Derek H. Ogle, [e-mail]

References

Ogle, D.H. 2016. Introductory Fisheries Analyses with R. Chapman & Hall/CRC, Boca Raton, FL.

Examples

# Create random lengths measured to nearest 0.1 unit
df1 <- data.frame(len=round(runif(50,0.1,9.9),1))

# Create length categories by 0.1 unit
df1$LCat1 <- lencat(df1$len,w=0.1)
xtabs(~LCat1,data=df1)

# length categories by 0.2 units
df1$LCat2 <- lencat(df1$len,w=0.2)
xtabs(~LCat2,data=df1)

# length categories by 0.2 units starting at 0.1
df1$LCat3 <- lencat(df1$len,w=0.2,startcat=0.1)
xtabs(~LCat3,data=df1)

# length categories as set by breaks
df1$LCat4 <- lencat(df1$len,breaks=c(0,2,4,7,10))
xtabs(~LCat4,data=df1)

## A Second example
# random lengths measured to nearest unit
df2 <- data.frame(len=round(runif(50,10,117),0))    

# length categories by 5 units
df2$LCat1 <- lencat(df2$len,w=5)
xtabs(~LCat1,data=df2)

# length categories by 5 units starting at 7
df2$LCat2 <- lencat(df2$len,w=5,startcat=7)
xtabs(~LCat2,data=df2)

# length categories by 10 units
df2$LCat3 <- lencat(df2$len,w=10)
xtabs(~LCat3,data=df2)

# length categories by 10 units starting at 5
df2$LCat4 <- lencat(df2$len,w=10,startcat=5)
xtabs(~LCat4,data=df2)

# length categories as set by breaks
df2$LCat5 <- lencat(df2$len,breaks=c(5,50,75,150))
xtabs(~LCat5,data=df2)

## A Third example
# random lengths measured to nearest 0.1 unit
df3 <- data.frame(len=round(runif(50,10,117),1))

# length categories by 5 units
df3$LCat1 <- lencat(df3$len,w=5)
xtabs(~LCat1,data=df3)

## A Fourth example
# random lengths measured to nearest 0.01 unit
df4 <- data.frame(len=round(runif(50,0.1,9.9),2))

# length categories by 0.1 unit
df4$LCat1 <- lencat(df4$len,w=0.1)
xtabs(~LCat1,data=df4)

# length categories by 0.1 unit, but without missing categories
df4$LCat2 <- lencat(df4$len,w=0.1,as.fact=TRUE)
xtabs(~LCat2,data=df4)

# length categories by 2 unit
df4$LCat3 <- lencat(df4$len,w=2)
xtabs(~LCat3,data=df4)

## A Fifth example -- with real data
# remove variables with "anu" and "radcap" just for simplicity
smb1 <- smb2 <- SMBassWB[,-c(8:20)]

# 10 mm length classes - in default LCat variable
smb1$LCat10 <- lencat(smb1$lencap,w=10)
head(smb1)
xtabs(~LCat10,data=smb1)

# Same as previous but returned as factor so levels with no fish still seen
smb1$LCat10A <- lencat(smb1$lencap,w=10,as.fact=TRUE)
head(smb1)
xtabs(~LCat10A,data=smb1)

# Same as previous but returned as a factor with unused levels dropped
smb1$LCat10B <- lencat(smb1$lencap,w=10,as.fact=TRUE,droplevels=TRUE)
head(smb1)
xtabs(~LCat10B,data=smb1)

# 25 mm length classes - in custom variable name
smb1$LCat25 <- lencat(smb1$lencap,w=25)
head(smb1)
xtabs(~LCat25,data=smb1)

# using values from psdVal for Smallmouth Bass
smb1$PSDCat1 <- lencat(smb1$lencap,breaks=psdVal("Smallmouth Bass"))
head(smb1)
xtabs(~PSDCat1,data=smb1)

# add category names
smb1$PSDCat2 <- lencat(smb1$lencap,breaks=psdVal("Smallmouth Bass"),use.names=TRUE)
head(smb1)
xtabs(~PSDCat2,data=smb1)

# same as above but drop the unused levels
smb1$PSDCat2A <- lencat(smb1$lencap,breaks=psdVal("Smallmouth Bass"),
                        use.names=TRUE,droplevels=TRUE)
head(smb1)
xtabs(~PSDCat2A,data=smb1)
str(smb1)

# same as above but not returned as a factor (returned as a character)
smb1$PSDcat2B <- lencat(smb1$lencap,breaks=psdVal("Smallmouth Bass"),
                        use.names=TRUE,as.fact=FALSE)
str(smb1)

## A Sixth example -- similar to fifth example but using the formula notation
# 10 mm length classes - in default LCat variable
smb2 <- lencat(~lencap,data=smb2,w=10)
head(smb2)

# 25 mm length classes - in custom variable name
smb2 <- lencat(~lencap,data=smb2,w=25,vname="LenCat25")
head(smb2)

# using values from psdVal for Smallmouth Bass
smb2 <- lencat(~lencap,data=smb2,breaks=psdVal("Smallmouth Bass"),vname="LenPsd")
head(smb2)

# add category names
smb2 <- lencat(~lencap,data=smb2,breaks=psdVal("Smallmouth Bass"),vname="LenPsd2",
               use.names=TRUE,droplevels=TRUE)
head(smb2)
str(smb2)

FSA documentation built on Aug. 27, 2023, 1:06 a.m.