Add a total radius-at-capture variable to a data.frame that contains one-fish-per-line (i.e., “wide” format) increments data.
addRadCap(df, in.pre = NULL, in.var = NULL, var.name = "radcap")A data.frame that contains the growth increment data in one-fish-per-line (i.e., “wide”) format.
A string that represents the common part of the increment variable names. See details.
A vector of variables in df that do not change. See details.
A string that indicates the name for the new total radius-at-capture variable in the new data.frame. Defaults to “radcap”.
A data.frame of increments in one-fish-per-line (i.e., “wide”) format with the total radius-at-capture appended in a variable named as given in var.name.
The columns that contain the original increment data can specified in a variety of ways. First, if all columns begin with the same prefix (and no other columns contain that prefix), then the prefix string may be given to in.pre=. Second, a sequence of column numbers may be given to in.var= with #:# (if the columns are contiguous) or as a vector (if the columns are not contiguous). Third, a vector of column names may be given to in.var=. Note that one, but not both, of in.var= or in.pre= must be specified by the user.
Note that the computed total radius-at-capture will only be the actual total radius-at-capture if all growth, including “plus-growth” in the current season, is recorded in the input data frame.
See gConvert for related functionality.
## Get data with radial measurements
data(SMBassWB,package="FSA")
head(SMBassWB)
#> species lake gear yearcap fish agecap lencap anu1 anu2 anu3 anu4 anu5 anu6
#> 1 SMB WB E 1988 5 1 71 1.90606 NA NA NA NA NA
#> 2 SMB WB E 1988 3 1 64 1.87707 NA NA NA NA NA
#> 3 SMB WB E 1988 2 1 57 1.09227 NA NA NA NA NA
#> 4 SMB WB E 1988 4 1 68 1.31848 NA NA NA NA NA
#> 5 SMB WB E 1988 6 1 72 1.59283 NA NA NA NA NA
#> 6 SMB WB E 1988 7 1 80 1.91602 NA NA NA NA NA
#> anu7 anu8 anu9 anu10 anu11 anu12 radcap
#> 1 NA NA NA NA NA NA 1.90606
#> 2 NA NA NA NA NA NA 1.87707
#> 3 NA NA NA NA NA NA 1.09736
#> 4 NA NA NA NA NA NA 1.33108
#> 5 NA NA NA NA NA NA 1.59283
#> 6 NA NA NA NA NA NA 1.91602
## convert radial measurements to increments
SMBi1 <- gConvert(SMBassWB,in.pre="anu",out.type="inc")
head(SMBi1)
#> species lake gear yearcap fish agecap lencap radcap inc1 inc2 inc3 inc4
#> 1 SMB WB E 1988 5 1 71 1.90606 1.90606 NA NA NA
#> 2 SMB WB E 1988 3 1 64 1.87707 1.87707 NA NA NA
#> 3 SMB WB E 1988 2 1 57 1.09736 1.09227 NA NA NA
#> 4 SMB WB E 1988 4 1 68 1.33108 1.31848 NA NA NA
#> 5 SMB WB E 1988 6 1 72 1.59283 1.59283 NA NA NA
#> 6 SMB WB E 1988 7 1 80 1.91602 1.91602 NA NA NA
#> inc5 inc6 inc7 inc8 inc9 inc10 inc11 inc12
#> 1 NA NA NA NA NA NA NA NA
#> 2 NA NA NA NA NA NA NA NA
#> 3 NA NA NA NA NA NA NA NA
#> 4 NA NA NA NA NA NA NA NA
#> 5 NA NA NA NA NA NA NA NA
#> 6 NA NA NA NA NA NA NA NA
## add the radius-at-capture measurement
SMBi1a <- addRadCap(SMBi1,in.pre="inc",var.name="radcap2")
head(SMBi1a)
#> species lake gear yearcap fish agecap lencap radcap inc1 inc2 inc3 inc4
#> 1 SMB WB E 1988 5 1 71 1.90606 1.90606 NA NA NA
#> 2 SMB WB E 1988 3 1 64 1.87707 1.87707 NA NA NA
#> 3 SMB WB E 1988 2 1 57 1.09736 1.09227 NA NA NA
#> 4 SMB WB E 1988 4 1 68 1.33108 1.31848 NA NA NA
#> 5 SMB WB E 1988 6 1 72 1.59283 1.59283 NA NA NA
#> 6 SMB WB E 1988 7 1 80 1.91602 1.91602 NA NA NA
#> inc5 inc6 inc7 inc8 inc9 inc10 inc11 inc12 radcap2
#> 1 NA NA NA NA NA NA NA NA 1.90606
#> 2 NA NA NA NA NA NA NA NA 1.87707
#> 3 NA NA NA NA NA NA NA NA 1.09227
#> 4 NA NA NA NA NA NA NA NA 1.31848
#> 5 NA NA NA NA NA NA NA NA 1.59283
#> 6 NA NA NA NA NA NA NA NA 1.91602