Repeat individual fish data (including lengths) from tallied counts.
Source:R/expandCounts.R
expandCounts.RdRepeat individual fish data, including lengths, from tallied counts and, optionally, add a random digit to length measurements to simulate actual length of fish in the bin. This is useful as a precursor to summaries that require information, e.g., lengths, of individual fish (e.g., length frequency histograms, means lengths).
Usage
expandCounts(
data,
cform,
lform = NULL,
removeCount = TRUE,
lprec = 0.1,
new.name = "newlen",
cwid = 0,
verbose = TRUE,
...
)Arguments
- data
A data.frame that contains variables in
cformandlform.- cform
A formula of the form
~countvarwherecountvargenerically represents the variable indatathat contains the counts of individuals. See details.- lform
An optional formula of the form
~lowerbin+upperbinwherelowerbinandupperbingenerically represent the variables indatathat identify the lower- and upper-values of the length bins. See details.- removeCount
A single logical that indicates if the variable that contains the counts of individuals (as given in
cform) should be removed form the returned data.frame. The default isTRUEsuch that the variable will be removed as the returned data.frame contains individuals and the counts of individuals in tallied bins is not relevant to an individual.- lprec
A single numeric that controls the precision to which the random lengths are recorded. See details.
- new.name
A single string that contains a name for the new length variable if random lengths are to be created.
- cwid
A single positive numeric that will be added to the lower length bin value in instances where the count exceeds one but only a lower (and not an upper) length were recorded. See details.
- verbose
A logical indicating whether progress message should be printed or not.
- ...
Not yet implemented.
Value
A data.frame of the same structure as data except that the variable in cform may be deleted and the variable in new.name may be added. The returned data.frame will have more rows than data because of the potential addition of new individuals expanded from the counts in cform.
Details
Fisheries data may be recorded as tallied counts in the field. For example, field biologists may have simply recorded that there were 10 fish in one group, 15 in another, etc. More specifically, the biologist may have recorded that there were 10 male Bluegill from the first sampling event between 100 and 124 mm, 15 male Bluegill from the first sampling event between 125 and 149 mm, and so on. At times, it may be necessary to expand these counts such that the repeated information appears in individual rows in a new data.frame. In this specific example, the tallied counts would be repeated such that the male, Bluegill, first sampling event, 100-124 mm information would be repeated 10 times; the male, Bluegill, first sampling event, 125-149 mm information would be repeated 15 times, and so on. This function facilitates this type of expansion.
Length data has often been collected in a “binned-and-tallied” format (e.g., 10 fish in the 100-124 mm group, 15 in the 125-149 mm group, etc.). This type of data collection does not facilitate easy or precise calculations of summary statistics of length (i.e., mean and standard deviations of length). Expanding the data as described above does not solve this problem because the length data are still essentially categorical (i.e., which group the fish belongs to rather than what it's actual length is). To facilitate computation of summary statistics, the data can be expanded as described above and then a length can be randomly selected from within the recorded length bin to serve as a “measured” length for that fish. This function performs this type of expansion by randomly selecting the length from a uniform distribution within the length bin (e.g., each value between 100 and 124 mm has the same probability of being selected).
This function makes some assumptions for some coding situations. First, it assumes that all lowerbin values are actually lower than all upperbin values. The function will throw an error if this is not true. Second, it assumes that if a lowerbin but no upperbin value is given then the lowerbin value is the exact measurement for those fish. Third, it assumes that if an upperbin but no lowerbin value is given that this is a data entry error and that the upperbin value should be the lowerbin value. Fourth, it assumes that it is a data entry error if varcount is zero or NA and lowerbin or upperbin contains values (i.e., why would there be lengths if no fish were captured?).
See also
See expandLenFreq for expanding length frequencies where individual fish measurements were made on individual fish in a subsample and the remaining fish were simply counted.
Author
Derek H. Ogle, DerekOgle51@gmail.com
Examples
# all need expansion
( d1 <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
lwr.bin=c(15,15.5,16,16,17,17),
upr.bin=c(15.5,16,16.5,16.5,17.5,17.5),
freq=c(6,4,2,3,1,1)) )
#> name lwr.bin upr.bin freq
#> 1 Johnson 15.0 15.5 6
#> 2 Johnson 15.5 16.0 4
#> 3 Jones 16.0 16.5 2
#> 4 Frank 16.0 16.5 3
#> 5 Frank 17.0 17.5 1
#> 6 Max 17.0 17.5 1
expandCounts(d1,~freq)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin
#> 1 Frank 17.0 17.5
#> 2 Max 17.0 17.5
#> 3 Johnson 15.0 15.5
#> 4 Johnson 15.0 15.5
#> 5 Johnson 15.0 15.5
#> 6 Johnson 15.0 15.5
#> 7 Johnson 15.0 15.5
#> 8 Johnson 15.0 15.5
#> 9 Johnson 15.5 16.0
#> 10 Johnson 15.5 16.0
#> 11 Johnson 15.5 16.0
#> 12 Johnson 15.5 16.0
#> 13 Jones 16.0 16.5
#> 14 Jones 16.0 16.5
#> 15 Frank 16.0 16.5
#> 16 Frank 16.0 16.5
#> 17 Frank 16.0 16.5
expandCounts(d1,~freq,~lwr.bin+upr.bin)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin newlen lennote
#> 1 Frank 17.0 17.5 17.3 Expanded length
#> 2 Max 17.0 17.5 17.3 Expanded length
#> 3 Johnson 15.0 15.5 15.2 Expanded length
#> 4 Johnson 15.0 15.5 15.4 Expanded length
#> 5 Johnson 15.0 15.5 15.4 Expanded length
#> 6 Johnson 15.0 15.5 15.0 Expanded length
#> 7 Johnson 15.0 15.5 15.3 Expanded length
#> 8 Johnson 15.0 15.5 15.0 Expanded length
#> 9 Johnson 15.5 16.0 15.9 Expanded length
#> 10 Johnson 15.5 16.0 15.5 Expanded length
#> 11 Johnson 15.5 16.0 15.9 Expanded length
#> 12 Johnson 15.5 16.0 15.9 Expanded length
#> 13 Jones 16.0 16.5 16.5 Expanded length
#> 14 Jones 16.0 16.5 16.2 Expanded length
#> 15 Frank 16.0 16.5 16.3 Expanded length
#> 16 Frank 16.0 16.5 16.0 Expanded length
#> 17 Frank 16.0 16.5 16.4 Expanded length
# some need expansion
( d2 <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
lwr.bin=c(15,15.5,16,16,17.1,17.3),
upr.bin=c(15.5,16,16.5,16.5,17.1,17.3),
freq=c(6,4,2,3,1,1)) )
#> name lwr.bin upr.bin freq
#> 1 Johnson 15.0 15.5 6
#> 2 Johnson 15.5 16.0 4
#> 3 Jones 16.0 16.5 2
#> 4 Frank 16.0 16.5 3
#> 5 Frank 17.1 17.1 1
#> 6 Max 17.3 17.3 1
expandCounts(d2,~freq)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin
#> 1 Frank 17.1 17.1
#> 2 Max 17.3 17.3
#> 3 Johnson 15.0 15.5
#> 4 Johnson 15.0 15.5
#> 5 Johnson 15.0 15.5
#> 6 Johnson 15.0 15.5
#> 7 Johnson 15.0 15.5
#> 8 Johnson 15.0 15.5
#> 9 Johnson 15.5 16.0
#> 10 Johnson 15.5 16.0
#> 11 Johnson 15.5 16.0
#> 12 Johnson 15.5 16.0
#> 13 Jones 16.0 16.5
#> 14 Jones 16.0 16.5
#> 15 Frank 16.0 16.5
#> 16 Frank 16.0 16.5
#> 17 Frank 16.0 16.5
expandCounts(d2,~freq,~lwr.bin+upr.bin)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin newlen lennote
#> 1 Frank 17.1 17.1 17.1 Observed length
#> 2 Max 17.3 17.3 17.3 Observed length
#> 3 Johnson 15.0 15.5 15.1 Expanded length
#> 4 Johnson 15.0 15.5 15.4 Expanded length
#> 5 Johnson 15.0 15.5 15.3 Expanded length
#> 6 Johnson 15.0 15.5 15.2 Expanded length
#> 7 Johnson 15.0 15.5 15.5 Expanded length
#> 8 Johnson 15.0 15.5 15.5 Expanded length
#> 9 Johnson 15.5 16.0 15.5 Expanded length
#> 10 Johnson 15.5 16.0 15.8 Expanded length
#> 11 Johnson 15.5 16.0 16.0 Expanded length
#> 12 Johnson 15.5 16.0 15.7 Expanded length
#> 13 Jones 16.0 16.5 16.1 Expanded length
#> 14 Jones 16.0 16.5 16.4 Expanded length
#> 15 Frank 16.0 16.5 16.0 Expanded length
#> 16 Frank 16.0 16.5 16.2 Expanded length
#> 17 Frank 16.0 16.5 16.3 Expanded length
# none need expansion
( d3 <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
lwr.bin=c(15,15.5,16,16,17.1,17.3),
upr.bin=c(15,15.5,16,16,17.1,17.3),
freq=c(6,4,2,3,1,1)) )
#> name lwr.bin upr.bin freq
#> 1 Johnson 15.0 15.0 6
#> 2 Johnson 15.5 15.5 4
#> 3 Jones 16.0 16.0 2
#> 4 Frank 16.0 16.0 3
#> 5 Frank 17.1 17.1 1
#> 6 Max 17.3 17.3 1
expandCounts(d3,~freq)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin
#> 1 Frank 17.1 17.1
#> 2 Max 17.3 17.3
#> 3 Johnson 15.0 15.0
#> 4 Johnson 15.0 15.0
#> 5 Johnson 15.0 15.0
#> 6 Johnson 15.0 15.0
#> 7 Johnson 15.0 15.0
#> 8 Johnson 15.0 15.0
#> 9 Johnson 15.5 15.5
#> 10 Johnson 15.5 15.5
#> 11 Johnson 15.5 15.5
#> 12 Johnson 15.5 15.5
#> 13 Jones 16.0 16.0
#> 14 Jones 16.0 16.0
#> 15 Frank 16.0 16.0
#> 16 Frank 16.0 16.0
#> 17 Frank 16.0 16.0
expandCounts(d3,~freq,~lwr.bin+upr.bin)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin newlen lennote
#> 1 Frank 17.1 17.1 17.1 Observed length
#> 2 Max 17.3 17.3 17.3 Observed length
#> 3 Johnson 15.0 15.0 15.0 Observed length
#> 4 Johnson 15.0 15.0 15.0 Observed length
#> 5 Johnson 15.0 15.0 15.0 Observed length
#> 6 Johnson 15.0 15.0 15.0 Observed length
#> 7 Johnson 15.0 15.0 15.0 Observed length
#> 8 Johnson 15.0 15.0 15.0 Observed length
#> 9 Johnson 15.5 15.5 15.5 Observed length
#> 10 Johnson 15.5 15.5 15.5 Observed length
#> 11 Johnson 15.5 15.5 15.5 Observed length
#> 12 Johnson 15.5 15.5 15.5 Observed length
#> 13 Jones 16.0 16.0 16.0 Observed length
#> 14 Jones 16.0 16.0 16.0 Observed length
#> 15 Frank 16.0 16.0 16.0 Observed length
#> 16 Frank 16.0 16.0 16.0 Observed length
#> 17 Frank 16.0 16.0 16.0 Observed length
# some need expansion, but different bin widths
( d4 <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
lwr.bin=c(15, 15, 16, 16, 17.1,17.3),
upr.bin=c(15.5,15.9,16.5,16.9,17.1,17.3),
freq=c(6,4,2,3,1,1)) )
#> name lwr.bin upr.bin freq
#> 1 Johnson 15.0 15.5 6
#> 2 Johnson 15.0 15.9 4
#> 3 Jones 16.0 16.5 2
#> 4 Frank 16.0 16.9 3
#> 5 Frank 17.1 17.1 1
#> 6 Max 17.3 17.3 1
expandCounts(d4,~freq)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin
#> 1 Frank 17.1 17.1
#> 2 Max 17.3 17.3
#> 3 Johnson 15.0 15.5
#> 4 Johnson 15.0 15.5
#> 5 Johnson 15.0 15.5
#> 6 Johnson 15.0 15.5
#> 7 Johnson 15.0 15.5
#> 8 Johnson 15.0 15.5
#> 9 Johnson 15.0 15.9
#> 10 Johnson 15.0 15.9
#> 11 Johnson 15.0 15.9
#> 12 Johnson 15.0 15.9
#> 13 Jones 16.0 16.5
#> 14 Jones 16.0 16.5
#> 15 Frank 16.0 16.9
#> 16 Frank 16.0 16.9
#> 17 Frank 16.0 16.9
expandCounts(d4,~freq,~lwr.bin+upr.bin)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin newlen lennote
#> 1 Frank 17.1 17.1 17.1 Observed length
#> 2 Max 17.3 17.3 17.3 Observed length
#> 3 Johnson 15.0 15.5 15.5 Expanded length
#> 4 Johnson 15.0 15.5 15.4 Expanded length
#> 5 Johnson 15.0 15.5 15.3 Expanded length
#> 6 Johnson 15.0 15.5 15.4 Expanded length
#> 7 Johnson 15.0 15.5 15.2 Expanded length
#> 8 Johnson 15.0 15.5 15.5 Expanded length
#> 9 Johnson 15.0 15.9 15.7 Expanded length
#> 10 Johnson 15.0 15.9 15.8 Expanded length
#> 11 Johnson 15.0 15.9 15.6 Expanded length
#> 12 Johnson 15.0 15.9 15.4 Expanded length
#> 13 Jones 16.0 16.5 16.1 Expanded length
#> 14 Jones 16.0 16.5 16.1 Expanded length
#> 15 Frank 16.0 16.9 16.1 Expanded length
#> 16 Frank 16.0 16.9 16.2 Expanded length
#> 17 Frank 16.0 16.9 16.2 Expanded length
# some need expansion but include zeros and NAs for counts
( d2a <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max","Max","Max","Max"),
lwr.bin=c(15, 15.5,16 ,16 ,17.1,17.3,NA,NA,NA),
upr.bin=c(15.5,16 ,16.5,16.5,17.1,17.3,NA,NA,NA),
freq=c(6,4,2,3,1,1,NA,0,NA)) )
#> name lwr.bin upr.bin freq
#> 1 Johnson 15.0 15.5 6
#> 2 Johnson 15.5 16.0 4
#> 3 Jones 16.0 16.5 2
#> 4 Frank 16.0 16.5 3
#> 5 Frank 17.1 17.1 1
#> 6 Max 17.3 17.3 1
#> 7 Max NA NA NA
#> 8 Max NA NA 0
#> 9 Max NA NA NA
expandCounts(d2a,~freq,~lwr.bin+upr.bin)
#> Results messages from expandCounts():
#> Rows 7, 8, 9 had zero or no counts in freq.
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin newlen lennote
#> 1 Max NA NA NA Observed length
#> 2 Max NA NA NA Observed length
#> 3 Max NA NA NA Observed length
#> 4 Frank 17.1 17.1 17.1 Observed length
#> 5 Max 17.3 17.3 17.3 Observed length
#> 6 Johnson 15.0 15.5 15.0 Expanded length
#> 7 Johnson 15.0 15.5 15.1 Expanded length
#> 8 Johnson 15.0 15.5 15.5 Expanded length
#> 9 Johnson 15.0 15.5 15.0 Expanded length
#> 10 Johnson 15.0 15.5 15.5 Expanded length
#> 11 Johnson 15.0 15.5 15.1 Expanded length
#> 12 Johnson 15.5 16.0 16.0 Expanded length
#> 13 Johnson 15.5 16.0 15.7 Expanded length
#> 14 Johnson 15.5 16.0 15.9 Expanded length
#> 15 Johnson 15.5 16.0 15.7 Expanded length
#> 16 Jones 16.0 16.5 16.4 Expanded length
#> 17 Jones 16.0 16.5 16.3 Expanded length
#> 18 Frank 16.0 16.5 16.2 Expanded length
#> 19 Frank 16.0 16.5 16.2 Expanded length
#> 20 Frank 16.0 16.5 16.0 Expanded length
# some need expansion but include NAs for upper values
( d2b <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
lwr.bin=c(15, 15.5,16 ,16 ,17.1,17.3),
upr.bin=c(NA ,NA ,16.5,16.5,17.1,17.3),
freq=c(6,4,2,3,1,1)) )
#> name lwr.bin upr.bin freq
#> 1 Johnson 15.0 NA 6
#> 2 Johnson 15.5 NA 4
#> 3 Jones 16.0 16.5 2
#> 4 Frank 16.0 16.5 3
#> 5 Frank 17.1 17.1 1
#> 6 Max 17.3 17.3 1
expandCounts(d2b,~freq,~lwr.bin+upr.bin)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin newlen lennote
#> 1 Frank 17.1 17.1 17.1 Observed length
#> 2 Max 17.3 17.3 17.3 Observed length
#> 3 Johnson 15.0 15.0 15.0 Observed length
#> 4 Johnson 15.0 15.0 15.0 Observed length
#> 5 Johnson 15.0 15.0 15.0 Observed length
#> 6 Johnson 15.0 15.0 15.0 Observed length
#> 7 Johnson 15.0 15.0 15.0 Observed length
#> 8 Johnson 15.0 15.0 15.0 Observed length
#> 9 Johnson 15.5 15.5 15.5 Observed length
#> 10 Johnson 15.5 15.5 15.5 Observed length
#> 11 Johnson 15.5 15.5 15.5 Observed length
#> 12 Johnson 15.5 15.5 15.5 Observed length
#> 13 Jones 16.0 16.5 16.0 Expanded length
#> 14 Jones 16.0 16.5 16.0 Expanded length
#> 15 Frank 16.0 16.5 16.5 Expanded length
#> 16 Frank 16.0 16.5 16.4 Expanded length
#> 17 Frank 16.0 16.5 16.1 Expanded length
# some need expansion but include NAs for upper values
( d2c <- data.frame(name=c("Johnson","Johnson","Jones","Frank","Frank","Max"),
lwr.bin=c(NA,NA, 16 ,16 ,17.1,17.3),
upr.bin=c(15,15.5,16.5,16.5,17.1,17.3),
freq=c(6,4,2,3,1,1)) )
#> name lwr.bin upr.bin freq
#> 1 Johnson NA 15.0 6
#> 2 Johnson NA 15.5 4
#> 3 Jones 16.0 16.5 2
#> 4 Frank 16.0 16.5 3
#> 5 Frank 17.1 17.1 1
#> 6 Max 17.3 17.3 1
expandCounts(d2c,~freq,~lwr.bin+upr.bin)
#> Results messages from expandCounts():
#> 2 rows had an individual measurement.
#> 4 rows with multiple measurements were expanded to 15 rows of individual measurements.
#> name lwr.bin upr.bin newlen lennote
#> 1 Frank 17.1 17.1 17.1 Observed length
#> 2 Max 17.3 17.3 17.3 Observed length
#> 3 Johnson 15.0 15.0 15.0 Observed length
#> 4 Johnson 15.0 15.0 15.0 Observed length
#> 5 Johnson 15.0 15.0 15.0 Observed length
#> 6 Johnson 15.0 15.0 15.0 Observed length
#> 7 Johnson 15.0 15.0 15.0 Observed length
#> 8 Johnson 15.0 15.0 15.0 Observed length
#> 9 Johnson 15.5 15.5 15.5 Observed length
#> 10 Johnson 15.5 15.5 15.5 Observed length
#> 11 Johnson 15.5 15.5 15.5 Observed length
#> 12 Johnson 15.5 15.5 15.5 Observed length
#> 13 Jones 16.0 16.5 16.0 Expanded length
#> 14 Jones 16.0 16.5 16.1 Expanded length
#> 15 Frank 16.0 16.5 16.5 Expanded length
#> 16 Frank 16.0 16.5 16.4 Expanded length
#> 17 Frank 16.0 16.5 16.1 Expanded length
if (FALSE) {
##!!##!!## Change path to where example file is and then run to demo
## Read in datafile (note periods in names)
df <- read.csv("c:/aaawork/consulting/R_WiDNR/Statewide/Surveysummaries2010.csv")
str(df)
## narrow variables for simplicity
df1 <- df[,c("County","Waterbody.Name","Survey.Year","Gear","Species",
"Number.of.Fish","Length.or.Lower.Length.IN","Length.Upper.IN",
"Weight.Pounds","Gender")]
## Sum the count to see how many fish there should be after expansion
sum(df1$Number.of.Fish)
## Simple expansion
df2 <- expandCounts(df1,~Number.of.Fish)
## Same expansion but include random component to lengths (thus new variable)
## also note default lprec=0.1
df3 <- expandCounts(df1,~Number.of.Fish,~Length.or.Lower.Length.IN+Length.Upper.IN)
}