| caphist.sum {FSA} | R Documentation |
This function summarizes the capture histories of individual fish. Results may be used in the Schnabel, Schumacher-Eschmeyer, or Jolly-Seber methods of estimating abundance.
caphist.sum(df,cols=NULL)
df |
a data.frame containing the capture histories (and, perhaps, other information. See details. |
cols |
a numerical vector of columns that contain the capture histories. See details. |
If the data.frame in df contains columns with non-capture history information then the cols argument should be used to identify which columns contain only the capture history information. Columns can be included by listing the column numbers (e.g., columns 2 through 7 could be included with cols=2:7). Columns can be excluded by including the column number preceded by a “minus” sign (e.g., columns 1 through 3 can be excluded with cols=-(1:3).
A list is returned with the following two components
caphist.sum |
A vector summarizing the frequency of fish with each capture history. |
schnabel.sum |
A data frame containing the number of fish captured in each sample (n), the number of marked fish captured in each sample (m), the number of marked fish returned to the population following the sample (R), and the number of marked fish in the population just prior to the sample (M). |
methodB.top |
a matrix containing the top of the Method B table used for the Jolly-Seber method (i.e., a contingency table of capture sample (columns) and last seen sample (rows)). |
methodB.bot |
a data.frame containng the bottom of the Method B table used for the Jolly-Seber method (i.e., the number of marked fish in the sample (m), the number of unmarked fish in the sample (u), the total number of fish in the sample (n), and the number of marked fish returned to the population following the sample (R). |
This function assumes that all unmarked captured fish are marked and returned to the population (i.e., no losses at the time of marking are allowed).
An error will be returned if a capture event occurs where no fish were collected (marked or unmarked).
Derek H. Ogle, dogle@northland.edu
# data.frame contains only capture histories data(PikeNYPartial1) caphist.sum(PikeNYPartial1) # fist column contains IDs & should be excluded data(CutthroatAL) caphist.sum(CutthroatAL,-1)