R: Convert .CSV File to an unmarkedFrame

csvToUMF {unmarked} | R Documentation

## Convert .CSV File to an unmarkedFrame

### Description

This function converts an appropriatedly formated comma-separated values file (.csv) to a format usable by unmarked's fitting functions (see Details).

### Usage

    csvToUMF(filename, long=FALSE, type, species, ...)

### Arguments

`filename` | string describing filename of file to read in
`long` | `FALSE` if file is in long format or `TRUE` if file is in long format (see Details)
`species` | if data is in long format with multiple species, then this can specify a particular species to extract if there is a column named "species".
`type` | specific type of unmarkedFrame.
`...` | further arguments to be passed to the unmarkedFrame constructor.

### Details

This function provides a quick way to take a .csv file with headers named as described below and provides the data required and returns of data in the format required by the model-fitting functions in `unmarked`. The .csv file can be in one of 2 formats: long or wide. See the first 2 lines of the examples for what these formats look like.

The .csv file is formatted as follows:

- col 1 is site labels.

- if data is in long format, col 2 is date of observation.

- next J columns are the observations (y) - counts or 0/1's.

- next is a series of columns for the site variables (one column per variable). The column header is the variable name.

- next is a series of columns for the observation-level variables. These are in sets of J columns for each variable, e.g., var1-1 var1-2 var1-3 var2-1 var2-2 var2-3, etc. The column header of the first variable in each group must indicate the variable name.

### Value

an unmarkedFrame object

### Author(s)

Ian Fiske ianfiske@gmail.com

### Examples

    # examine a correctly formatted long .csv
    head(read.csv(system.file("csv","frog2001pcru.csv", package="unmarked")))

    # examine a correctly formatted wide .csv
    head(read.csv(system.file("csv","widewt.csv", package="unmarked")))

    # convert them!
    dat1 <- csvToUMF(system.file("csv","frog2001pcru.csv", package="unmarked"),
                     long = TRUE, type = "unmarkedFrameOccu")
    dat2 <- csvToUMF(system.file("csv","frog2001pfer.csv", package="unmarked"),
                     long = TRUE, type = "unmarkedFrameOccu")
    dat3 <- csvToUMF(system.file("csv","widewt.csv", package="unmarked"),
                     long = FALSE, type = "unmarkedFrameOccu")

[Package unmarked version 1.0.0 Index]