csvToUMF.RdThis function converts an appropriatedly formated comma-separated values file (.csv) to a format usable by unmarked's fitting functions (see Details).
csvToUMF(filename, long=FALSE, type, species, ...)
| filename | string describing filename of file to read in |
|---|---|
| long |
|
| 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. |
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.
an unmarkedFrame object
Ian Fiske ianfiske@gmail.com
# examine a correctly formatted long .csv head(read.csv(system.file("csv","frog2001pcru.csv", package="unmarked")))#> RouteNumStopNum JulianDate Pcru MinAfterSunset Wind Sky Temperature #> 1 211202.0 72 3 48 1 0 8.3 #> 2 211202.0 72 3 64 1 0 7.8 #> 3 211202.0 72 3 72 1 0 7.8 #> 4 211202.0 72 3 81 1 0 7.8 #> 5 211202.0 72 3 90 1 0 7.8 #> 6 211202.1 72 3 97 1 1 7.2# examine a correctly formatted wide .csv head(read.csv(system.file("csv","widewt.csv", package="unmarked")))#> site y.1 y.2 y.3 elev forest length date.1 date.2 #> 1 1 0 0 0 -1.1729446 -1.156228147 1.824549 -1.761481 0.3099471 #> 2 2 0 0 0 -1.1265010 -0.501483710 1.629241 -2.904339 -1.0471958 #> 3 3 0 0 0 -0.1976283 -0.101362109 1.458615 -1.690053 -0.4757672 #> 4 4 0 0 0 -0.1047411 0.007761963 1.686399 -2.190053 -0.6900529 #> 5 5 0 0 0 -1.0336137 -1.192602838 1.280934 -1.832910 0.1670899 #> 6 6 0 0 0 -0.8478392 0.917129237 1.808289 -2.618624 0.1670899 #> date.3 ivel.1 ivel.2 ivel.3 #> 1 1.3813757 -0.5060353 -0.5060353 -0.5060353 #> 2 0.5956614 -0.9336151 -0.9907486 -1.1621491 #> 3 1.4528042 -1.1355754 -1.3388644 -1.6099164 #> 4 1.2385185 -0.8193481 -0.9272669 -1.1970640 #> 5 1.3813757 0.6375563 0.8803737 1.0422520 #> 6 1.3813757 -1.3288666 -1.0422624 -0.8989603# 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")