Convert Data to RMark Input Format
A single-session capthist object is formed by RMarkInput into a dataframe that may be passed directly to RMark.
RMarkInput(object, grouped = FALSE, covariates = TRUE) unRMarkInput(df, covariates = TRUE)
object |
secr capthist object |
grouped |
logical for whether to replace each group of identical capture histories with a single line |
covariates |
logical or character vector; see Details |
df |
dataframe with fields ‘ch’ and ‘freq’ |
To convert a multi-session object first collapse the sessions with
join.
If covariates is TRUE the all columns of individual covariates
in the input are appended as columns in the output. If
covariates is a character-valued vector then only the specified
covariates will be appended.
If both grouped and covariates are specified in
RMarkInput, grouped will be ignored, with a warning.
For RMarkInput –
Dataframe with fields ch and freq. ‘ch’ is a character string of 0's
and 1's. If grouped = FALSE the rownames are retained and the
value of ‘freq’ is 1 or -1. Negative values of ‘freq’ indicate
removal.
The dataframe also includes individual covariates specified with
covariates.
The attribute ‘intervals’ is copied from ‘object’, if present; otherwise it is set to a vector of zeros (indicating a closed-population sample).
For unRMarkInput –
A single-session capthist object with no traps attribute and hence no detector type (i.e. non-spatial capture histories). Covariates are copied as requested.
In versions before 2.4.0, a spurious occasion was added by
RMarkInput when grouped = FALSE. Thanks to Jeff Stetz for
spotting this.
The default value for grouped changed to FALSE in secr 2.4.0
Laake, J. and Rexstad E. (2008) Appendix C. RMark - an alternative approach to building linear models in MARK. In: Cooch, E. and White, G. (eds) Program MARK: A Gentle Introduction. 6th edition. Available at http://www.phidot.org/software/mark/docs/book/.
## ovenCH is a 5-year mist-netting dataset
ovenRD <- RMarkInput (join(ovenCH))
head(ovenRD)
unRMarkInput(ovenRD)
RMarkInput(deermouse.ESG, covariates = FALSE, grouped = TRUE)
RMarkInput(deermouse.ESG, covariates = TRUE)
## Not run:
## fit robust-design model in RMark (MARK must be installed)
## may need to set MarkPath, e.g., MarkPath <- 'c:/MARK'
library(RMark)
ovenRD.data <- process.data(ovenRD, model = "Robust",
time.interval = attr(ovenRD, "intervals"))
ovenRD.model <- mark(data = ovenRD.data, model = "Robust",
model.parameters = list(p = list(formula = ~1, share = TRUE),
GammaDoublePrime = list(formula = ~1),
GammaPrime = list(formula = ~1),
f0 = list(formula = ~1)))
cleanup(ask = FALSE)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.