RMarkInput {secr} | R Documentation |
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 then 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.
From secr 4.6.6, missing values (.) in input capture histories are converted to NA in the output, with a warning. The resulting capthist is unusable until the NAs are removed.
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. Most recent edition available at 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)
library(RMark)
MarkPath <- 'c:/MARK' ## adjust for your installation
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)