xtable | R Documentation |
Functions to format various objects following model selection and
multimodel inference to LaTeX or HTML tables. These functions extend the
methods from the xtable
package (Dahl 2014).
## S3 method for class 'aictab'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, include.AICc = TRUE,
include.LL = TRUE, include.Cum.Wt = FALSE, ...)
## S3 method for class 'anovaOD'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, ...)
## S3 method for class 'bictab'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, include.BIC = TRUE, include.LL = TRUE,
include.Cum.Wt = FALSE, ...)
## S3 method for class 'boot.wt'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, include.AICc = TRUE, include.AICcWt = FALSE, ...)
## S3 method for class 'countDist'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, table.countDist = "distance", ...)
## S3 method for class 'checkParms'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, include.variable = TRUE, include.max.se =
TRUE, include.n.high.se = TRUE, ...)
## S3 method for class 'countHist'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, table.countHist = "count", ...)
## S3 method for class 'detHist'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, table.detHist = "freq", ...)
## S3 method for class 'detTime'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, table.detTime = "freq", ...)
## S3 method for class 'dictab'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, include.DIC = TRUE, include.Cum.Wt = FALSE, ...)
## S3 method for class 'ictab'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE, nice.names = TRUE,
include.IC = TRUE, include.Cum.Wt = FALSE, ...)
## S3 method for class 'mb.chisq'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE, nice.names = TRUE,
include.detection.histories = TRUE, ...)
## S3 method for class 'modavg'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE, nice.names = TRUE,
print.table = FALSE, ...)
## S3 method for class 'modavgCustom'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, print.table = FALSE, ...)
## S3 method for class 'modavgEffect'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, print.table = FALSE, ...)
## S3 method for class 'modavgIC'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE, nice.names = TRUE,
print.table = FALSE, ...)
## S3 method for class 'modavgPred'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, ...)
## S3 method for class 'modavgShrink'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, print.table = FALSE, ...)
## S3 method for class 'multComp'
xtable(x, caption = NULL, label = NULL,
align = NULL, digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, print.table = FALSE, ...)
## S3 method for class 'summaryOD'
xtable(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, auto = FALSE,
nice.names = TRUE, ...)
x |
an object of class |
caption |
a character vector of length 1 or 2 storing the caption or title of
the table. If the vector is of length 2, the second item is the
short caption used when LaTeX generates a list of tables. The
default value is |
label |
a character vector storing the LaTeX label or HTML anchor. The default
value is |
align |
a character vector of length equal to the number of columns of the table specifying the alignment of the elements. Note that the rownames are considered as an additional column and require an alignment value. |
digits |
a numeric vector of length one or equal to the number of columns in the table (including the rownames) specifying the number of digits to display in each column. |
display |
a character vector of length equal to the number of columns
(including the rownames) specifying the format of each column. For
example, use |
auto |
Logical, indicating whether to apply automatic format when no value
is passed to |
nice.names |
logical. If |
include.AICc |
logical. If |
include.BIC |
logical. If |
include.DIC |
logical. If |
include.IC |
logical. If |
include.LL |
logical. If |
include.Cum.Wt |
logical. If |
include.AICcWt |
logical. If |
include.detection.histories |
logical. If |
include.variable |
logical. If |
include.max.se |
logical. If |
include.n.high.se |
logical. If |
print.table |
logical. If |
table.detHist |
character string specifying, either |
table.detTime |
character string specifying, either |
table.countDist |
character string specifying, either
|
table.countHist |
character string specifying, either
|
... |
additional arguments passed to the function. |
xtable
creates an object of the xtable
class inheriting
from the data.frame
class. This object can then be used with
print.xtable
for added flexibility such as suppressing row names,
modifying caption placement, and format tables in LaTeX or HTML
format.
Marc J. Mazerolle
Dahl, D. B. (2014) xtable: Export tables to LaTeX or HTML. R package version 1.7-3. https://cran.r-project.org/package=xtable.
aictab
, boot.wt
, dictab
,
formatC
, ictab
, mb.chisq
,
modavg
, modavgCustom
,
modavgIC
, modavgEffect
,
modavgPred
, modavgShrink
,
multComp
, summaryOD
, anovaOD
,
xtable
, print.xtable
if(require(xtable)) {
##model selection example
data(dry.frog)
##setup candidate models
Cand.models <- list( )
Cand.models[[1]] <- lm(log_Mass_lost ~ Shade + Substrate +
cent_Initial_mass + Initial_mass2,
data = dry.frog)
Cand.models[[2]] <- lm(log_Mass_lost ~ Shade + Substrate +
cent_Initial_mass + Initial_mass2 +
Shade:Substrate, data = dry.frog)
Cand.models[[3]] <- lm(log_Mass_lost ~ cent_Initial_mass +
Initial_mass2, data = dry.frog)
Model.names <- c("additive", "interaction", "no shade")
##model selection table - AICc
out <- aictab(cand.set = Cand.models, modnames = Model.names)
xtable(out)
##exclude AICc and LL
xtable(out, include.AICc = FALSE, include.LL = FALSE)
##remove row names and add caption
print(xtable(out, caption = "Model selection based on AICc"),
include.rownames = FALSE, caption.placement = "top")
##model selection table - BIC
out2 <- bictab(cand.set = Cand.models, modnames = Model.names)
xtable(out2)
##exclude AICc and LL
xtable(out2, include.BIC = FALSE, include.LL = FALSE)
##remove row names and add caption
print(xtable(out2, caption = "Model selection based on BIC"),
include.rownames = FALSE, caption.placement = "top")
##model-averaged estimate of Initial_mass2
mavg.mass <- modavg(cand.set = Cand.models, parm = "Initial_mass2",
modnames = Model.names)
#model-averaged estimate
xtable(mavg.mass, print.table = FALSE)
#table with contribution of each model
xtable(mavg.mass, print.table = TRUE)
##model-averaged predictions for first 10 observations
preds <- modavgPred(cand.set = Cand.models, modnames = Model.names,
newdata = dry.frog[1:10, ])
xtable(preds)
}
##example of diagnostics
## Not run:
if(require(unmarked)){
##distance sampling example from ?distsamp
data(linetran)
ltUMF <- with(linetran, {
unmarkedFrameDS(y = cbind(dc1, dc2, dc3, dc4),
siteCovs = data.frame(Length, area, habitat),
dist.breaks = c(0, 5, 10, 15, 20),
tlength = linetran$Length * 1000, survey = "line",
unitsIn = "m")
})
##summarize counts across distance classes
xtable(countDist(ltUMF), table.countDist = "distance")
##summarize counts across all sites
xtable(countDist(ltUMF), table.countDist = "count")
##Half-normal detection function
fm1 <- distsamp(~ 1 ~ 1, ltUMF)
##determine parameters with highest SE's
xtable(checkParms(fm1))
}
## End(Not run)
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