R/sjPlotOdds.R
sjp.glm.Rd
Plot odds or incident rate ratios with confidence intervalls as dot plot.
Depending on the type
argument, this function may also plot model
assumptions for generalized linear models, or marginal effects
(predicted probabilities or events).
sjp.glm(fit, type = "dots", vars = NULL, group.estimates = NULL, remove.estimates = NULL, sort.est = TRUE, title = NULL, legend.title = NULL, axis.labels = NULL, axis.title = NULL, geom.size = NULL, geom.colors = "Set1", wrap.title = 50, wrap.labels = 25, axis.lim = NULL, grid.breaks = 0.5, trns.ticks = TRUE, show.intercept = FALSE, show.values = TRUE, show.p = TRUE, show.ci = FALSE, show.legend = FALSE, show.summary = FALSE, show.scatter = TRUE, point.alpha = 0.2, point.color = NULL, jitter.ci = FALSE, digits = 2, vline.type = 2, vline.color = "grey70", coord.flip = TRUE, y.offset = 0.15, facet.grid = TRUE, prnt.plot = TRUE, ...)
fit  Fitted generalized linear model ( 

type  Type of plot. Use one of following:

vars  Numeric vector with column indices of selected variables or a character vector with
variable names of selected variables from the fitted model, which should be used to plot
 depending on 
group.estimates  Numeric or character vector, indicating a group identifier for each estimate. Dots and confidence intervals of estimates are coloured according to their group association. See 'Examples'. 
remove.estimates  Character vector with coefficient names that indicate
which estimates should be removed from the plot.

sort.est  Logical, determines whether estimates should be sorted according to their values.
If 
title  character vector, used as plot title. Depending on plot type and function,
will be set automatically. If 
legend.title  Character vector, used as title for the plot legend. Note that
only some plot types have legends (e.g. 
axis.labels  character vector with labels used as axis labels. Optional argument, since in most cases, axis labels are set automatically. 
axis.title  Character vector of length one or two (depending on
the plot function and type), used as title(s) for the x and y axis.
If not specified, a default labelling is chosen. To set multiple
axis titles (e.g. with 
geom.size  size resp. width of the geoms (bar width, line thickness or point size, depending on plot type and function). Note that bar and bin widths mostly need smaller values than dot sizes. 
geom.colors  User defined color palette for geoms. If 
wrap.title  numeric, determines how many chars of the plot title are displayed in one line and when a line break is inserted. 
wrap.labels  numeric, determines how many chars of the value, variable or axis labels are displayed in one line and when a line break is inserted. 
axis.lim  Numeric vector of length 2, defining the range of the plot axis.
Depending on plot type, may effect either x or yaxis, or both.
For multiple plot outputs (e.g., from 
grid.breaks  numeric; sets the distance between breaks for the axis,
i.e. at every 
trns.ticks  Logical, if 
show.intercept  Logical, if 
show.values  Logical, whether values should be plotted or not. 
show.p  Logical, adds significance levels to values, or value and variable labels. 
show.ci  Logical, if 
show.legend  logical, if 
show.summary  Logical, if 
show.scatter  Logical, if 
point.alpha  Alpha value of pointgeoms in the scatter plots. Only applies,
if 
point.color  Color of of pointgeoms in the scatter plots. Only applies,
if 
jitter.ci  Logical, if 
digits  Numeric, amount of digits after decimal point when rounding estimates and values. 
vline.type  Linetype of the vertical "zero point" line. Default is 
vline.color  Color of the vertical "zero point" line. Default value is 
coord.flip  logical, if 
y.offset  numeric, offset for text labels when their alignment is adjusted
to the top/bottom of the geom (see 
facet.grid 

prnt.plot  logical, if 
...  Other arguments passed down to further functions. Currently, following arguments are supported:

(Insisibily) returns, depending on the plot type
The ggplotobject (plot
). For multiple plots and if facet.grid = FALSE
) a plot.list
is returned.
A data frame data
with the data used to build the ggplotobject(s), or a list of data frames (data.list
).
type = "slope"
the predicted values
are based on the intercept's estimate and each specific term's estimate.
All other covariates are set to zero (i.e. ignored), which corresponds
to family(fit)$linkinv(eta = b0 + bi * xi)
(where xi
is the estimate).
This plot type can be seen as equivalent to type = "slope"
for sjp.lm
,
just for glm objects. This plot type may give similar results as
type = "pred"
, however, type = "slope"
does not adjust
for other predictors.
type = "eff"
computes marginal effects of all higher order
terms in the model. The predicted values computed by type = "eff"
are adjusted for all other covariates, by setting them to the mean
(as returned by the allEffects
function).
You can pass further arguments down to allEffects
for flexible
function call via the ...
argument.
type = "pred"
the predicted values
of the response are computed, based on the predict.glm
method. Corresponds to predict(fit, type = "response")
.
This plot type requires the vars
argument to select specific terms
that should be used for the xaxis and  optional  as grouping factor.
Hence, vars
must be a character vector with the names of
one or two model predictors. See 'Examples'.