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, ...)Fitted generalized linear model (glm- or logistf-object).
Type of plot. Use one of following:
"dots"(or "glm" or "or" (default)) for odds or incident rate ratios (forest plot). Note that this type plots the exponentiated estimates, thus being appropriate only for specific link-functions.
"eff"to plot marginal effects of predicted probabilities or incidents for each model term, where all remaining co-variates are set to the mean (see 'Details'). Use facet.grid to decide whether to plot each coefficient as separate plot or as integrated faceted plot.
"pred"to plot predicted values for the response, related to specific model predictors. See 'Details'.
"ma"to check model assumptions. Note that the only relevant argument for this option is fit. All other arguments are ignored.
"vif"to plot Variance Inflation Factors.
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 type - estimates, fixed effects slopes or predicted values
(mean, probabilities, incidents rates, ...). See 'Examples'.
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'.
Character vector with coefficient names that indicate
which estimates should be removed from the plot.
remove.estimates = "est_name" would remove the estimate est_name. Default
is NULL, i.e. all estimates are printed.
Logical, determines whether estimates should be sorted according to their values.
If group.estimates is not NULL, estimates are sorted
according to their group assignment.
character vector, used as plot title. Depending on plot type and function,
will be set automatically. If title = "", no title is printed.
For effect-plots, may also be a character vector of length > 1,
to define titles for each sub-plot or facet.
Character vector, used as title for the plot legend. Note that
only some plot types have legends (e.g. type = "pred" or when
grouping estimates with group.estimates).
character vector with labels used as axis labels. Optional argument, since in most cases, axis labels are set automatically.
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 type = "eff" for many predictors),
axis.title must be a character vector of same length of plots
that are printed. In this case, each plot gets an own axis title
(applying, for instance, to the y-axis for type = "eff").
Note: Some plot types do not support this argument. In such
cases, use the return value and add axis titles manually with
labs, e.g.: $plot.list[[1]] + labs(x = ...)
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.
User defined color palette for geoms. If group.estimates
is not specified, must either be vector with two color values or a specific
color palette code (see 'Details' in sjp.grpfrq). Else, if
group.estimates is specified, geom.colors must be a vector
of same length as groups. See 'Examples'.
numeric, determines how many chars of the plot title are displayed in one line and when a line break is inserted.
numeric, determines how many chars of the value, variable or axis labels are displayed in one line and when a line break is inserted.
Numeric vector of length 2, defining the range of the plot axis.
Depending on plot type, may effect either x- or y-axis, or both.
For multiple plot outputs (e.g., from type = "eff" or
type = "slope" in sjp.glm), axis.lim may
also be a list of vectors of length 2, defining axis limits for each
plot (only if non-faceted).
numeric; sets the distance between breaks for the axis,
i.e. at every grid.breaks'th position a major grid is being printed.
Logical, if TRUE, the grid lines have exponential
distances (equidistant), i.e. they visually have the same distance from
one panel grid to the next. If FALSE, grids are
plotted on every grid.breaks's position, thus the grid lines become narrower with
higher odds ratio values.
Logical, if TRUE, the intercept of the fitted model is also plotted.
Default is FALSE. For glm's, please note that due to exponential
transformation of estimates, the intercept in some cases can not be calculated, thus the
function call is interrupted and no plot printed.
Logical, whether values should be plotted or not.
Logical, adds significance levels to values, or value and variable labels.
Logical, if TRUE, depending on type, a confidence
interval or region is added to the plot. For frequency plots, the
confidence interval for the relative frequencies are shown.
logical, if TRUE, and depending on plot type and
function, a legend is added to the plot.
Logical, if TRUE, a summary with model statistics
is added to the plot.
Logical, if TRUE (default), adds a scatter plot of
data points to the plot. Only applies for slope-type or predictions plots.
For most plot types, dots are jittered to avoid overplotting, hence the
points don't reflect exact values in the data.
Alpha value of point-geoms in the scatter plots. Only applies,
if show.scatter = TRUE.
Color of of point-geoms in the scatter plots. Only applies,
if show.scatter = TRUE.
Logical, if TRUE and show.ci = TRUE and confidence
bands are displayed as error bars, adds jittering to lines and error bars
to avoid overlapping.
Numeric, amount of digits after decimal point when rounding estimates and values.
Linetype of the vertical "zero point" line. Default is 2 (dashed line).
Color of the vertical "zero point" line. Default value is "grey70".
logical, if TRUE, the x and y axis are swapped.
numeric, offset for text labels when their alignment is adjusted
to the top/bottom of the geom (see hjust and vjust).
TRUE to arrange the lay out of of multiple plots
in a grid of an integrated single plot. This argument calls
facet_wrap or facet_grid
to arrange plots. Use plot_grid to plot multiple plot-objects
as an arranged grid with grid.arrange.
logical, if TRUE (default), plots the results as graph. Use FALSE if you don't
want to plot any graphs. In either case, the ggplot-object will be returned as value.
Other arguments passed down to further functions. Currently, following arguments are supported:
?effects::effectAny arguments accepted by the effect resp.
allEffects function, for type = "eff".
widthThe width-argument for error bars.
alphaThe alpha-argument for confidence bands.
levelThe level-argument confidence bands.
(Insisibily) returns, depending on the plot type
The ggplot-object (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 ggplot-object(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 co-variates 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 co-variates, 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 x-axis and - optional - as grouping factor.
Hence, vars must be a character vector with the names of
one or two model predictors. See 'Examples'.