R: Plot polynomials for (generalized) linear regression

sjp.poly {sjPlot}

R Documentation

Plot polynomials for (generalized) linear regression

Description

This function plots a scatter plot of a term poly.term against a response variable x and adds - depending on the amount of numeric values in poly.degree - multiple polynomial curves. A loess-smoothed line can be added to see which of the polynomial curves fits best to the data.

Usage

sjp.poly(x, poly.term, poly.degree, poly.scale = FALSE, fun = NULL,
  axis.title = NULL, geom.colors = NULL, geom.size = 0.8,
  show.loess = TRUE, show.loess.ci = TRUE, show.p = TRUE,
  show.scatter = TRUE, point.alpha = 0.2, point.color = "#404040",
  loess.color = "#808080", prnt.plot = TRUE)

Arguments

`x`	A vector, representing the response variable of a linear (mixed) model; or a linear (mixed) model as returned by `lm` or `lmer`.
`poly.term`	If `x` is a vector, `poly.term` should also be a vector, representing the polynomial term (independent variabl) in the model; if `x` is a fitted model, `poly.term` should be the polynomial term's name as character string. See 'Examples'.
`poly.degree`	Numeric, or numeric vector, indicating the degree of the polynomial. If `poly.degree` is a numeric vector, multiple polynomial curves for each degree are plotted. See 'Examples'.
`poly.scale`	Logical, if `TRUE`, `poly.term` will be scaled before linear regression is computed. Default is `FALSE`. Scaling the polynomial term may have an impact on the resulting p-values.
`fun`	Linear function when modelling polynomial terms. Use `fun = "lm"` for linear models, or `fun = "glm"` for generalized linear models. When `x` is not a vector, but a fitted model object, the function is detected automatically. If `x` is a vector, `fun` defaults to `"lm"`.
`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 `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 = ...)`
`geom.colors`	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'.
`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.
`show.loess`	Logical, if `TRUE`, an additional loess-smoothed line is plotted.
`show.loess.ci`	Logical, if `TRUE`, a confidence region for the loess-smoothed line will be plotted.
`show.p`	Logical, if `TRUE` (default), p-values for polynomial terms are printed to the console.
`show.scatter`	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.
`point.alpha`	Alpha value of point-geoms in the scatter plots. Only applies, if `show.scatter = TRUE`.
`point.color`	Color of of point-geoms in the scatter plots. Only applies, if `show.scatter = TRUE`.
`loess.color`	Color of the loess-smoothed line. Only applies, if `show.loess = TRUE`.
`prnt.plot`	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.

Details

For each polynomial degree, a simple linear regression on x (resp. the extracted response, if x is a fitted model) is performed, where only the polynomial term poly.term is included as independent variable. Thus, lm(y ~ x + I(x^2) + ... + I(x^i)) is repeatedly computed for all values in poly.degree, and the predicted values of the reponse are plotted against the raw values of poly.term. If x is a fitted model, other covariates are ignored when finding the best fitting polynomial.

This function evaluates raw polynomials, not orthogonal polynomials. Polynomials are computed using the poly function, with argument raw = TRUE.

To find out which polynomial degree fits best to the data, a loess-smoothed line (in dark grey) can be added (with show.loess = TRUE). The polynomial curves that comes closest to the loess-smoothed line should be the best fit to the data.

Value

(Insisibily) returns

plot: the ggplot-object with the complete plot
df: the data frame that was used for setting up the ggplot-object
cutpoints: a data frame that indicates x-values and predicted y-values of each direction change in the loess curvature

Examples

library(sjmisc)
data(efc)
# linear fit. loess-smoothed line indicates a more
# or less cubic curve
sjp.poly(efc$c160age, efc$quol_5, 1)

# quadratic fit
sjp.poly(efc$c160age, efc$quol_5, 2)

# linear to cubic fit
sjp.poly(efc$c160age, efc$quol_5, 1:4, show.scatter = FALSE)


# fit sample model
fit <- lm(tot_sc_e ~ c12hour + e17age + e42dep, data = efc)
# inspect relationship between predictors and response
sjp.lm(fit, type = "slope", show.loess = TRUE, show.scatter = FALSE)
# "e17age" does not seem to be linear correlated to response
# try to find appropiate polynomial. Grey line (loess smoothed)
# indicates best fit. Looks like x^4 has the best fit,
# however, only x^3 has significant p-values.
sjp.poly(fit, "e17age", 2:4, show.scatter = FALSE)

## Not run: 
# fit new model
fit <- lm(tot_sc_e ~ c12hour + e42dep + e17age + I(e17age^2) + I(e17age^3),
          data = efc)
# plot marginal effects of polynomial term
sjp.lm(fit, type = "poly", poly.term = "e17age")
## End(Not run)

[Package sjPlot version 2.4.1 Index]