Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
warnings = FALSE,
fig.width = 6,
fig.height = 4
)
library(rms)
## ----setup--------------------------------------------------------------------
#the regression modelling by F. Harrell
library(rms)
#the extension for plotting the rms summary objects
library(ormPlot)
#to modify plots
library(ggplot2)
## ----eval=FALSE---------------------------------------------------------------
# #show first 6 rows
# head(educ_data)
## ----echo=FALSE, results="asis"-----------------------------------------------
pander::pandoc.table(head(educ_data), split.tables=Inf)
## ---- eval = FALSE------------------------------------------------------------
# #show variable explanation
# help(educ_data)
## -----------------------------------------------------------------------------
#q.effect determines for what range the odds ratios are given on plots
dd <- datadist(educ_data, q.effect = c(0.5, 0.75))
#set it also to options
options(datadist="dd")
## -----------------------------------------------------------------------------
#see help(orm) for further info
orm_model<-orm(educ_3 ~ Rural + sex + n_siblings + cran_rzs + height_rzs +
FW_rzs + YOBc + (YOBc * sex) + (YOBc * Rural), data = educ_data)
## -----------------------------------------------------------------------------
plot(orm_model, cran_rzs)
## -----------------------------------------------------------------------------
plot(orm_model, cran_rzs, Rural, sex)
## -----------------------------------------------------------------------------
p<-plot(orm_model, cran_rzs, Rural, sex,
xlab = "Cranial volume (residuals to age an birth date)",
facet_labels = list(Rural = c("Urban", "Rural"),sex=c("Male","Female")))
colors <- c("#4a9878", "#0a191e", "#d8b65c")
educ_names <- c("Primary", "Secondary", "Tertiary")
# further modifing like any other ggplot
final_plot<-p + labs(color = "Education", fill = "Education") +
scale_color_manual(values = colors, labels = educ_names) +
scale_fill_manual(values = colors, labels = educ_names)
final_plot
## ----eval = FALSE-------------------------------------------------------------
# ggsave("educ_cran.svg",final_plot, height = 8 ,width = 8)
## ----fig.width=7, fig.height=4------------------------------------------------
forestplot(summary(orm_model))
## ----fig.width=6--------------------------------------------------------------
# you can use also use plot instead of forestplot
plots<-forestplot(summary(orm_model), return_ggplots=T)
plots[[1]]
plots[[2]]
## ---- fig.width=7-------------------------------------------------------------
p1 <- plots[[1]] +
scale_x_discrete(labels=c("Mean", "Lower CI", "Upper CI"),
position = "top",
name = NULL)
# the x axis is actually y axis because the cordinates are flipped with coord_flip()
p2 <- plots[[2]] + scale_y_continuous(breaks = c(0.5, 0.7, 0.9, 1.1),
position = "right")
forestplot<-join_ggplots(p1,p2)
## ---- eval=FALSE--------------------------------------------------------------
# ggsave("forestplot.svg",forestplot)
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