inst/tinytest/unusual-formulas.R

In pbreheny/visreg: Visualization of Regression Models

suppressPackageStartupMessages(library(lme4))
suppressPackageStartupMessages(library(locfit))
suppressPackageStartupMessages(library(mgcv))
suppressPackageStartupMessages(library(survival))
suppressPackageStartupMessages(library(splines))

fit <- lm(Ozone ~ Solar.R + poly(Wind, 4) + poly(Temp, 4), airquality)
visreg(fit, "Wind")
visreg(fit, "Temp")

fit <- lm(Ozone ~ I(Solar.R/2) + Wind + Temp, data=airquality)
visreg(fit, "Solar.R")
fit <- lm(Ozone ~ I(Solar.R^2) + Wind + Temp, data=airquality)
visreg(fit, "Solar.R")
fit <- lm(Ozone ~ I(Solar.R+2) + Wind + Temp, data=airquality)
visreg(fit, "Solar.R")
fit <- lm(Ozone ~ I(Solar.R*2) + Wind + Temp, data=airquality)
visreg(fit, "Solar.R")
fit <- lm(Ozone ~ I(Solar.R/Wind) + Temp, data=airquality)
visreg(fit, "Solar.R")

# lme4
data(Orthodont, package="nlme")
Orthodont$nsex <- as.numeric(Orthodont$Sex=="Male")
fit <- lmer(distance ~ age + (age|Subject) + (0+nsex|Subject) + (0 + nsex:age|Subject), data=Orthodont) |> suppressMessages()
visreg(fit, "age")

data(ethanol, package="locfit")
fit <- locfit(NOx~lp(E, nn=0.5), data=ethanol)
visreg(fit, "E")
fit <- locfit(NOx~lp(E,C,nn=0.5,scale=0), data=ethanol)
visreg(fit, "E", by="C")

# splines
fit <- lm(Ozone ~ Solar.R + bs(Wind, 4) + ns(Temp, 4), airquality)
visreg(fit, "Wind")
visreg(fit, "Temp")

# survival
fit <- coxph(Surv(time, status) ~ ph.ecog + pspline(age,4), cancer)
visreg(fit, "age")
visreg(fit, "age", type="contrast")

# mgcv
capture.output(dat <- gamSim(2,n=200,dist="normal",scale=0.1)$data) |> invisible()
fit <- gam(y~s(x)+s(z), data=dat)
visreg(fit, "x")
fit <- gam(y~s(x, z),data=dat)
visreg(fit, "x")
visreg(fit, "z")
fit <- gam(y~te(x,z,k=7),data=dat, method="REML")
visreg(fit, "x", by="z")
fit <- gam(y~ti(x,z,k=7), data=dat, method="REML")
visreg(fit, "x", by="z")
visreg2d(fit, "x", "z")