Replace matplot with the plot method in examples

inst/examples/ex-bernsteinPoly.R

@@ -9,9 +9,9 @@ bMat1 <- bernsteinPoly(x1, degree = 4, intercept = TRUE)
 ## generalized Bernstein polynomials basis over [- 2, 2]
 bMat2 <- bernsteinPoly(x2, degree = 4, intercept = TRUE)
 
-op <- par(mfrow = c(1, 2), mar = c(2.5, 2.5, 0.2, 0.1), mgp = c(1.5, 0.5, 0))
-matplot(x1, bMat1, type = "l", ylab = "y")
-matplot(x2, bMat2, type = "l", ylab = "y")
+op <- par(mfrow = c(1, 2))
+plot(bMat1)
+plot(bMat2)
 
 ## the first and second derivative matrix
 d1Mat1 <- bernsteinPoly(x1, degree = 4, derivs = 1, intercept = TRUE)
@@ -20,10 +20,10 @@ d1Mat2 <- bernsteinPoly(x2, degree = 4, derivs = 1, intercept = TRUE)
 d2Mat2 <- bernsteinPoly(x2, degree = 4, derivs = 2, intercept = TRUE)
 
 par(mfrow = c(2, 2))
-matplot(x1, d1Mat1, type = "l", ylab = "y")
-matplot(x2, d1Mat2, type = "l", ylab = "y")
-matplot(x1, d2Mat1, type = "l", ylab = "y")
-matplot(x2, d2Mat2, type = "l", ylab = "y")
+plot(d1Mat1)
+plot(d1Mat2)
+plot(d2Mat1)
+plot(d2Mat2)
 
 ## reset to previous plotting settings
 par(op)

inst/examples/ex-cSpline.R

@@ -6,16 +6,11 @@ knots <- c(0.3, 0.5, 0.6)
 ### when 'scale = TRUE' (by default)
 csMat <- cSpline(x, knots = knots, degree = 2)
 
-op <- par(mar = c(2.5, 2.5, 0.2, 0.1), mgp = c(1.5, 0.5, 0))
-matplot(x, csMat, type = "l", ylab = "C-spline basis")
-abline(v = knots, lty = 2, col = "gray")
+plot(csMat, ylab = "C-spline basis", mark_knots = "internal")
 isMat <- deriv(csMat)
 msMat <- deriv(csMat, derivs = 2)
-matplot(x, isMat, type = "l", ylab = "scaled I-spline basis")
-matplot(x, msMat, type = "l", ylab = "scaled M-spline basis")
-
-## reset to previous plotting settings
-par(op)
+plot(isMat, ylab = "scaled I-spline basis")
+plot(msMat, ylab = "scaled M-spline basis")
 
 ### when 'scale = FALSE'
 csMat <- cSpline(x, knots = knots, degree = 2, scale = FALSE)

inst/examples/ex-iSpline.R

@@ -1,16 +1,13 @@
 library(splines2)
 
-## Example given in the reference paper by Ramsay (1988)
+## an example given in Ramsay (1988)
 x <- seq.int(0, 1, by = 0.01)
 knots <- c(0.3, 0.5, 0.6)
 isMat <- iSpline(x, knots = knots, degree = 2)
 
 op <- par(mar = c(2.5, 2.5, 0.2, 0.1), mgp = c(1.5, 0.5, 0))
-matplot(x, isMat, type = "l", ylab = "I-spline basis")
-abline(v = knots, lty = 2, col = "gray")
-
-## reset to previous plotting settings
-par(op)
+plot(isMat, ylab = "I-spline basis", mark_knots = "internal")
+par(op) # reset to previous plotting settings
 
 ## the derivative of I-splines is M-spline
 msMat1 <- iSpline(x, knots = knots, degree = 2, derivs = 1)

inst/examples/ex-mSpline.R

@@ -6,8 +6,7 @@ knots <- c(0.3, 0.5, 0.6)
 msMat <- mSpline(x, knots = knots, degree = 2, intercept = TRUE)
 
 op <- par(mar = c(2.5, 2.5, 0.2, 0.1), mgp = c(1.5, 0.5, 0))
-matplot(x, msMat, type = "l", ylab = "y")
-abline(v = knots, lty = 2, col = "gray")
+plot(msMat, mark_knots = "internal")
 
 ## derivatives of M-splines
 dmsMat <- mSpline(x, knots = knots, degree = 2,
@@ -32,16 +31,12 @@ dMat1 <- mSpline(x, knots = knots, degree = 3, intercept = TRUE,
 dMat2 <- deriv(pMat)
 
 par(mfrow = c(2, 2))
-matplot(x, pMat, type = "l", ylab = "Periodic Basis")
-abline(v = seq.int(0, max(x)), lty = 2, col = "grey")
-matplot(x, iMat, type = "l", ylab = "Integrals from 0")
+plot(pMat, ylab = "Periodic Basis", mark_knots = "boundary")
+plot(iMat, ylab = "Integrals from 0")
 abline(v = seq.int(0, max(x)), h = seq.int(0, max(x)), lty = 2, col = "grey")
-matplot(x, dMat1, type = "l", ylab = "1st derivatives by 'derivs=1'")
-abline(v = seq.int(0, max(x)), lty = 2, col = "grey")
-matplot(x, dMat2, type = "l", ylab = "1st derivatives by 'deriv()'")
-abline(v = seq.int(0, max(x)), lty = 2, col = "grey")
-## reset to previous plotting settings
-par(op)
+plot(dMat1, ylab = "1st derivatives by 'derivs=1'", mark_knots = "boundary")
+plot(dMat2, ylab = "1st derivatives by 'deriv()'", mark_knots = "boundary")
+par(op) # reset to previous plotting settings
 
 ### default placement of internal knots for periodic splines
 default_knots <- function(x, df, intercept = FALSE,
@@ -56,12 +51,13 @@ df <- 8
 degree <- 3
 intercept <- TRUE
 internal_knots <- default_knots(x, df, intercept)
+
 ## 1. specify df
-spline_basis1 =  splines2::mSpline(x, degree = degree, df = df,
-                                   periodic = TRUE, intercept = intercept)
+spline_basis1 =  mSpline(x, degree = degree, df = df,
+                         periodic = TRUE, intercept = intercept)
 ## 2. specify knots
-spline_basis2 =  splines2::mSpline(x, degree = degree, knots = internal_knots,
-                                   periodic = TRUE, intercept = intercept)
+spline_basis2 =  mSpline(x, degree = degree, knots = internal_knots,
+                         periodic = TRUE, intercept = intercept)
 
 all.equal(internal_knots, knots(spline_basis1))
 all.equal(spline_basis1, spline_basis2)