4.0.1 to cran

Author: guyabel

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: fanplot
 Type: Package
 Title: Visualisation of Sequential Probability Distributions Using Fan Charts
-Version: 4.0.0
+Version: 4.0.1
 Authors@R: c(person(c("Guy", "J."), "Abel", role = c("aut", "cre"),
                     email = "g.j.abel@gmail.com",
                     comment = c(ORCID = "0000-0002-4893-5687")))
@@ -13,13 +13,18 @@ Description: Visualise sequential distributions using a range of plotting
     different styles, including fan chart type plots, where a set of coloured
     polygon, with shadings corresponding to the percentile values are layered
     to represent different uncertainty levels. Full details in R Journal article; Abel (2015) <doi:10.32614/RJ-2015-002>.
-License: GPL-2
+License: GPL-3
+Encoding: UTF-8
 URL: http://guyabel.github.io/fanplot/
 BugReports: https://github.com/guyabel/fanplot/issues/
-Imports:
-    methods
 Depends: 
     R (>= 2.10)
+Imports:
+    methods
 Suggests: 
-    shiny
+    shiny,
+    RColorBrewer,
+    colorspace,
+    zoo
 LazyData: true
+RoxygenNote: 7.3.3

NAMESPACE

@@ -1,8 +1,2 @@
 exportPattern("^[[:alpha:]]+")
-importFrom("grDevices", "adjustcolor", "heat.colors")
-importFrom("graphics", "box", "boxplot", "lines", "plot", "polygon", "rect", "text")
-importFrom("stats", "lag", "median", "pnorm", "qnorm", "quantile", "runif", "time", "ts")
-importFrom("methods", "is")
-
-
-
+importFrom("methods", "is")

NEWS.md

@@ -1,3 +1,7 @@
+# fanplot 4.0.1
+
+* updated suggests for demo file, as required for CRAN
+
 # fanplot 4.0.0
 
 * Added a `NEWS.md` file to track changes to the package.
@@ -6,6 +10,6 @@
 * Expanded README
 * Added hex
 * Github actions working
-* Transferred blog posts from `https://gjabel.wordpress.com/` 
+* Transferred blog posts from `https://gjabel.wordpress.com/` to `https://guyabel.github.io/fanplot/`
 
 

R/fan.R

@@ -2,7 +2,7 @@ fan <-
   function(data = NULL, data.type="simulations", style = "fan", type = "percentile",
            probs = if(type=="percentile") seq(0.01, 0.99, 0.01) else c(0.5, 0.8, 0.95), 
            start = 1, frequency = 1, anchor = NULL, anchor.time=NULL,
-           fan.col = heat.colors, alpha = if (style == "spaghetti") 0.5 else 1, 
+           fan.col = grDevices::heat.colors, alpha = if (style == "spaghetti") 0.5 else 1, 
            n.fan = NULL,
            ln = if(length(probs)<10) probs else 
              probs[round(probs,2) %in% round(seq(0.1, 0.9, 0.1),2)],
@@ -31,7 +31,7 @@ fan <-
     ##
     ##data classes
     ##
-    if(is(data, "mts")[1]){
+    if(methods::is(data, "mts")[1]){
       start<-start(data)[1]
       frequency<-frequency(data)
     }
@@ -59,7 +59,7 @@ fan <-
       #work out quantiles
       if(data.type=="simulations"){
         pp<-as.matrix(data)
-        pp<-apply(pp,2,quantile,probs=p)
+        pp<-apply(pp,2,stats::quantile,probs=p)
       }
       if(data.type=="values"){
         pp<-as.matrix(data)
@@ -86,18 +86,18 @@ fan <-
 
 
       #ts info
-      if(!is(data, "zoo")[1]){
-        ppts <- ts(pp, start = start, frequency = frequency)
-        tt<-time(ppts)
+      if(!methods::is(data, "zoo")[1]){
+        ppts <- stats::ts(pp, start = start, frequency = frequency)
+        tt<-stats::time(ppts)
         tt<-as.numeric(tt)
         if(!is.null(anchor)){
-          ppts <- ts(pp, start = time(lag(ppts))[1], frequency = frequency)
-          tt <- time(ppts)
+          ppts <- stats::ts(pp, start = stats::time(stats::lag(ppts))[1], frequency = frequency)
+          tt <- stats::time(ppts)
           tt<-as.numeric(tt)
         }
       }
-      if(is(data, "zoo")[1]){
-        tt<-time(data)
+      if(methods::is(data, "zoo")[1]){
+        tt<-stats::time(data)
         if(!is.null(anchor))
           tt<-c(anchor.time,tt)
       }
@@ -112,7 +112,7 @@ fan <-
         fan.col<-fan.col(floor(n/2))
       if(!is.null(n.fan))
         fan.col<-fan.col(n.fan)
-      fan.col<-adjustcolor(fan.col,alpha.f=alpha)
+      fan.col <- grDevices::adjustcolor(fan.col,alpha.f=alpha)
       if(is.null(ln.col))
         ln.col<-fan.col[1]
     }
@@ -124,7 +124,7 @@ fan <-
       fan.fill<-function(ts1, ts2, tt, fan.col="grey"){
         xx <- cbind(tt,rev(tt)) 
         yy <- cbind(as.vector(ts1),rev(as.vector(ts2)))
-        polygon(xx,yy, col=fan.col, border=fan.col)
+        graphics::polygon(x = xx, y = yy, col = fan.col, border = fan.col)
       }
       #plot(cpi, type = "l", xlim = c(y0-5, y0+3), ylim = c(-2, 7))
       #plot(NULL, type = "n", xlim = c(1, 945),  ylim = range(th.mcmc), ylab = "Theta")
@@ -142,7 +142,7 @@ fan <-
       x<-pp[,1]
       for(i in 1:nrow(pp)){
         for(j in 1:floor(n/2)){
-          rect(xleft=tt[i]-0.5*space, ybottom=pp[i,j], xright=tt[i]+0.5*space, ytop=pp[i,n-j+1], col=fan.col[floor(n/2)+1-j], border=fan.col[floor(n/2)+1-j])
+          graphics::rect(xleft=tt[i]-0.5*space, ybottom=pp[i,j], xright=tt[i]+0.5*space, ytop=pp[i,n-j+1], col=fan.col[floor(n/2)+1-j], border=fan.col[floor(n/2)+1-j])
         }
       }
     }
@@ -169,12 +169,12 @@ fan <-
         #plot lines
         if(style=="fan"){
           for(i in match(ln0, p))
-            lines(x=tt, y=pp[,i], col=ln.col)
+            graphics::lines(x=tt, y=pp[,i], col=ln.col)
         }
         if(style=="boxfan"){
           for(i in 1:nrow(pp)){
             for(j in match(ln0, p)){
-              lines(x=tt[i]+c(-0.5,0.5)*space, y=rep(pp[i,j],2), col=ln.col)
+              graphics::lines(x=tt[i]+c(-0.5,0.5)*space, y=rep(pp[i,j],2), col=ln.col)
             }
           }
         }
@@ -202,9 +202,9 @@ fan <-
         rlab<-round(rlab, 5)
         for(i in match(rlab, p)){
           if(style=="fan")
-            text(tt[length(tt)], pp[nrow(pp),i], colnames(pp)[i], pos=rpos, offset=roffset, cex=rcex, col=rcol)
+            graphics::text(tt[length(tt)], pp[nrow(pp),i], colnames(pp)[i], pos=rpos, offset=roffset, cex=rcex, col=rcol)
           if(style=="boxfan")
-            text(tt[length(tt)]+0.5*space, pp[nrow(pp),i], colnames(pp)[i], pos=rpos, offset=roffset, cex=rcex, col=rcol)
+            graphics::text(tt[length(tt)]+0.5*space, pp[nrow(pp),i], colnames(pp)[i], pos=rpos, offset=roffset, cex=rcex, col=rcol)
         }
         if(is.na(sum(match(rlab,p))))
           print("some right labels not plotted as conflict with precentiles given in probs")
@@ -224,9 +224,9 @@ fan <-
           llab<-rlab
         for(i in match(llab, p)){
           if(style=="fan")
-            text(tt[1], pp[1,i],  colnames(pp)[i], pos=lpos, offset=loffset, cex=lcex, col=lcol)
+            graphics::text(tt[1], pp[1,i],  colnames(pp)[i], pos=lpos, offset=loffset, cex=lcex, col=lcol)
           if(style=="boxfan")
-            text(tt[1]-0.5*space, pp[1,i], colnames(pp)[i], pos=lpos, offset=loffset, cex=lcex, col=lcol)
+            graphics::text(tt[1]-0.5*space, pp[1,i], colnames(pp)[i], pos=lpos, offset=loffset, cex=lcex, col=lcol)
         }
         if(is.na(sum(match(llab,p))))
           print("some left labels not plotted as conflict with precentiles given in probs")
@@ -237,28 +237,28 @@ fan <-
     if(style=="fan" | style=="boxfan"){
       if(med.ln==TRUE & data.type=="simulations"){
         pp<-data
-        pm<-apply(pp,2,median)
+        pm<-apply(pp,2,stats::median)
         if(!is.null(anchor))
           pm<-c(anchor,pm)
         if(is.null(med.col))
           med.col<-ln.col
         if(style=="fan"){
-          lines(x=tt, y=pm, col=med.col)
+          graphics::lines(x=tt, y=pm, col=med.col)
         }
         if(style=="boxfan"){
           for(i in 1:nrow(pp)){
             #lines(x=(i-1)/frequency+c(-0.5,0.5)*space, y=rep(pm[i],2), col=med.col)
-            lines(x=tt[i]+c(-0.5,0.5)*space, y=rep(pm[i],2), col=med.col)
+            graphics::lines(x=tt[i]+c(-0.5,0.5)*space, y=rep(pm[i],2), col=med.col)
           }
         }
         if(!is.null(rlab) & style %in% c("fan","spaghetti"))
-          text(tt[length(tt)], pm[length(pm)], medlab, pos=rpos, offset=roffset, cex=rcex, col=rcol)
+          graphics::text(tt[length(tt)], pm[length(pm)], medlab, pos=rpos, offset=roffset, cex=rcex, col=rcol)
         if(!is.null(rlab) & style=="boxfan")
-          text(tt[length(tt)]+0.5*space, pm[length(pm)], medlab, pos=rpos, offset=roffset, cex=rcex, col=rcol)
+          graphics::text(tt[length(tt)]+0.5*space, pm[length(pm)], medlab, pos=rpos, offset=roffset, cex=rcex, col=rcol)
         if(any(llab==TRUE,is.numeric(llab)) & style %in% c("fan","spaghetti"))
-          text(tt[1], pm[1], medlab, pos=lpos, offset=loffset, cex=lcex, col=lcol)
+          graphics::text(tt[1], pm[1], medlab, pos=lpos, offset=loffset, cex=lcex, col=lcol)
         if(any(llab==TRUE,is.numeric(llab)) & style=="boxfan")
-          text(tt[1]-0.5*space, pm[1], medlab, pos=lpos, offset=loffset, cex=lcex, col=lcol)
+          graphics::text(tt[1]-0.5*space, pm[1], medlab, pos=lpos, offset=loffset, cex=lcex, col=lcol)
       }
     }
 
@@ -272,9 +272,9 @@ fan <-
       #add ancohor
       if(!is.null(anchor))
         ps<-cbind(rep(anchor,nrow(ps)),ps)
-      spag.col<-adjustcolor(ln.col,alpha.f=alpha)
+      spag.col <- grDevices::adjustcolor(ln.col,alpha.f=alpha)
       for(i in 1:nrow(ps))
-        lines(x=tt, y=ps[i,], col=spag.col)
+        graphics::lines(x=tt, y=ps[i,], col=spag.col)
     }
 
     ##
@@ -288,12 +288,12 @@ fan <-
       if(!is.null(anchor))
         print("anchor ignored for boxplots plots")
       #single time series to use for at=time 
-      p<-ts(pp[1,], start=start, frequency=frequency)
+      p<-stats::ts(pp[1,], start=start, frequency=frequency)
       #plot(NULL, type = "n", xlim = c(1, 10),  ylim = range(pp), ylab = "Theta")
       for(i in 1:n)
-        boxplot(pp[,i], add=TRUE, at=time(p)[i], boxwex=space, xaxt = "n", yaxt = "n",...)
+        graphics::boxplot(pp[,i], add=TRUE, at=stats::time(p)[i], boxwex=space, xaxt = "n", yaxt = "n",...)
     }
-    box()
+    graphics::box()
   }
 
 

R/fan0.R

@@ -2,7 +2,7 @@ fan0 <-
   function(data = NULL, data.type = "simulations", style = "fan", type = "percentile",
            probs = if(type=="percentile") seq(0.01, 0.99, 0.01) else c(0.5, 0.8, 0.95), 
            start = 1, frequency = 1, anchor = NULL, anchor.time=NULL,
-           fan.col = heat.colors, alpha = if (style == "spaghetti") 0.5 else 1, 
+           fan.col = grDevices::heat.colors, alpha = if (style == "spaghetti") 0.5 else 1, 
            n.fan = NULL,
            ln = NULL, ln.col = if(style=="spaghetti") "gray" else NULL, 
            med.ln = if(type=="interval") TRUE else FALSE, med.col= "orange",

R/psplitnorm.R

@@ -34,7 +34,7 @@ function(x, mode = 0, sd = 1, skew = 0, sd1 = NULL, sd2 = NULL) {
   k[] <- x #change name of x to match formula
   k1 <- k <= mode
   k2 <- k > mode
-  f[k1] <- (c[k1] * sqrt(2 * pi) * sd1[k1] * pnorm((k[k1] - mode[k1])/sd1[k1]))
-  f[k2] <- (1 - c[k2] * sqrt(2 * pi) * sd2[k2] * (1 - pnorm((k[k2] - mode[k2])/sd2[k2])))
+  f[k1] <- (c[k1] * sqrt(2 * pi) * sd1[k1] * stats::pnorm((k[k1] - mode[k1])/sd1[k1]))
+  f[k2] <- (1 - c[k2] * sqrt(2 * pi) * sd2[k2] * (1 - stats::pnorm((k[k2] - mode[k2])/sd2[k2])))
   return(f)
 }

R/qsplitnorm.R

@@ -36,7 +36,7 @@ function(p, mode = 0, sd = 1, skew = 0, sd1 = NULL, sd2 = NULL) {
   p <- psplitnorm(mode, mode = mode, sd1 = sd1, sd2 = sd2) 
   alpha1 <- alpha <= p
   alpha2 <- alpha > p
-  f[alpha1] <- (mode[alpha1] + sd1[alpha1] * qnorm( alpha[alpha1]/(c[alpha1] * sqrt(2 * pi) * sd1[alpha1])))
-  f[alpha2] <- (mode[alpha2] + sd2[alpha2] * qnorm((alpha[alpha2]+ c[alpha2] * sqrt(2 * pi) * sd2[alpha2] - 1)/(c[alpha2] * sqrt(2 * pi) * sd2[alpha2])))
+  f[alpha1] <- (mode[alpha1] + sd1[alpha1] * stats::qnorm( alpha[alpha1]/(c[alpha1] * sqrt(2 * pi) * sd1[alpha1])))
+  f[alpha2] <- (mode[alpha2] + sd2[alpha2] * stats::qnorm((alpha[alpha2]+ c[alpha2] * sqrt(2 * pi) * sd2[alpha2] - 1)/(c[alpha2] * sqrt(2 * pi) * sd2[alpha2])))
   f
 }

R/rsplitnorm.R

@@ -26,7 +26,7 @@ function(n, mode = 0, sd = 1, skew = 0, sd1 = NULL, sd2 = NULL) {
   }
   if (any(findInterval(skew, c(-1,1), rightmost.closed=TRUE)!=1) )
     stop("skew must be between -1 and 1")
-  u <- runif(n)
+  u <- stats::runif(n)
   f <- qsplitnorm(u, mode = mode, sd = sd, skew = skew, sd1 = sd1, sd2 = sd2)
   f
 }

README.Rmd

@@ -22,7 +22,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/guyabel/fanplot/workflows/R-CMD-check/badge.svg)](https://github.com/guyabel/fanplot/actions)
 <!-- badges: end -->
 
-<img src='https://raw.githubusercontent.com/guyabel/fanplot/master/hex/logo_transp.png' align="right" height="200" style="float:right; height:200px;"/>
+<!-- <img src='https://raw.githubusercontent.com/guyabel/fanplot/master/hex/logo_transp.png' align="right" height="180" style="padding-left: 20px; padding-bottom: 20px;" /> -->
 
 Visualise sequential distributions using a range of plotting styles. Sequential distribution data can be input as either simulations or values corresponding to percentiles over time. Plots are added to existing graphic devices using the fan function. Users can choose from four different styles, including fan chart type plots, where a set of coloured polygon, with shadings corresponding to the percentile values are layered to represent different uncertainty levels.
 

README.md

@@ -14,7 +14,7 @@ superseded](https://img.shields.io/badge/lifecycle-superseded-blue.svg)](https:/
 [![R-CMD-check](https://github.com/guyabel/fanplot/workflows/R-CMD-check/badge.svg)](https://github.com/guyabel/fanplot/actions)
 <!-- badges: end -->
 
-<img src='https://raw.githubusercontent.com/guyabel/fanplot/master/hex/logo_transp.png' align="right" height="200" style="float:right; height:200px;"/>
+<!-- <img src='https://raw.githubusercontent.com/guyabel/fanplot/master/hex/logo_transp.png' align="right" height="180" style="padding-left: 20px; padding-bottom: 20px;" /> -->
 
 Visualise sequential distributions using a range of plotting styles.
 Sequential distribution data can be input as either simulations or