updated priors vignette so that it works, exported required functions

CHANGELOG.md

@@ -31,6 +31,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Replace deprecated `rlang::UQ` syntax with the recommended `!!`
 - Explicitly use `PEcAn.uncertainty::read.ensemble.output` in `PEcAn.utils::get.results`. Otherwise, it would sometimes use the deprecated `PEcAn.utils::read.ensemble.output` version.
 - History page would not pass the hostname parameter when showing a running workflow, this would result in the running page showing an error.
+- Fixed Priors vignette (#2439)
 
 ### Changed
 - Updated modules/rtm PROSPECT docs

modules/priors/DESCRIPTION

@@ -15,7 +15,8 @@ Depends:
     PEcAn.utils
 Imports:
     PEcAn.logger,
-    ggplot2
+    ggplot2,
+    MASS
 Suggests:
     testthat
 Encoding: UTF-8

modules/priors/NAMESPACE

@@ -1,15 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(plot,posterior.density)
-S3method(plot,prior.density)
-S3method(plot,trait)
 export(create.density.df)
 export(fit.dist)
 export(get.quantiles.from.density)
 export(get.sample)
+export(plot_densities)
+export(plot_posterior.density)
+export(plot_prior.density)
+export(plot_trait)
 export(pr.dens)
 export(pr.samp)
 export(prior.fn)
+export(priorfig)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)

modules/priors/R/plots.R

@@ -1,46 +1,46 @@
 ##--------------------------------------------------------------------------------------------------#
 ##' Plots a prior density from a parameterized probability distribution  
 ##'
-##' @name plot.prior.density
+##' @name plot_prior.density
 ##' @title Add Prior Density
 ##' @param prior.density 
 ##' @param base.plot a ggplot object (grob), created by \code{\link{create.base.plot}} if none provided
 ##' @param prior.color color of line to be plotted
 ##' @return plot with prior density added
 ##' @seealso \code{\link{pr.dens}}
 ##' @author David LeBauer
-##' @export
+##' @export plot_prior.density
 ##' @examples
 ##' \dontrun{
-##' plot.prior.density(pr.dens('norm', 0, 1))
+##' plot_prior.density(pr.dens('norm', 0, 1))
 ##' }
-plot.prior.density <- function(prior.density, base.plot = NULL, prior.color = "black") {
+plot_prior.density <- function(prior.density, base.plot = NULL, prior.color = "black") {
   if (is.null(base.plot)) {
     base.plot <- create.base.plot()
   }
   new.plot <- base.plot + geom_line(data = prior.density, aes(x = x, y = y), color = prior.color)
   return(new.plot)
-} # plot.prior.density
+} # plot_prior.density
 
 
 ##--------------------------------------------------------------------------------------------------#
 ##'  Add posterior density to a plot
 ##'
-##' @name plot.posterior.density
+##' @name plot_posterior.density
 ##' @title Add posterior density. 
 ##' @param posterior.density 
 ##' @param base.plot a ggplot object (grob), created by \code{\link{create.base.plot}} if none provided
 ##' @return plot with posterior density line added
-##' @export
+##' @export plot_posterior.density
 ##' @importFrom ggplot2 geom_line aes
 ##' @author David LeBauer
-plot.posterior.density <- function(posterior.density, base.plot = NULL) {
+plot_posterior.density <- function(posterior.density, base.plot = NULL) {
   if (is.null(base.plot)) {
     base.plot <- create.base.plot()
   }
   new.plot <- base.plot + geom_line(data = posterior.density, aes(x = x, y = y))
   return(new.plot)
-} # plot.posterior.density
+} # plot_posterior.density
 
 
 ##--------------------------------------------------------------------------------------------------#
@@ -54,6 +54,7 @@ plot.posterior.density <- function(posterior.density, base.plot = NULL) {
 ##' @param xlim limits for x axis
 ##' @author David LeBauer
 ##' @return plot / grob of prior distribution with data used to inform the distribution 
+##' @export
 ##' @importFrom ggplot2 ggplot aes theme_bw scale_x_continuous scale_y_continuous element_blank element_text geom_rug geom_line geom_point
 priorfig <- function(priordata = NA, priordensity = NA, trait = "", xlim = "auto", fontsize = 18) {
   if (is.data.frame(priordata)) {
@@ -78,7 +79,7 @@ priorfig <- function(priordata = NA, priordensity = NA, trait = "", xlim = "auto
           axis.text.x = element_text(size = fontsize),
           axis.title.y = element_blank(),   ## hide y axis label
           axis.title.x = element_text(size = fontsize * 0.9), 
-          plot.title = element_text(size = fontsize * 1.1))
+          plot_title = element_text(size = fontsize * 1.1))
 
   if (is.data.frame(priordata)) {
     priordata   <- subset(priordata, subset = !is.na(x))
@@ -101,7 +102,7 @@ priorfig <- function(priordata = NA, priordensity = NA, trait = "", xlim = "auto
 ##--------------------------------------------------------------------------------------------------#
 ##' Plot trait density and data
 ##'
-##' @name plot.trait
+##' @name plot_trait
 ##' @title Plot trait density
 ##' @param trait character, name of trait to be plotted
 ##' @param prior named distribution with parameters
@@ -111,18 +112,18 @@ priorfig <- function(priordata = NA, priordensity = NA, trait = "", xlim = "auto
 ##' @return plot (grob) object
 ##' @author David LeBauer
 ##' @importFrom ggplot2 theme_bw aes scale_x_continuous labs element_text element_blank
-##' @export
+##' @export plot_trait
 ##' @examples
 ##' \dontrun{
 ##' prior1 <- data.frame(distn = 'norm',
 ##'                      parama = 20,
 ##'                      paramb = 5)
 ##' data1  <- data.frame(Y = c(19, 21), se = c(1,1))
-##' plot.trait(trait = 'Vcmax',
+##' plot_trait(trait = 'Vcmax',
 ##'           prior = prior1,
 ##'           trait.df = data1)
 ##' }
-plot.trait <- function(trait,
+plot_trait <- function(trait,
                        prior = NULL,
                        posterior.sample = NULL,
                        trait.df = NULL,
@@ -132,23 +133,23 @@ plot.trait <- function(trait,
                        logx = FALSE) {
 
   ## Determine plot components
-  plot.posterior <- !is.null(posterior.sample)
-  plot.prior     <- !is.null(prior)
-  plot.data      <- !is.null(trait.df)
+  plot_posterior <- !is.null(posterior.sample)
+  plot_prior     <- !is.null(prior)
+  plot_data      <- !is.null(trait.df)
 
   ## get units for plot title
   units <- trait.lookup(trait)$units
 
-  if(plot.data)  trait.df <- jagify(trait.df)
+  if(plot_data)  trait.df <- jagify(trait.df)
 
-  if (plot.prior) {
-    prior.color   <- ifelse(plot.posterior, "grey", "black")
+  if (plot_prior) {
+    prior.color   <- ifelse(plot_posterior, "grey", "black")
     prior.density <- create.density.df(distribution = prior)
     prior.density <- prior.density[prior.density$x > 0, ]
   } else {
     prior.density <- data.frame(x = NA, y = NA)
   }
-  if (plot.posterior) {
+  if (plot_posterior) {
     posterior.density <- create.density.df(samps = posterior.sample)
     posterior.density <- posterior.density[posterior.density$x > 0, ]
   } else {
@@ -170,13 +171,13 @@ plot.trait <- function(trait,
   x.ticks <<- pretty(c(0, x.lim[2]))
 
   base.plot <- create.base.plot() + theme_bw()
-  if (plot.prior) {
-    base.plot <- plot.prior.density(prior.density, base.plot = base.plot, prior.color = prior.color)
+  if (plot_prior) {
+    base.plot <- plot_prior.density(prior.density, base.plot = base.plot, prior.color = prior.color)
   }
-  if (plot.posterior) {
-    base.plot <- plot.posterior.density(posterior.density, base.plot = base.plot)
+  if (plot_posterior) {
+    base.plot <- plot_posterior.density(posterior.density, base.plot = base.plot)
   }
-  if (plot.data) {
+  if (plot_data) {
     base.plot <- plot_data(trait.df, base.plot = base.plot, ymax = y.lim[2])
   }
 
@@ -191,38 +192,39 @@ plot.trait <- function(trait,
           axis.ticks.y = element_blank(), 
           axis.line.y = element_blank(), 
           legend.position = "none", 
-          plot.title = element_text(size = fontsize$title), 
+          plot_title = element_text(size = fontsize$title), 
           panel.grid.major = element_blank(), 
           panel.grid.minor = element_blank(), 
           panel.border = element_blank())
   return(trait.plot)
-} # plot.trait
+} # plot_trait
 
 
 ##--------------------------------------------------------------------------------------------------#
 ##' Plot probability density and data
 ##'
-##' @name plot.densities
+##' @name plot_densities
 ##' @title Plot Trait Probability Densities
-##' @param sensitivity.results list containing sa.samples and sa.splines 
+##' @param sensitivity.results list containing sa.samples and sa.splines
+##' @export plot_densities
 ##' @param outdir directory in which to generate figure as pdf 
 ##' @author David LeBauer
 ##' @return outputs plots in outdir/sensitivity.analysis.pdf file 
-plot.densities <- function(density.plot.inputs, outdir, ...) {
-  trait.samples       <- density.plot.inputs$trait.samples
-  trait.df            <- density.plot.inputs$trait.df
-  prior.trait.samples <- density.plot.inputs$trait.df
+plot_densities <- function(density.plot_inputs, outdir, ...) {
+  trait.samples       <- density.plot_inputs$trait.samples
+  trait.df            <- density.plot_inputs$trait.df
+  prior.trait.samples <- density.plot_inputs$trait.df
 
   traits <- names(trait.samples)
   pdf(paste0(outdir, "trait.densities.pdf"), height = 12, width = 20)
 
   for (trait in traits) {
-    density.plot <- plot.density(trait.sample = trait.samples[, trait], 
+    density.plot <- plot_density(trait.sample = trait.samples[, trait], 
                                  trait.df = trait.df[[trait]], ...)
     print(sensitivity.plot)
   }
   dev.off()
-} # plot.densities
+} # plot_densities
 
 
 ##--------------------------------------------------------------------------------------------------#
@@ -233,7 +235,7 @@ plot.densities <- function(density.plot.inputs, outdir, ...) {
 ##' @param priordensity density dataframe generated by \code{\link{create.density.df}}
 ##' @param quantiles default is the median and 95\% CI;
 ##' @author David LeBauer
-##' @export
+##' @export get.quantiles.from.density
 ##' @examples
 ##' prior.df <- create.density.df(distribution = list('norm',0,1))
 ##' get.quantiles.from.density(prior.df)

modules/priors/R/priors.R

@@ -24,28 +24,28 @@ fit.dist <- function(trait.data, trait = colnames(trait.data),
   }
   ## warning(immediate. = TRUE)
   nostart.dists <- dists[dists %in% c("weibull", "lognormal", "gamma", "normal")]
-  a <- lapply(nostart.dists, function(x) suppressWarnings(fitdistr(trait.data, x)))
+  a <- lapply(nostart.dists, function(x) suppressWarnings(MASS::fitdistr(trait.data, x)))
   names(a) <- nostart.dists
   if ("f" %in% dists) {
     print(trait)
     if (trait == "tt") {
-      a[["f"]] <- suppressWarnings(fitdistr(trait.data, "f", 
+      a[["f"]] <- suppressWarnings(MASS::fitdistr(trait.data, "f", 
                                             start = list(df1 = 100, df2 = 200)))
     } else if (trait == "sla") {
-      a[["f"]] <- suppressWarnings(fitdistr(trait.data, "f", 
+      a[["f"]] <- suppressWarnings(MASS::fitdistr(trait.data, "f", 
                                             start = list(df1 = 6, df2 = 1)))
     } else if (trait == "rrr") {
-      a[["f"]] <- suppressWarnings(fitdistr(trait.data, "f", 
+      a[["f"]] <- suppressWarnings(MASS::fitdistr(trait.data, "f", 
                                             start = list(df1 = 6, df2 = 1)))
     } else if (trait == "q") {
-      a[["f"]] <- suppressWarnings(fitdistr(trait.data, "f", 
+      a[["f"]] <- suppressWarnings(MASS::fitdistr(trait.data, "f", 
                                             start = list(df1 = 1, df2 = 2)))
     } else {
       PEcAn.logger::logger.severe(paste(trait, "not supported!"))
     }
   }
   if ("beta" %in% dists) {
-    a[["beta"]] <- suppressWarnings(fitdistr(trait.data, "beta", 
+    a[["beta"]] <- suppressWarnings(MASS::fitdistr(trait.data, "beta", 
                                              start = list(shape1 = 2, shape2 = 1)))
   }
   aicvalues <- lapply(a, AIC)