Remove deprecated ggplot2 functions

11 files changed, 63 insertions, 42 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 1671e72..4011db0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -12,15 +12,16 @@ Imports:
     gridExtra,
     lme4,
     loo,
-    Matrix,
+    Matrix (>= 1.5-0),
     methods,
     pbapply,
     Rcpp (>= 0.12.0),
+    rlang,
     RSpectra,
     rstan (>= 2.18.1),
     rstantools (>= 2.0.0),
     stats
-Suggests: covr, devtools, knitr, pkgdown, raster, rmarkdown, rlang, roxygen2, testthat
+Suggests: covr, devtools, knitr, pkgdown, raster, rmarkdown, roxygen2, testthat
 VignetteBuilder: knitr
 Description: Fit Bayesian hierarchical models of animal abundance and occurrence
     via the 'rstan' package, the R interface to the 'Stan' C++ library.
@@ -34,7 +35,7 @@ License: GPL (>=3)
 URL: https://kenkellner.com/ubms/
 BugReports: https://github.com/kenkellner/ubms/issues
 Encoding: UTF-8
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.2
 Biarch: true
 LinkingTo: 
     BH (>= 1.66.0),
diff --git a/NAMESPACE b/NAMESPACE
index 2032258..9b3d89a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -52,7 +52,7 @@ import(Rcpp)
 importClassesFrom(rstan,stanfit)
 importFrom(RSpectra,eigs)
 importFrom(ggplot2,aes)
-importFrom(ggplot2,aes_string)
+importFrom(ggplot2,after_stat)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
@@ -93,6 +93,7 @@ importFrom(methods,callNextMethod)
 importFrom(methods,new)
 importFrom(pbapply,pblapply)
 importFrom(pbapply,pboptions)
+importFrom(rlang,sym)
 importFrom(rstan,extract)
 importFrom(rstan,get_elapsed_time)
 importFrom(rstan,get_stancode)
diff --git a/R/distsamp.R b/R/distsamp.R
index 021b489..b42b8e0 100644
--- a/R/distsamp.R
+++ b/R/distsamp.R
@@ -417,32 +417,33 @@ setMethod("sim_fitted", "ubmsFitDistsamp", function(object, submodel, samples, .
 #Histogram---------------------------------------------------------------------
 
 #' @importFrom graphics hist
-#' @importFrom ggplot2 geom_histogram
+#' @importFrom ggplot2 geom_histogram after_stat
 setMethod("hist", "ubmsFitDistsamp", function(x, draws=30, ...){
   samples <- get_samples(x, draws)
   hist_data <- get_hist_data(x)
   mean_line <- get_mean_line(x)
-
-  out <- ggplot(hist_data, aes_string(x="x")) +
-    geom_histogram(aes_string(y="..density.."),fill='transparent',
+  
+  xval <- sym("x"); val <- sym("val"); ind <- sym("ind"); dens <- sym("density")
+  out <- ggplot(hist_data, aes(x={{xval}})) +
+    geom_histogram(aes(y=after_stat({{dens}})),fill='transparent',
                    col='black',breaks=x@response@dist_breaks)
 
   #Adjust the histogram height to match the density line
   bar_height <- ggplot2::ggplot_build(out)$data[[1]]$y[1]
   adj_factor <- max(mean_line$val, na.rm=TRUE) / bar_height
 
-  out <- ggplot(hist_data, aes_string(x="x")) +
-    geom_histogram(aes_string(y=paste0("..density..*",adj_factor)),fill='transparent',
+  out <- ggplot(hist_data, aes(x={{xval}})) +
+    geom_histogram(aes(y=after_stat({{dens}})*adj_factor),fill='transparent',
                    col='black',breaks=x@response@dist_breaks)
 
   if(draws > 0){
     sample_lines <- get_sample_lines(x, samples)
     out <- out +
-      geom_line(data=sample_lines, aes_string(x="x", y="val", group="ind"),
+      geom_line(data=sample_lines, aes(x={{xval}}, y={{val}}, group={{ind}}),
               alpha=0.3)
   }
   out +
-    geom_line(data=mean_line, aes_string(x="x", y="val"), col='red') +
+    geom_line(data=mean_line, aes(x={{xval}}, y={{val}}), col='red') +
     labs(x=paste0("Distance (", x@response@units_in,")"), y="Density") +
     theme_bw() +
     theme(panel.grid.major=element_blank(), panel.grid.minor=element_blank(),
diff --git a/R/gof.R b/R/gof.R
index fe7c7bd..4143ca6 100644
--- a/R/gof.R
+++ b/R/gof.R
@@ -15,13 +15,17 @@ setMethod("show", "ubmsGOF", function(object){
 
 #' @importFrom ggplot2 ggplot aes geom_abline geom_point theme_bw labs
 #' @importFrom ggplot2 facet_wrap theme element_blank element_text element_rect
-#' @importFrom ggplot2 geom_label unit aes_string ggtitle
+#' @importFrom ggplot2 geom_label unit ggtitle
+#' @importFrom rlang sym
 setMethod("plot", "ubmsGOF", function(x, ...){
+  obs <- sym("obs")
+  sim <- sym("sim")
+  lab <- sym("lab")
   ppval <- data.frame(lab=paste("P =", round(x@post_pred_p, 3)))
-  ggplot(x@samples, aes_string(x="obs", y="sim")) +
-    geom_abline(aes(intercept=0, slope=1),size=1.2, col='red') +
+  ggplot(x@samples, aes(x={{obs}}, y={{sim}})) +
+    geom_abline(aes(intercept=0, slope=1), linewidth=1.2, col='red') +
     geom_point(alpha=0.4) +
-    geom_label(data=ppval, aes_string(x=-Inf, y=Inf, label="lab"),
+    geom_label(data=ppval, aes(x=-Inf, y=Inf, label={{lab}}),
                hjust=-0.2, vjust=1.4, size=5,
                fill='white', label.size=0,
                label.padding=unit(0.1, "lines")) +
diff --git a/R/plot_effects.R b/R/plot_effects.R
index cf3f73a..5eb3ffa 100644
--- a/R/plot_effects.R
+++ b/R/plot_effects.R
@@ -98,9 +98,11 @@ marg_numeric_plot <- function(object, submodel, covariate, quant,
     plot_df$lower <- stats::lowess(plot_df$lower, f=smooth)[[2]]
     plot_df$upper <- stats::lowess(plot_df$upper, f=smooth)[[2]]
   }
-
-  ggplot(data=plot_df, aes_string(x="covariate", y="mn")) +
-    geom_ribbon(aes_string(ymin="lower", ymax="upper"), alpha=0.3) +
+  
+  covariate <- sym("covariate"); mn <- sym("mn")
+  lower <- sym("lower"); upper <- sym("upper")
+  ggplot(data=plot_df, aes(x={{covariate}}, y={{mn}})) +
+    geom_ribbon(aes(ymin={{lower}}, ymax={{upper}}), alpha=0.3) +
     geom_line() +
     labs(x = covariate, y = sm@name) +
     plot_theme() +
@@ -117,9 +119,11 @@ marg_factor_plot <- function(object, submodel, covariate, quant, draws){
 
   plot_df <- get_margplot_data(object, submodel, covariate, quant,
                                samples, newdata)
-
-  ggplot(data=plot_df, aes_string(x="covariate", y="mn")) +
-    geom_errorbar(aes_string(ymin="lower", ymax="upper"), width=0.4) +
+  
+  covariate <- sym("covariate"); mn <- sym("mn")
+  lower <- sym("lower"); upper <- sym("upper")
+  ggplot(data=plot_df, aes(x={{covariate}}, y={{mn}})) +
+    geom_errorbar(aes(ymin={{lower}}, ymax={{upper}}), width=0.4) +
     geom_point(size=2) +
     labs(x = covariate, y = sm@name) +
     plot_theme() +
diff --git a/R/plot_posteriors.R b/R/plot_posteriors.R
index 65e8449..65150c2 100644
--- a/R/plot_posteriors.R
+++ b/R/plot_posteriors.R
@@ -52,8 +52,9 @@ setMethod("plot_posteriors", "ubmsFit", function(object, pars=NULL, density=FALS
   plot_dat$parameter <- factor(plot_dat$parameter, levels=pars)
 
   if(density){
+    samples <- sym("samples"); chain <- sym("chain")
     out <- ggplot(data=plot_dat) +
-      stat_density(aes_string(x="samples", col="chain"), geom="line",
+      stat_density(aes(x={{samples}}, col={{chain}}), geom="line",
                    position="identity", ...) +
       labs(x="Value", y="Density") +
       facet_wrap("parameter", scales="free") +
@@ -61,8 +62,9 @@ setMethod("plot_posteriors", "ubmsFit", function(object, pars=NULL, density=FALS
       theme(strip.text=element_text(size=12),
             strip.background=element_rect("white"))
   } else {
+    samples <- sym("samples")
     out <- ggplot(data=plot_dat) +
-      geom_histogram(aes_string(x="samples"),fill='gray90',col='black', ...) +
+      geom_histogram(aes(x={{samples}}),fill='gray90',col='black', ...) +
       labs(x="Value", y="Count") +
       facet_wrap("parameter", scales="free") +
       plot_theme() +
diff --git a/R/residuals.R b/R/residuals.R
index a34b5e7..6e9d31c 100644
--- a/R/residuals.R
+++ b/R/residuals.R
@@ -129,8 +129,9 @@ plot_pearson_residuals <- function(x, res, xlab, name){
             })
   pl_dat <- do.call("rbind", pl_dat)
   pl_dat <- pl_dat[stats::complete.cases(pl_dat),]
-
-  ggplot(data=pl_dat, aes_string(x="x", y="y")) +
+  
+  x <- sym("x"); y <- sym("y")
+  ggplot(data=pl_dat, aes(x={{x}}, y={{y}})) +
     geom_hline(aes(yintercept=0), linetype=2) +
     geom_point() +
     facet_wrap("ind") +
@@ -145,12 +146,14 @@ plot_binned_residuals <- function(x, res, xlab, name, nbins){
                   get_binned_residuals(x[i,], res[i,], i, nbins)})
   pl_dat <- do.call("rbind", pl_dat)
   pl_dat <- pl_dat[stats::complete.cases(pl_dat),]
-
-  ggplot(data=pl_dat, aes_string(x="x_bar", y="y_bar")) +
-    geom_ribbon(aes_string(ymin="y_lo", ymax="y_hi"), alpha=0.1) +
+  
+  x_bar <- sym("x_bar"); y_bar <- sym("y_bar")
+  y_lo <- sym("y_lo"); y_hi <- sym("y_hi")
+  ggplot(data=pl_dat, aes(x={{x_bar}}, y={{y_bar}})) +
+    geom_ribbon(aes(ymin={{y_lo}}, ymax={{y_hi}}), alpha=0.1) +
     geom_hline(aes(yintercept=0), linetype=2) +
-    geom_line(aes_string(y="y_hi"), col='gray', size=1.1) +
-    geom_line(aes_string(y="y_lo"), col='gray', size=1.1)+
+    geom_line(aes(y={{y_hi}}), col='gray', linewidth=1.1) +
+    geom_line(aes(y={{y_lo}}), col='gray', linewidth=1.1)+
     geom_point() +
     facet_wrap("ind") +
     ggtitle(paste(name, "submodel residuals plot")) +
diff --git a/R/spatial.R b/R/spatial.R
index 5c76f06..bf690b9 100644
--- a/R/spatial.R
+++ b/R/spatial.R
@@ -75,10 +75,11 @@ plot_RSR <- function(coords, A, threshold, focal_site){
     neighbors$type <- "Neighbors"
     focal <- rbind(focal, neighbors)
   }
+  x <- sym("x"); y <- sym("y"); type <- sym("type")
 
-  ggplot(focal, aes_string(x="x",y="y")) +
+  ggplot(focal, aes(x={{x}},y={{y}})) +
     geom_point(data=plot_dat, alpha=0.3) +
-    geom_point(aes_string(col="type")) +
+    geom_point(aes(col={{type}})) +
     scale_color_manual(values=c("red","blue")) +
     plot_theme() +
     theme(legend.text=element_text(size=14),
@@ -278,9 +279,11 @@ plot_spatial <- function(object, param=c('state','eta'), sites=TRUE, cell_size=N
     est <- Kmat %*% colMeans(b)
   }
   plot_data <- cbind(as.data.frame(coords), est=est)
+  
+  x <- sym(nms[1]); y <- sym(nms[2]); est <- sym("est")
 
-  out <- ggplot(data=plot_data, aes_string(x=nms[1], y=nms[2])) +
-    geom_tile(aes_string(fill="est"), width=cell_size, height=cell_size) +
+  out <- ggplot(data=plot_data, aes(x={{x}}, y={{y}})) +
+    geom_tile(aes(fill={{est}}), width=cell_size, height=cell_size) +
     scale_fill_gradientn(colors=terrain.colors(10)) +
     labs(fill=param) +
     plot_theme() +
@@ -292,15 +295,17 @@ plot_spatial <- function(object, param=c('state','eta'), sites=TRUE, cell_size=N
     if(inherits(object, "ubmsFitOccuTTD")){
       coords_samp$obs <- as.numeric(coords_samp$obs < object@response@surveyLength)
     }
+    
+    obs <- sym("obs")
 
     if(inherits(object, c("ubmsFitOccu","ubmsFitOccuTTD","ubmsFitOccuRN"))){
       coords_samp$obs <- factor(coords_samp$obs)
-      out <- out + geom_point(data=coords_samp, aes_string(col="obs"),
+      out <- out + geom_point(data=coords_samp, aes(col={{obs}}),
                             size=1, pch=19) +
         scale_color_manual(values=c("gray","black")) +
         labs(color="Detected")
     } else {
-      out <- out + geom_point(data=coords_samp, aes_string(size="obs"), pch=19) +
+      out <- out + geom_point(data=coords_samp, aes(size={{obs}}), pch=19) +
         #scale_color_manual(values=c("gray","black")) +
         labs(size="Minimum\ncount")
     }
diff --git a/man/gof.Rd b/man/gof.Rd
index c4e8307..6b25158 100644
--- a/man/gof.Rd
+++ b/man/gof.Rd
@@ -32,12 +32,12 @@ checks
 }
 \section{Functions}{
 \itemize{
-\item \code{gof,ubmsFitOccu-method}: Applies the MacKenzie-Bailey chi-square goodness of fit test for
+\item \code{gof(ubmsFitOccu)}: Applies the MacKenzie-Bailey chi-square goodness of fit test for
 ocupancy models (MacKenzie and Bailey 2004).
 
-\item \code{gof,ubmsFitAbun-method}: A goodness-of-fit test for N-mixture type models based on Pearson's chi-square.
-}}
+\item \code{gof(ubmsFitAbun)}: A goodness-of-fit test for N-mixture type models based on Pearson's chi-square.
 
+}}
 \references{
 MacKenzie, D. I., & Bailey, L. L. (2004). Assessing the
  fit of site-occupancy models. Journal of Agricultural, Biological,
diff --git a/src/Makevars b/src/Makevars
index e7a95c7..1a7240d 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -14,7 +14,7 @@ PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppPa
 PKG_LIBS+= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 
 # COMMENT THIS OUT WHEN TESTING CLANG COMPILER
-CXX_STD = CXX14
+# CXX_STD = CXX14
 
 
 all: $(SHLIB)
diff --git a/src/Makevars.win b/src/Makevars.win
index a16dabe..01e474c 100644
--- a/src/Makevars.win
+++ b/src/Makevars.win
@@ -7,7 +7,7 @@ PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::Cx
 PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")
 PKG_LIBS+= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 
-CXX_STD = CXX14
+# CXX_STD = CXX14
 
 all: $(SHLIB)