better plot margins

DESCRIPTION

@@ -27,6 +27,7 @@ Imports:
     posterior (>= 1.0.0),
     loo (>= 2.3.1),
     parallel,
+    collapse,
     pbapply,
     tweedie,
     MASS,

R/as.data.frame.mvgam.R

@@ -54,8 +54,10 @@ as.data.frame.mvgam = function(x,
 
   # Get a string of all possible variables to extract
   all_vars <- variables(x)
-  all_orig_vars <- unique(unlist(purrr::map(all_vars, 'orig_name')))
-  all_alias_vars <- unique(unlist(purrr::map(all_vars, 'alias')))
+  all_orig_vars <- unlist(purrr::map(all_vars, 'orig_name'))
+  all_alias_vars <- unlist(purrr::map(all_vars, 'alias'))
+
+  all_orig_walias <- all_orig_vars[!is.na(all_alias_vars)]
   all_alias_vars <- all_alias_vars[!is.na(all_alias_vars)]
 
   # All possible var sets to extract
@@ -191,7 +193,7 @@ as.data.frame.mvgam = function(x,
           names_to_use[[i]] <- NA
         } else {
           if(any(all_alias_vars == variable[i])){
-            vars_to_extract[[i]] <- unname(unlist(purrr::map(all_vars, 'orig_name'))[
+            vars_to_extract[[i]] <- unname(all_orig_walias[
               which(all_alias_vars == variable[i])])
             names_to_use[[i]] <- variable[i]
           } else {

R/globals.R

@@ -8,4 +8,4 @@ utils::globalVariables(c("y", "year", "smooth_vals", "smooth_num",
                          "mod_call", "particles", "obs", "mgcv_model",
                          "param_name", "outcome", "mgcv_plottable",
                          "term", "data_test", "object", "row_num", "trends_test",
-                         "trend"))
+                         "trend", "trend_series", "trend_y", "."))

R/plot.mvgam.R

@@ -160,8 +160,6 @@ plot.mvgam = function(x, type = 'residuals',
     n_plots <- n_smooths
     if (n_plots==0) stop("No suitable terms to plot - plot.mvgam() only handles smooths of 2 or fewer dimensions.")
     pages <- 1
-    .pardefault <- par(no.readonly=T)
-    par(.pardefault)
 
     if (n_plots > 4) pages <- 2
     if (n_plots > 8) pages <- 3
@@ -179,7 +177,13 @@ plot.mvgam = function(x, type = 'residuals',
     if (c<1) r <- c <- 1
     if (c*r < ppp) c <- c + 1
     if (c*r < ppp) r <- r + 1
-    oldpar<-par(mfrow=c(r,c))
+
+    .pardefault <- par(no.readonly=T)
+    par(.pardefault)
+    oldpar<-par(mfrow=c(r,c),
+                mar=c(2.5, 2.3, 2, 2),
+                oma = c(1, 1, 0, 0),
+                mgp = c(1.5, 0.5, 0))
 
     } else { ppp<-1;oldpar<-par()}
 

R/plot_mvgam_factors.R

@@ -46,11 +46,20 @@ plot_mvgam_factors = function(object, plot = TRUE){
     .pardefault <- par(no.readonly=T)
     par(.pardefault)
     if(object$n_lv <= 2){
-      par(mfrow = c(1, 2))
+      par(mfrow = c(1, 2),
+          mar=c(2.5, 2.3, 2, 2),
+          oma = c(1, 1, 0, 0),
+          mgp = c(1.5, 0.5, 0))
     } else if(object$n_lv <= 4){
-      par(mfrow = c(2, 2))
+      par(mfrow = c(2, 2),
+          mar=c(2.5, 2.3, 2, 2),
+          oma = c(1, 1, 0, 0),
+          mgp = c(1.5, 0.5, 0))
     } else {
-      par(mfrow = c(3, 2))
+      par(mfrow = c(3, 2),
+          mar=c(2.5, 2.3, 2, 2),
+          oma = c(1, 1, 0, 0),
+          mgp = c(1.5, 0.5, 0))
     }
   }
 

R/plot_mvgam_pterms.R

@@ -55,11 +55,17 @@ if(length(pterms) > 0){
   }
 
   if(length(pterms) == 2){
-    par(mfrow = c(2, 1))
+    par(mfrow = c(2, 1),
+        mar=c(2.5, 2.3, 2, 2),
+        oma = c(1, 1, 0, 0),
+        mgp = c(1.5, 0.5, 0))
   }
 
   if(length(pterms) %in% c(3, 4)){
-    par(mfrow = c(2, 2))
+    par(mfrow = c(2, 2),
+        mar=c(2.5, 2.3, 2, 2),
+        oma = c(1, 1, 0, 0),
+        mgp = c(1.5, 0.5, 0))
   }
 
   for(i in 1:length(pterms)){