diff --git a/R/compare_spatial_vars.R b/R/compare_spatial_vars.R
index 2bb9ae9..ad46b78 100644
--- a/R/compare_spatial_vars.R
+++ b/R/compare_spatial_vars.R
@@ -13,7 +13,6 @@
 #' @param ref.years numeric vector with first and last year (years from start) for comparison period
 #' @param plot logical. do you want to generate a plot
 #'
-#' @inheritParams make_atlantis_diagnostic_figures
 #'
 #' @importFrom magrittr "%>%"
 #'
@@ -195,10 +194,10 @@ compare_spatial_vars = function(param.dir,
 
         #species ref box
         ref.data.box =boxes %>%
-          left_join(filter(ref.data,species == spp.names[s]))
+          dplyr::left_join(filter(ref.data,species == spp.names[s]))
 
         init.data.box = boxes %>%
-          left_join(filter(init.data,species == spp.names[s]))
+          dplyr::left_join(filter(init.data,species == spp.names[s]))
 
         plot.data.ls = list()
         for(r in 1:length(run.names)){
@@ -223,7 +222,7 @@ compare_spatial_vars = function(param.dir,
             dplyr::mutate(polygon = as.factor(polygon))
 
           plot.data.ls[[r]] = boxes %>%
-            left_join(plot.data.spp, by = 'polygon')
+            dplyr::left_join(plot.data.spp, by = 'polygon')
 
         }
         plot.data = dplyr::bind_rows(plot.data.ls)
@@ -294,10 +293,10 @@ compare_spatial_vars = function(param.dir,
 
         #species ref box
         ref.data.box =boxes %>%
-          left_join(filter(ref.data,species == fleet.combs$species[sf] & fleet == fleet.combs$fleet[sf]))
+          dplyr::left_join(filter(ref.data,species == fleet.combs$species[sf] & fleet == fleet.combs$fleet[sf]))
 
         init.data.box = boxes %>%
-          left_join(filter(init.data,species == fleet.combs$species[sf]))
+          dplyr::left_join(filter(init.data,species == fleet.combs$species[sf]))
 
         plot.data.ls = list()
         for(r in 1:length(run.names)){
@@ -329,7 +328,7 @@ compare_spatial_vars = function(param.dir,
           }
 
           plot.data.ls[[r]] = boxes %>%
-            left_join(plot.data.spp, by = 'polygon')
+            dplyr::left_join(plot.data.spp, by = 'polygon')
 
         }
         plot.data = dplyr::bind_rows(plot.data.ls)
diff --git a/R/process_atl_output.R b/R/process_atl_output.R
index eb306cd..a49cb4e 100644
--- a/R/process_atl_output.R
+++ b/R/process_atl_output.R
@@ -10,6 +10,7 @@
 #' @param system String. "Windows" or "Linux"
 #' @param process.all Boolean. Global option to process all components
 #' @param plot.spatial.overlap Boolean
+#' @param plot.catch.fleet Boolean
 #'
 #' @inheritParams make_atlantis_diagnostic_figures
 #'
diff --git a/man/process_atl_output.Rd b/man/process_atl_output.Rd
index 0acf395..86f07df 100644
--- a/man/process_atl_output.Rd
+++ b/man/process_atl_output.Rd
@@ -94,6 +94,8 @@ process_atl_output(
 
 \item{plot.catch}{logical. Plots annual catch(mt) age based catch (numbers) and age based \%ages}
 
+\item{plot.catch.fleet}{Boolean}
+
 \item{plot.spatial.catch}{logical. Plots showing the spatial (box/level) structure of groups' catch}
 
 \item{plot.mortality}{logical. Plots Mortality (F, M1, M2) from two output sources (Mort, SpecificMort)}