From 9e40fb09677e7cda305930e4834c2d50e4b84272 Mon Sep 17 00:00:00 2001
From: lizadams <lizadams@email.unc.edu>
Date: Fri, 13 Feb 2026 15:51:23 -0500
Subject: [PATCH 1/2] update plot examples

---
 docs/AMET_QuickStart_Guide_v16.md | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/docs/AMET_QuickStart_Guide_v16.md b/docs/AMET_QuickStart_Guide_v16.md
index 28a95ea3..ccaf7316 100644
--- a/docs/AMET_QuickStart_Guide_v16.md
+++ b/docs/AMET_QuickStart_Guide_v16.md
@@ -122,16 +122,16 @@ To compile these programs, edit the Makefile file that is located in the **src**
 > cd $AMETBASE/tools_src
 cd combine/src
 edit the combine Makefile
-> Make
+> make
 > cd bldoverlay/src
 edit the bldoverlay Makefile
-> Make
+> make
 > cd ../sitecmp/scr
 edit the sitecmp Makefile
-> Make
+> make
 > cd ../sitecmp_dailyo3/scr
 edit the sitecmp_dailyo3 Makefile
-> Make
+> make
 ```
 
 *Note: AMETBASE is the root AMET installation directory on your system*
@@ -209,6 +209,12 @@ Go to the output directory to view the plots:
 cd $AMETBASE/output/metExample_wrf/spatial_surface
 ```
 
+View the rmse of Temperature
+
+```
+okular metExample_wrf.rmse.T.20160701-20160801.pdf
+```
+
 Use the following command to navigate to the air quality analysis example project directory:
 
 ```
@@ -217,12 +223,18 @@ cd $AMETBASE/scripts_analysis/aqExample
 Edit the AMETBASE and AMET\_DATABASE variables to be consistent with the AMET installation on your system. Save and run the script:
 
 ```
-./run_scatterplot.csh |& tee scatterplot.log
+./run_scatterplot_density_ggplot.csh |& tee run_scatterplot_density_ggplot.log
 ```
 
 Go to the output directory and view the
 plots:
 
 ```
-cd $AMETBASE/output/aqExample/scatterplot
+cd $AMETBASE/output/aqExample/scatterplot_density_ggplot
+```
+
+View a density scatterplot of Temperature
+
+```
+okular metExample_wrf_T_1_scatterplot_density_ggplot.pdf
 ```

From bc99695f8fb06403f74fadfad2d9416b5b42b1ca Mon Sep 17 00:00:00 2001
From: lizadams <lizadams@email.unc.edu>
Date: Wed, 18 Feb 2026 11:45:43 -0500
Subject: [PATCH 2/2] add prism package

---
 docs/AMET_Install_Guide_v16.md | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/docs/AMET_Install_Guide_v16.md b/docs/AMET_Install_Guide_v16.md
index fe8ce8cb..67a62682 100644
--- a/docs/AMET_Install_Guide_v16.md
+++ b/docs/AMET_Install_Guide_v16.md
@@ -242,6 +242,7 @@ After you have installed the basic R software, AMET also requires the following
 * lubridate
 * maps
 * mapdata
+* prism
 * plotly
 * plotrix
 * processx
@@ -260,7 +261,7 @@ The easiest way to install R packages, is through the R package manager.  Once R
 ```
 > sudo R
 
-> install.packages(c("akima","data.table","date","dplyr","dygraphs","fields","ggplot2","grid","gridExtra","hexbin","htmltools","htmlwidgets","lattice","latticeExtra","leaflet","leaflet.extras","leafpop","lubridate","maps","mapdata","plotly","plotrix","processx","reshape2","RColorBrewer","RMySQL","RMariaDB","stats","webshot","xts","pandoc"),repos="http://cran.r-project.org")
+> install.packages(c("akima","data.table","date","dplyr","dygraphs","fields","ggplot2","grid","gridExtra","hexbin","htmltools","htmlwidgets","lattice","latticeExtra","leaflet","leaflet.extras","leafpop","lubridate","maps","mapdata","prism","plotly","plotrix","processx","reshape2","RColorBrewer","RMySQL","RMariaDB","stats","webshot","xts","pandoc"),repos="http://cran.r-project.org")
 
 ```
 
@@ -407,17 +408,17 @@ edit the sitecmp_dailyo3 Makefile
 > make |& tee make.log
 ```
 
-Note, the combine script directory contains a script called linkem that needs to be edited to point to your CMAQv5.5+ REPO directory to obtain the species definition files.
+Note, the combine script directory contains a script called linkem that needs to be edited to point to your CMAQ REPO directory to obtain the species definition files.
 
 ```
 cd $AMETBASE/tools_src/combine/scripts/spec_def_files
 vi linkem.csh
 ```
 
-Modify the set src = line to point to the CMAQv5.5+ Repository.
+Modify the set src = line to point to the CMAQv6.0 Repository.
 
 ```
-set src = /path_to/CMAQ/CMAQv5.5+/build/CMAQ_REPO_v5.5+/CCTM/src/MECHS
+set src = /path_to/CMAQ/CMAQv6.0/build/CMAQ_REPO_v6.0/CCTM/src/MECHS
 
 modify to the path for your CMAQ installation directory