Skip to content

minor updates #261

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
lizadams wants to merge 2 commits into
base: develop
Choose a base branch
from
Open

minor updates #261

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
9e40fb0
update plot examples
lizadams Feb 13, 2026
bc99695
add prism package
lizadams Feb 18, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 5 additions & 4 deletions docs/AMET_Install_Guide_v16.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -242,6 +242,7 @@ After you have installed the basic R software, AMET also requires the following
* lubridate
* maps
* mapdata
* prism
* plotly
* plotrix
* processx
Expand All @@ -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")

```

Expand Down Expand Up @@ -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

Expand Down
24 changes: 18 additions & 6 deletions docs/AMET_QuickStart_Guide_v16.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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*
Expand Down Expand Up @@ -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:

```
Expand All @@ -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
```