diff --git a/docs/README.md b/docs/README.md
index 02bfc5e74676e5cafb415fea29034a953db92cdd..3eba4574ac99d18f25b025e271ae740b8995026d 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -17,8 +17,8 @@ to use *nshmp-haz-v2* as well as underlying model implementation details.
* [Developer Basics](./pages/Developer-Basics.md)
* [Calculation Configuration](./pages/Calculation-Configuration.md)
* [Site Specification](./pages/Site-Specification.md)
- * Examples [on GitLab](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples)
- or [in a local copy](../etc/examples/README.md)
+ * [Examples](../../etc/examples/README.md) (or
+ [on GitLab](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples))
* [Hazard Model](./pages/Hazard-Model.md)
* [Model Structure](./pages/Model-Structure.md)
* [Model Files](./pages/Model-Files.md)
diff --git a/docs/pages/About-the-NSHMP.md b/docs/pages/About-the-NSHMP.md
index 76f1ce136ff5508bc522ac1bd565acd1c76ac8a6..2ee3a89ea3da645cc77555b5faad65e554e5b928 100644
--- a/docs/pages/About-the-NSHMP.md
+++ b/docs/pages/About-the-NSHMP.md
@@ -24,8 +24,8 @@ U.S. and its territories to consider the best available science.
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Building-&-Running.md b/docs/pages/Building-&-Running.md
index beda1c7e49678f53b0e980ef35b1c9ff84ee0ba8..3a1bd0cc06218166c9e7bdfe7462d917a87b7f97 100644
--- a/docs/pages/Building-&-Running.md
+++ b/docs/pages/Building-&-Running.md
@@ -2,7 +2,12 @@
## Related Pages
-TODO
+* Building & Running
+ * [Developer Basics](./Developer-Basics.md)
+ * [Calculation Configuration](./Calculation-Configuration.md)
+ * [Site Specification](./Site-Specification.md)
+ * [Examples](../../etc/examples/README.md) (or
+ [on GitLab](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples))
## Build & Run Options
@@ -11,12 +16,12 @@ TODO
## Build and Run Locally
-Building and running *nshmp-haz* requires prior installation of Git and Java. Please see the
-[developer basics](developer-basics) page for system configuration guidance.
+Building and running *nshmp-haz-v2* requires prior installation of Git and Java. Please see the
+[developer basics](./Developer-Basics.md) page for system configuration guidance.
### Building
-Navigate to a location on your system where you want *nshmp-haz* code to reside, clone the
+Navigate to a location on your system where you want *nshmp-haz-v2* code to reside, clone the
repository, and compile:
```bash
@@ -40,16 +45,16 @@ measures. For example:
java -cp path/to/nshmp-haz.jar gov.usgs.earthquake.nshmp.HazardCalc model sites [config]
```
-At a minimum, the hazard source [model](Hazard-Model.md) and the [site](Site-Specification.md)(s) at
-which to perform calculations must be specified. The source model should specified a path to a
+At a minimum, the hazard source [model](./Hazard-Model.md) and the [site](./Site-Specification.md)(s)
+at which to perform calculations must be specified. The source model should specified a path to a
directory. A single site may be specified with a string; multiple sites must be specified using
either a comma-delimited (CSV) or [GeoJSON](http://geojson.org) file. The path to a custom
-[configuration](Calculation-Configuration.md) file containing user-specific settings may optionally
+[configuration](./Calculation-Configuration.md) file containing user-specific settings may optionally
be supplied as a third argument. It can be used to override any calculation settings; if absent
-[default](Calculation-Configuration.md) values are used.
+[default](./Calculation-Configuration.md) values are used.
-See the [examples](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples)
-directory for more details.
+See the [examples](../../etc/examples/README.md) directory for more details (or
+[on GitLab](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples))
### Computing Disaggregations
@@ -63,11 +68,11 @@ java -cp nshmp-haz.jar gov.usgs.earthquake.nshmp.DisaggCalc model sites returnPe
Disaggregations build on and output `HazardCalc` results along with other disaggregation specific
files. Disaggregations also have some independent
-[configuration](Calculation-Configuration.md#config-disagg) options.
+[configuration](./Calculation-Configuration.md#config-disagg) options.
## Run with [Docker](https://docs.docker.com/install/)
-To ensure you are have the latest *nshmp-haz* update, always first pull the image from Docker:
+To ensure you are have the latest *nshmp-haz-v2* update, always first pull the image from Docker:
```bash
docker pull usgs/nshmp-haz
@@ -75,13 +80,15 @@ docker pull usgs/nshmp-haz
### Docker Memory on Mac
-By default, Docker Desktop for Mac is set to use 2 GB runtime memory. To run *nshmp-haz*, the
+By default, Docker Desktop for Mac is set to use 2 GB runtime memory. To run *nshmp-haz-v2*, the
memory available to Docker must be [increased](https://docs.docker.com/docker-for-mac/#advanced)
to a minimum of 4 GB.
### Running
-The *nshmp-haz* application may be run as a Docker container which mitigates the need to install
+TODO: is there a Docker image for nshmp-haz-v2?
+
+The *nshmp-haz-v2* application may be run as a Docker container which mitigates the need to install
Git, Java, or other dependencies besides Docker. A public image is available on
Docker hub at [https://hub.docker.com/r/usgs/nshmp-haz](https://hub.docker.com/r/usgs/nshmp-haz)
which can be run with:
@@ -113,24 +120,26 @@ Where: (TODO links below need checking)
* hazard = `HazardCalc`
* rate = `RateCalc`
-* `MODEL` is the [USGS model (NSHM)](USGS-Models.md) to run:
+* `MODEL` is the [USGS model (NSHM)](./USGS-Models.md) to run:
* CONUS-2018: [Conterminous U.S. 2018](https://code.usgs.gov/ghsc/nshmp/nshm-conus)
* HAWAII-2021: [Hawaii 2021](https://code.usgs.gov/ghsc/nshmp/nshm-hawaii)
* `RETURN_PERIOD`, in years, is only required when running a disaggregation
+TODO: what should these examples point to? links to example files? or where to look for the samples?
+
* Other arguments:
- * (required) The absolute path to a GeoJSON or CSV [site(s)](Site-Specification.md) file
- * CSV example: `$(pwd)/my-csv-sites.csv:/app/sites.csv`
+ * (required) The absolute path to a GeoJSON or CSV [site(s)](./Site-Specification.md) file
+ * CSV example: `$(pwd)/my-csv-sites.csv:/app/sites.csv` [`sites.csv`](../../etc/examples/3-sites-file/sites.csv)
* GeoJSON example: `$(pwd)/my-geojson-sites.geojson:/app/sites.geojson`
- * (optional) The absolute path to a [configuration](Calculation-Configuration.md) file
+ * (optional) The absolute path to a [configuration](./Calculation-Configuration.md) file
* Example: `$(pwd)/my-custom-config.json:/app/config.json`
* (required) The absolute path to an output directory
* Example: `$(pwd)/my-hazard-output:/app/output`
### Run Customization
-When running *nshmp-haz* with Docker the initial (Xms) and maximum (Xmx) JVM memory sizes can
+When running *nshmp-haz-v2* with Docker the initial (Xms) and maximum (Xmx) JVM memory sizes can
be set with the environment flag (-e, -env):
```bash
@@ -148,8 +157,8 @@ Where:
---
-[**Documentation Index**](docs/README.md)
+* [**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Calculation-Configuration.md b/docs/pages/Calculation-Configuration.md
index f76ae63869ab00c8ded58ff593b0be92cf47cc18..78210b1dd0a5e916ca9004d79a95cc26adebea66 100644
--- a/docs/pages/Calculation-Configuration.md
+++ b/docs/pages/Calculation-Configuration.md
@@ -1,50 +1,55 @@
# Calculation Configuration
-A `calc-config.json` file _may_ reside at the root of every [hazard model](hazard-model). This
+A `calc-config.json` file _may_ reside at the root of every [hazard model](./Hazard-Model.md). This
file, if present, will override any built-in default calculation configuration parameters, as
-listed below. See the [examples](/usgs/nshmp-haz/tree/master/etc/examples) directory, or any
-[USGS model](usgs-models), for concrete examples (TODO decide if last sentence needed and check
-links).
+listed below. See the [examples](../../etc/examples/README.md) directory, or any
+[USGS model](./Usgs-Models.md), for concrete examples.
## Calculation Configuration Parameters
Calculation configuration parameters are optional (i.e. defaults are used for missing values) and
-may be overridden. See [building and running](building-&-running) and the
-[examples](/usgs/nshmp-haz/tree/master/etc/examples) for details.
-
-(TODO needs updated javadoc links)
+may be overridden. See [building and running](./Building-&-Running.md) and the
+[examples](../../etc/examples/README.md) for details.
Parameter | Type | Default | Notes |
--------- | ---- | ------- | ----- |
__`hazard`__
- `.exceedanceModel` |`String` | `TRUNCATION_3SIGMA_UPPER` | [`ExceedanceModel`](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/calc/ExceedanceModel.html)
- `.truncationLevel` |`Double` | `3.0` | [1](notes)
- `.imts` |`String[]` | `[ PGV, PGA, SA0P01, SA0P02, SA0P03, SA0P05, SA0P075, SA0P1, SA0P15, SA0P2, SA0P25, SA0P3, SA0P4, SA0P5, SA0P75, SA1P0, SA1P5, SA2P0, SA3P0, SA4P0, SA5P0, SA7P5, SA10P0 ]` | [`Imt`](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/gmm/Imt.html)
+ `.exceedanceModel` |`String` | `TRUNCATION_3SIGMA_UPPER` | [`ExceedanceModel`][url-exceedance]
+ `.truncationLevel` |`Double` | `3.0` | [1](#notes)
+ `.imts` |`String[]` | `[ PGV, PGA, SA0P01, SA0P02, SA0P03, SA0P05, SA0P075, SA0P1, SA0P15, SA0P2, SA0P25, SA0P3, SA0P4, SA0P5, SA0P75, SA1P0, SA1P5, SA2P0, SA3P0, SA4P0, SA5P0, SA7P5, SA10P0 ]` | [`Imt`][url-imt]
`.customImls` |`Map<String, Double[]>` | `{}` (empty object) | [2](#notes)
`.gmmUncertainty` |`Boolean` | `false` | [3](#notes)
- `.valueFormat` |`String` | `ANNUAL_RATE` | [`ValueFormat`](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/calc/ValueFormat.html)
+ `.valueFormat` |`String` | `ANNUAL_RATE` | [`ValueFormat`][url-valueformat]
__`deagg`__
`.bins` |`Object` | | [4](#notes)
`.contributorLimit` |`Double` | `0.1` | [5](#notes)
__`rate`__
`.bins` |`Object` | | [6](#notes)
`.distance` |`Double` | `20` km
- `.distributionFormat` |`String` | `INCREMENTAL` | [`DistributionFormat`](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/calc/DistributionFormat.html)
+ `.distributionFormat` |`String` | `INCREMENTAL` | [`DistributionFormat`][url-distribution]
`.timespan` |`Double` | `30` years
- `.valueFormat` |`String` | `ANNUAL_RATE` | [`ValueFormat`](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/calc/ValueFormat.html)
+ `.valueFormat` |`String` | `ANNUAL_RATE` | [`ValueFormat`][url-valueformat]
__`site`__
- `.vs30` |`Double` | `760.0` | [`Site`](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/calc/Site.html)
+ `.vs30` |`Double` | `760.0` | [`Site`][url-site]
`.vsInferred` |`Boolean` | `true`
`.z1p0` |`Double` | `null` | [7](#notes)
`.z2p5` |`Double` | `null` | [7](#notes)
__`output`__ |
`.directory` |`String` | `hazout`
- `.dataTypes` |`String[]` | `[ TOTAL ]` | [`DataType`](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/calc/DataType.html)
+ `.dataTypes` |`String[]` | `[ TOTAL ]` | [`DataType`][url-datatype]
__`performance`__
`.optimizeGrids` |`Boolean` | `true` | [8](#notes)
`.smoothGrids` |`Boolean` | `true` | [9](#notes)
`.systemPartition` |`Integer` | `1000` | [10](#notes)
- `.threadCount` |`String` | `ALL` | [`ThreadCount`](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/calc/ThreadCount.html)
+ `.threadCount` |`String` | `ALL` | [`ThreadCount`][url-sheets]
+
+[url-exceedance]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/calc/ExceedanceModel.html
+[url-imt]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/Imt.html
+[url-valueformat]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/calc/ValueFormat.html
+[url-distribution]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/calc/DistributionFormat.html
+[url-site]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/calc/Site.html
+[url-datatype]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/calc/DataType.html
+[url-sheets]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/calc/ThreadCount.html
## Notes
@@ -54,7 +59,7 @@ __`performance`__
been defined, this value en/disables this feature.
3. `hazard.customImls`: Hazard is computed at default intensity measure levels (IMLs) for every
supported intenisty measure type (IMT), but a user can specify different IMLs as needed (see
- this [example](/usgs/nshmp-haz/blob/master/etc/examples/2-custom-config/config.json) and the
+ this [example](../../etc/examples/2-custom-config/README.md) and the
table of default IMLs, below).
4. `disagg.bins`: This field maps to a data container that specifies the following default ranges
and intervals for distance, magnitude, and epsilon binning: `"bins": { "rMin": 0.0, "rMax":
@@ -82,22 +87,28 @@ not listed use the values of the next highest spectral period.
IMT | IMLs
-----------|-----
-PGV | 0.237, 0.355, 0.532, 0.798, 1.19, 1.80, 2.69, 4.04, 6.06, 9.09, 13.6, 20.5, 30.7, 46.0, 69.0, 103.0, 155.0, 233.0, 349.0, 525.0
-PGA | 0.00233, 0.00350, 0.00524, 0.00786, 0.0118, 0.0177, 0.0265, 0.0398, 0.0597, 0.0896, 0.134, 0.202, 0.302, 0.454, 0.680, 1.02, 1.53, 2.30, 3.44, 5.17
-T ≤ 0.01 s | 0.00233, 0.00350, 0.00524, 0.00786, 0.0118, 0.0177, 0.0265, 0.0398, 0.0597, 0.0896, 0.134, 0.202, 0.302, 0.454, 0.680, 1.02, 1.53, 2.30, 3.44, 5.17
-T ≤ 0.02 s | 0.00283, 0.00424, 0.00637, 0.00955, 0.0143, 0.0215, 0.0322, 0.0483, 0.0725, 0.109, 0.163, 0.245, 0.367, 0.551, 0.826, 1.24, 1.86, 2.79, 4.18, 6.27
-T ≤ 0.05 s | 0.00333, 0.00499, 0.00749, 0.0112, 0.0169, 0.0253, 0.0379, 0.0569, 0.0853, 0.128, 0.192, 0.288, 0.432, 0.648, 0.972, 1.46, 2.19, 3.28, 4.92, 7.38
-T ≤ 2 s | 0.00250, 0.00375, 0.00562, 0.00843, 0.0126, 0.0190, 0.0284, 0.0427, 0.0640, 0.0960, 0.144, 0.216, 0.324, 0.486, 0.729, 1.09, 1.64, 2.46, 3.69, 5.54
-T ≤ 3 s | 0.00200, 0.00300, 0.00449, 0.00674, 0.0101, 0.0152, 0.0228, 0.0341, 0.0512, 0.0768, 0.115, 0.173, 0.259, 0.389, 0.583, 0.875, 1.31, 1.97, 2.95, 4.43
-T ≤ 4 s | 0.00133, 0.00200, 0.00300, 0.00449, 0.00674, 0.0101, 0.0152, 0.0228, 0.0341, 0.0512, 0.0768, 0.115, 0.173, 0.259, 0.389, 0.583, 0.875, 1.31, 1.97, 2.95
-T ≤ 5 s | 0.000999, 0.00150, 0.00225, 0.00337, 0.00506, 0.00758, 0.0114, 0.0171, 0.0256, 0.0384, 0.0576, 0.0864, 0.130, 0.194, 0.292, 0.437, 0.656, 0.984, 1.48, 2.21
-T ≤ 7.5 s | 0.000499, 0.000749, 0.00112, 0.00169, 0.00253, 0.00379, 0.00569, 0.00853, 0.0128, 0.0192, 0.0288, 0.0432, 0.0648, 0.0972, 0.146, 0.219, 0.328, 0.492, 0.738, 1.11
-T ≤ 10 s | 0.000333, 0.000499, 0.000749, 0.00112, 0.00169, 0.00253, 0.00379, 0.00569, 0.00853, 0.0128, 0.0192, 0.0288, 0.0432, 0.0648, 0.0972, 0.146, 0.219, 0.328, 0.492, 0.738
+PGV | 0.237, 0.355, 0.532, 0.798, 1.19, 1.80, 2.69, 4.04, <br>6.06, 9.09, 13.6, 20.5, 30.7, 46.0, 69.0, 103.0, 155.0, <br>233.0, 349.0, 525.0
+PGA | 0.00233, 0.00350, 0.00524, 0.00786, 0.0118, 0.0177, <br>0.0265, 0.0398, 0.0597, 0.0896, 0.134, 0.202, 0.302, 0.454, <br>0.680, 1.02, 1.53, 2.30, 3.44, 5.17
+T ≤ 0.01 s | 0.00233, 0.00350, 0.00524, 0.00786, 0.0118, 0.0177, <br>0.0265, 0.0398, 0.0597, 0.0896, 0.134, 0.202, 0.302, 0.454, <br>0.680, 1.02, 1.53, 2.30, 3.44, 5.17
+T ≤ 0.02 s | 0.00283, 0.00424, 0.00637, 0.00955, 0.0143, 0.0215, <br>0.0322, 0.0483, 0.0725, 0.109, 0.163, 0.245, 0.367, 0.551, 0.826, <br>1.24, 1.86, 2.79, 4.18, 6.27
+T ≤ 0.05 s | 0.00333, 0.00499, 0.00749, 0.0112, 0.0169, 0.0253, <br>0.0379, 0.0569, 0.0853, 0.128, 0.192, 0.288, 0.432, 0.648, 0.972, <br>1.46, 2.19, 3.28, 4.92, 7.38
+T ≤ 2 s | 0.00250, 0.00375, 0.00562, 0.00843, 0.0126, 0.0190, <br>0.0284, 0.0427, 0.0640, 0.0960, 0.144, 0.216, 0.324, 0.486, <br>0.729, 1.09, 1.64, 2.46, 3.69, 5.54
+T ≤ 3 s | 0.00200, 0.00300, 0.00449, 0.00674, 0.0101, 0.0152, <br>0.0228, 0.0341, 0.0512, 0.0768, 0.115, 0.173, 0.259, 0.389, <br>0.583, 0.875, 1.31, 1.97, 2.95, 4.43
+T ≤ 4 s | 0.00133, 0.00200, 0.00300, 0.00449, 0.00674, 0.0101, <br>0.0152, 0.0228, 0.0341, 0.0512, 0.0768, 0.115, 0.173, 0.259, <br>0.389, 0.583, 0.875, 1.31, 1.97, 2.95
+T ≤ 5 s | 0.000999, 0.00150, 0.00225, 0.00337, 0.00506, 0.00758, <br>0.0114, 0.0171, 0.0256, 0.0384, 0.0576, 0.0864, 0.130, 0.194, <br>0.292, 0.437, 0.656, 0.984, 1.48, 2.21
+T ≤ 7.5 s | 0.000499, 0.000749, 0.00112, 0.00169, 0.00253, 0.00379, <br>0.00569, 0.00853, 0.0128, 0.0192, 0.0288, 0.0432, 0.0648, <br>0.0972, 0.146, 0.219, 0.328, 0.492, 0.738, 1.11
+T ≤ 10 s | 0.000333, 0.000499, 0.000749, 0.00112, 0.00169, 0.00253, <br>0.00379, 0.00569, 0.00853, 0.0128, 0.0192, 0.0288, 0.0432, <br>0.0648, 0.0972, 0.146, 0.219, 0.328, 0.492, 0.738
---
-[**Documentation Index**](docs/README.md)
+* [**Documentation Index**](../README.md)
+* [Building & Running](./Building-&-Running.md)
+ * [Developer Basics](./Developer-Basics.md)
+ * [Calculation Configuration](./Calculation-Configuration.md)
+ * [Site Specification](./Site-Specification.md)
+ * [Examples](../../etc/examples/README.md) (or
+ [on GitLab](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples))
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Developer-Basics.md b/docs/pages/Developer-Basics.md
index 791ab835ba2ff357ca3f5eeebb7f7984250574e1..d2e8a181bb7b9b147651e94c8b194e02b05a0185 100644
--- a/docs/pages/Developer-Basics.md
+++ b/docs/pages/Developer-Basics.md
@@ -53,7 +53,7 @@ git clone https://code.usgs.gov/ghsc/nshmp/nshmp-haz.git
## Eclipse Integration (Optional)
Eclipse provides automatic compilation, syntax highlighting, and integration with Git, among
-other useful features. To build or modify *nshmp-haz* using [Eclipse](http://www.eclipse.org/),
+other useful features. To build or modify *nshmp-haz-v2* using [Eclipse](http://www.eclipse.org/),
install the [Eclipse IDE for Java Developers](https://www.eclipse.org/downloads/packages/) or
[Eclipse IDE for Enterprise Java and Web Developers](https://www.eclipse.org/downloads/packages/),
if you plan on developing web services. Import the project into Eclipse: `File > Import >
@@ -61,8 +61,14 @@ Gradle > Existing Gradle Project`
---
-[**Documentation Index**](docs/README.md)
+* [**Documentation Index**](../README.md)
+* [Building & Running](./Building-&-Running.md)
+ * [Developer Basics](./Developer-Basics.md)
+ * [Calculation Configuration](./Calculation-Configuration.md)
+ * [Site Specification](./Site-Specification.md)
+ * [Examples](../../etc/examples/README.md) (or
+ [on GitLab](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples))
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Ground-Motion-Models.md b/docs/pages/Ground-Motion-Models.md
index 4527f365d49015e3ec01ff5d2f87b17689467f8b..fc7f55a0fc1765a79a40de315c92303be892427d 100644
--- a/docs/pages/Ground-Motion-Models.md
+++ b/docs/pages/Ground-Motion-Models.md
@@ -161,8 +161,8 @@ modify model output.
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Hazard-Model.md b/docs/pages/Hazard-Model.md
index fa537064e7b1edd2749ea6f8b96afc061a2c1035..92171f52705a817a88bc2e6ffd415e0e62ebc734 100644
--- a/docs/pages/Hazard-Model.md
+++ b/docs/pages/Hazard-Model.md
@@ -34,8 +34,8 @@ support modeling of complex logic trees.
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Logic-Trees-&-Uncertainty.md b/docs/pages/Logic-Trees-&-Uncertainty.md
index b5db0a58a50c9d746a5e143544afce4dbfb7f19b..57c05cda56f5b175c5b25e6d5c7546cc236cfff8 100644
--- a/docs/pages/Logic-Trees-&-Uncertainty.md
+++ b/docs/pages/Logic-Trees-&-Uncertainty.md
@@ -1,7 +1,7 @@
# USGS Models: Logic Trees & Uncertainty
The following page details the logic trees of epistemic uncertainty considered in NSHMs supported
-by *nshmp-haz*. Logic trees are represented in a NSHM using files ending in `-tree.json`.
+by *nshmp-haz-v2*. Logic trees are represented in a NSHM using files ending in `-tree.json`.
[[_TOC_]]
@@ -125,8 +125,8 @@ alternative models.
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Magnitude-Frequency-Distributions.md b/docs/pages/Magnitude-Frequency-Distributions.md
index 9fd7e7c0651e685b2d84c50dc4abcb354c4d6398..0d041cc9cf7fc331c58fd65a78dd3978eb9d3c7a 100644
--- a/docs/pages/Magnitude-Frequency-Distributions.md
+++ b/docs/pages/Magnitude-Frequency-Distributions.md
@@ -286,8 +286,8 @@ TODO: convert example to JSON format (or see `mfd-config.json` section above)
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Model-Editions.md b/docs/pages/Model-Editions.md
index bdecc204a43e7217ee27f0814c21ddcb1454fab9..c47e2f31391cbd8366b912e1ebe43789a967e016 100644
--- a/docs/pages/Model-Editions.md
+++ b/docs/pages/Model-Editions.md
@@ -102,8 +102,8 @@ TODO: Update model links
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Model-Files.md b/docs/pages/Model-Files.md
index c1c485fad79a1878d7ae750058d13241d5bba31a..ca478d5ee6404e6d7cd72bf82c542316daf0a311 100644
--- a/docs/pages/Model-Files.md
+++ b/docs/pages/Model-Files.md
@@ -186,8 +186,8 @@ is composed of an array of rupture-sets.
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Model-Structure.md b/docs/pages/Model-Structure.md
index df34c9fc4d2eb3099ec9f8daebd79434c72f1868..e7230c6b1853ae5180dc3b1b5c40acdc915eb5e7 100644
--- a/docs/pages/Model-Structure.md
+++ b/docs/pages/Model-Structure.md
@@ -196,8 +196,8 @@ See also: [Subduction Intraslab Source Type](source-types#subduction-intraslab-s
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Rupture-Scaling-Relations.md b/docs/pages/Rupture-Scaling-Relations.md
index 3e29c61b7efe7f30e2267db379940163f38845b8..e78cd91a9453fda27a1dc0c87b9926cb492b7ed2 100644
--- a/docs/pages/Rupture-Scaling-Relations.md
+++ b/docs/pages/Rupture-Scaling-Relations.md
@@ -70,8 +70,8 @@ relationships for subduction zone earthquakes. Seismological Research Letters 68
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Site-Specification.md b/docs/pages/Site-Specification.md
index 3b3dfb4975584118c9c98c80f3e6ed542c96f9e4..40808da9fb11d14ff433021c05275620321cbd2e 100644
--- a/docs/pages/Site-Specification.md
+++ b/docs/pages/Site-Specification.md
@@ -2,18 +2,22 @@
(TODO update etc and/or javadoc links)
+~~TODO: add README for `etc/nshm` directory so it can be linked here~~
+
+TODO: where is `etc/peer`? is it needed?
+
The sites at which to perform hazard and related calculations may be defined in a variety of
ways. Examples of the file formats described below are available in the resource directory:
-[`etc/nshm`](/usgs/nshmp-haz/tree/master/etc/nshm).
+[`etc/nshm`](../../etc/nshm/README.md).
-__Note on Coordinates:__ *nshmp-haz* supports longitude and latitude values in the closed
+__Note on Coordinates:__ *nshmp-haz-v2* supports longitude and latitude values in the closed
ranges `[-360° ‥ 360°]` and `[-90° ‥ 90°]`. Note, however, that mixing site and/or source
coordinates across the antimeridian (the -180° to 180° transition) will yield unexpected results.
For Pacific models and calculations, always use positive or negative longitudes exclusively.
## Site String
-For the case of running a single site of interest, most *nshmp-haz* programs accept a
+For the case of running a single site of interest, most *nshmp-haz-v2* programs accept a
comma-delimited string of the form: `name,lon,lat[,vs30,vsInf[,z1p0,z2p5]]`, where `vs30`, `vsInf`,
`z1p0`, and `z2p5` are optional. Note that if `vs30` is supplied, so too must `vsInf`. Likewise if
`z1p0` is supplied, so too must `z2p5`. If the string contains any spaces, escape them or wrap the
@@ -21,7 +25,7 @@ entire string in double quotes.
For any site parameter values that are not supplied on the command line or in the file formats
below, the following defaults are used (see the `site` member of the
-[configuration](calculation-configuration) file):
+[configuration](./Calculation-Configuration.md) file):
```text
name: Unnamed
@@ -47,7 +51,7 @@ it's 'default' basin depth scale factor.
## GeoJSON Format (\*.geojson)
Although more verbose than the comma-delimited format, [GeoJSON](http://geojson.org) is a more
-versatile format for encoding geographic data. *nshmp-haz* uses GeoJSON for both lists of sites
+versatile format for encoding geographic data. *nshmp-haz-v2* uses GeoJSON for both lists of sites
and to define map regions. If you encounter problems when formatting JSON files, use
[JSONLint](http://jsonlint.com) or [GeoJSONLint](http://geojsonlint.com) for validation.
@@ -79,19 +83,19 @@ A site list is expected as a `FeatureCollection` of `Point` features. For exampl
As with the CSV format, the minimum required data is a `geometry` `coordinates` array. All
`properties` are optional. When using GeoJSON, the `title` property maps to the name of the site.
-Additional properties, if present, are ignored by *nshmp-haz* but permitted as they may be
+Additional properties, if present, are ignored by *nshmp-haz-v2* but permitted as they may be
relevant for other applications. For example, [styling
properties](https://help.github.com/articles/mapping-geojson-files-on-github/#styling-features)
may be used to improve rendering in mapping applications. For a fully fledged example, see the
-[NSHM test sites](/usgs/nshmp-haz/blob/master/etc/nshm/sites-nshmp.geojson) file.
+[NSHM test sites](../../etc/nshm/sites-nshmp.geojson) file.
### Map Regions
-GeoJSON is also used to define *nshmp-haz* map regions. For example, see the file that defines a
+GeoJSON is also used to define *nshmp-haz-v2* map regions. For example, see the file that defines a
region commonly used when creating hazard and other maps for the
-[Los Angeles basin](/usgs/nshmp-haz/blob/master/etc/nshm/map-la-basin.geojson).
+[Los Angeles basin](../../etc/nshm/map-la-basin.geojson).
-A map region is expected as a `Polygon` `FeatureCollection`. Currently, *nshmp-haz* only supports
+A map region is expected as a `Polygon` `FeatureCollection`. Currently, *nshmp-haz-v2* only supports
a `FeatureCollection` with 1 or 2 polygons. When a single polygon is defined, it must consist of a
single, simple closed loop. Additional arrays that define holes in the polygon (per the GeoJSON
spec) are not processed and results are undefined for self-intersecting coordinate arrays. This
@@ -106,13 +110,20 @@ have a feature `id` of `Extents`, and *must* be rectangular (in a mercator proje
parallel to lines of latitude and longitude. Any points in the 'calculation' polygon outside the
'extents' polygon are ignored; hazard values at any points within the 'extents' polygon but
outside the 'calculation' polygon are set to zero. For an example, see the
-[NSHMP Western US](/usgs/nshmp-haz/blob/master/etc/nshm/map-wus.geojson) map site file.
+[NSHMP Western US](../../etc/nshm/map-wus.geojson) map site file.
+
(TODO This needs updating; link to conus-2018 active crust map-region.geojson).
---
-[**Documentation Index**](docs/README.md)
+* [**Documentation Index**](../README.md)
+* [Building & Running](./Building-&-Running.md)
+ * [Developer Basics](./Developer-Basics.md)
+ * [Calculation Configuration](./Calculation-Configuration.md)
+ * [Site Specification](./Site-Specification.md)
+ * [Examples](../../etc/examples/README.md) (or
+ [on GitLab](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples))
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/Source-Types.md b/docs/pages/Source-Types.md
index baaf1f4f1dd59092ca1ac931607d1883b7b464c2..b6a0382a37ce8dd6d2026cafecdf097f935369d1 100644
--- a/docs/pages/Source-Types.md
+++ b/docs/pages/Source-Types.md
@@ -12,15 +12,15 @@ geometry itself is unknown or very poorly defined.
[[_TOC_]]
-Source models for use with *nshmp-haz* are defined using [JSON](https://www.json.org) and
-[GeoJSON](https://geojson.org). *nshmp-haz* makes determinations about how to represent a source
+Source models for use with *nshmp-haz-v2* are defined using [JSON](https://www.json.org) and
+[GeoJSON](https://geojson.org). *nshmp-haz-v2* makes determinations about how to represent a source
based on a GeoJSON geometry type in conjunction with supporting JSON configuration files. Example
source configuration files, `*-config.json`, are provided with each source type description.
Configuration files must be fully specified with `null` JSON member values used to specify 'do
nothing' where appropriate. Any configuration member value in ALL_CAPS indicates the value is one
of a fixed number of options commonly referred to as an enum.
-__Note on Coordinates:__ *nshmp-haz* supports longitude and latitude values in the closed ranges
+__Note on Coordinates:__ *nshmp-haz-v2* supports longitude and latitude values in the closed ranges
`[-360°‥360°]` and `[-90°‥90°]`. Note, however, that mixing site and/or source coordinates across
the antimeridian (the -180° to 180° transition) will yield unexpected results. For Pacific models
and calculations, always use positive or negative longitudes exclusively.
@@ -347,8 +347,8 @@ using an `slab-config.json` file.
---
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/docs/pages/USGS-Models.md b/docs/pages/USGS-Models.md
index 7d28b81b6ef0ae551dfcaae2b615d13cd0eee62e..6a686b0634a1d312cec7f849d06ac553e5a5661c 100644
--- a/docs/pages/USGS-Models.md
+++ b/docs/pages/USGS-Models.md
@@ -6,7 +6,7 @@ years. This window is narrowing, however, and updates are also being undertaken
models for states and territories outside the conterminous U.S. These pages describe the models
that are available and some of the history and versions of each. The models are intended for use
with the USGS probabilistic earthquake hazard codebase:
-[*nshmp-haz*](https://github.com/usgs/nshmp-haz).
+[*nshmp-haz-v2*](https://github.com/usgs/nshmp-haz).
As specified in this documentation, NSHM files are organized by tectonic setting and then further
by source type. For larger models, such as that of the conterminous U.S., sources are commonly
@@ -32,8 +32,8 @@ Each model region has a dedicated repository with version tags marking different
* [Model Editions](model-editions.md)
* [Logic Trees & Uncertainty](logic-trees-&-uncertainty.md)
-[**Documentation Index**](docs/README.md)
+[**Documentation Index**](../README.md)
---
- [U.S. Geological Survey](https://www.usgs.gov)
+ [U.S. Geological Survey](https://www.usgs.gov)
National Seismic Hazard Mapping Project ([NSHMP](https://earthquake.usgs.gov/hazards/))
diff --git a/etc/nshm/README.md b/etc/nshm/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..96c4ee61ad93dacd36ce1a1b84edb4634a9b7194
--- /dev/null
+++ b/etc/nshm/README.md
@@ -0,0 +1,3 @@
+# NSHM site and map files
+
+This directory contains the sites, map, and boundary files used in NSHM calculations.