diff --git a/docs/README.md b/docs/README.md
index 3ef557e3b0a1c7ae9a581ccf271151734bc4857e..3b01c8111d2ea2fbbc09726dc75f05281e69a259 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -1,9 +1,9 @@
# Documentation: nshmp-haz
-***nshmp-haz*** is a USGS developed software stack that supports probabilistic seismic hazard
-(PSHA) and related analyses. It is maintained by the National Seismic Hazard Model Project
-([NSHMP](https://earthquake.usgs.gov/hazards/)) within the U.S. Geological Survey's
-([USGS](https://www.usgs.gov)) earthquake hazards program ([EHP](http://earthquake.usgs.gov)).
+***nshmp-haz*** is a U.S. Geological Survey ([USGS](https://www.usgs.gov)) developed software stack
+that supports probabilistic seismic hazard (PSHA) and related analyses. It is maintained by the
+National Seismic Hazard Model Project ([NSHMP](https://earthquake.usgs.gov/hazards/)) within the
+USGS's earthquake hazards program ([EHP](http://earthquake.usgs.gov)).
*nshmp-haz* supports high performance seismic hazard calculations required to generate detailed
maps over large areas and supports a variety of USGS web services and applications related to
@@ -31,7 +31,7 @@ to use *nshmp-haz* as well as underlying model implementation details.
## Other Pages & References
-* [nshmp-lib](/ghsc/nshmp/nshmp-lib): USGS hazard modeling library
+* [nshmp-lib](https://code.usgs.gov/ghsc/nshmp/nshmp-lib): USGS hazard modeling library
* [Functional PSHA](pages/Functional-PSHA.md)
* [Probabilistic Seismic Hazard Analysis, a Primer
[PDF]](http://www.opensha.org/sites/opensha.org/files/PSHA_Primer_v2_0.pdf)
diff --git a/docs/pages/Building-&-Running.md b/docs/pages/Building-&-Running.md
index 2184c25f133d3b1789c83d9e00905c377765a83d..8983bde40eaaae5f4373660275b0926bc897c824 100644
--- a/docs/pages/Building-&-Running.md
+++ b/docs/pages/Building-&-Running.md
@@ -40,15 +40,16 @@ 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) and the [site](site-specification)(s) at
+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) 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) values are used.
+[default](Calculation-Configuration.md) values are used.
-See the [examples](/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples) directory for more details.
+See the [examples](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples)
+directory for more details.
### Computing Disaggregations
@@ -62,7 +63,7 @@ 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#config-disagg) options.
+[configuration](Calculation-Configuration.md#config-disagg) options.
## Run with [Docker](https://docs.docker.com/install/)
@@ -112,17 +113,17 @@ Where: (TODO links below need checking)
* hazard = `HazardCalc`
* rate = `RateCalc`
-* `MODEL` is the [USGS model (NSHM)](usgs-models) to run:
- * CONUS-2018: [Conterminous U.S. 2018](https://github.com/usgs/nshm-conus)
+* `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
* Other arguments:
- * (required) The absolute path to a GeoJSON or CSV [site(s)](site-specification) file
+ * (required) The absolute path to a GeoJSON or CSV [site(s)](Site-Specification.md) file
* CSV example: `$(pwd)/my-csv-sites.csv:/app/sites.csv`
* GeoJSON example: `$(pwd)/my-geojson-sites.geojson:/app/sites.geojson`
- * (optional) The absolute path to a [configuration](calculation-configuration) 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`
diff --git a/docs/pages/Magnitude-Frequency-Distributions.md b/docs/pages/Magnitude-Frequency-Distributions.md
index 660adb59fca2dae9615e63619014ba7fcca7b2ee..2abe4485aeca04ea41e49ff535dc0a88bb974c02 100644
--- a/docs/pages/Magnitude-Frequency-Distributions.md
+++ b/docs/pages/Magnitude-Frequency-Distributions.md
@@ -48,6 +48,8 @@ tree of rates for a source is also present in a model. Example:
## Tapered Gutenberg–Richter
+TODO: Need a new link for tapered GR MFD
+
A [tapered Gutenberg-Richter](http://scec.ess.ucla.edu/~ykagan/moms_index.html) MFD is similar to
Gutenberg-Richter, above, but with an exponential taper applied with a corner magnitude of `mCut`.
The `a`-value member is optional when a logic tree of rates for a source is also present in a
@@ -98,8 +100,6 @@ example:
}
```
-**mfd-config.json:**
-
MFD confguration files:
* mfd-map.json
@@ -255,6 +255,8 @@ Depending on the types of MFDs being modeled, a rate file may contain Gutenberg-
or magnitude-specific rates. The branches of a rate-tree commonly have the generic ID's:
`[R1, R2, R3, ...]` to support matching rate-trees across source-tree branches.
+TODO: convert example to JSON format (or see `mfd-config.json` section above)
+
```xml
<!-- (optional) A magnitude uncertainty model that will be
applied to every source: