Merge pull request #109 from GEMScienceTools/small-fixes

Make the RMTK library installable

MANIFEST.in

@@ -0,0 +1,3 @@
+include README.md LICENSE
+
+recursive-include rmtk/*.*

README.md

@@ -3,7 +3,7 @@ Risk Modeller's Toolkit (RMTK)
 
 This is the web repository of the Risk Modeller's Toolkit (RMTK). 
 The RMTK is a suite of tools developed by scientists working at the
-Global Earthquake Model (GEM) Foundation. The main purpouse
+Global Earthquake Model (GEM) Foundation. The main purpose
 of the RMTK is to provide a suite of tools for the creation of seismic
 risk input models and for the post-processing and visualisation of 
 OpenQuake risk results.

RMTK.ipynb

@@ -41,25 +41,25 @@
     "Currently, the Plotting module of the Risk Modeller's Toolkit can generate plots for the following outputs:\n",
     "\n",
     "### Collapse maps\n",
-    "Collapse maps represent the spatial distribution of the estimated mean number of assets that will collapse (or exceed the ultimate damage state described in the fragility model - e.g. destruction, complete). To use this feature click [here](rmtk/plotting/collapse_maps/plot_collapse_maps.ipynb).\n",
+    "Collapse maps represent the spatial distribution of the estimated mean number of assets that will collapse (or exceed the ultimate damage state described in the fragility model - e.g. destruction, complete). To use this feature click [here](notebooks/plotting/collapse_maps/plot_collapse_maps.ipynb).\n",
     "\n",
     "### Damage distribution\n",
-    "The OpenQuake-engine can calculate the damage distribution for a given earthquake scenario. This module can be used to plot the total damage distribution (i.e. mean number of assets in each damage state), as well as the distribution of damage for building classes or typologies (i.e. mean number of assets in each damage state, according to each building class). To use this feature click [here](rmtk/plotting/damage_dist/plot_damage_dist.ipynb).\n",
+    "The OpenQuake-engine can calculate the damage distribution for a given earthquake scenario. This module can be used to plot the total damage distribution (i.e. mean number of assets in each damage state), as well as the distribution of damage for building classes or typologies (i.e. mean number of assets in each damage state, according to each building class). To use this feature click [here](notebooks/plotting/damage_dist/plot_damage_dist.ipynb).\n",
     "\n",
     "### Loss maps\n",
-    "Risk maps (or loss maps) represent the spatial distribution of the estimated losses (economic or human) within the region of interest. These maps can be derived for earthquake scenarios (single events) or considering probabilistic hazard. In the former case, the spatial distribution of the mean losses are illustrated on the loss map. For the latter case, the losses corresponding to a given return period are presented in the loss map. To use this feature click [here](rmtk/plotting/risk_maps/plot_risk_maps.ipynb).\n",
+    "Risk maps (or loss maps) represent the spatial distribution of the estimated losses (economic or human) within the region of interest. These maps can be derived for earthquake scenarios (single events) or considering probabilistic hazard. In the former case, the spatial distribution of the mean losses are illustrated on the loss map. For the latter case, the losses corresponding to a given return period are presented in the loss map. To use this feature click [here](notebooks/plotting/risk_maps/plot_risk_maps.ipynb).\n",
     "\n",
     "### Hazard maps\n",
-    "Hazard maps present the expected ground motion (e.g. peak ground acceleration, peak ground velocity, spectral acceleration at a given period of vibration) for a given level of frequency (represented by a probability of exceedance within a given time span (e.g. 10% in 50 years) or return periods in years (e.g. 475-year). To use this feature click [here](rmtk/plotting/hazard_outputs/plot_hazard_maps.ipynb).\n",
+    "Hazard maps present the expected ground motion (e.g. peak ground acceleration, peak ground velocity, spectral acceleration at a given period of vibration) for a given level of frequency (represented by a probability of exceedance within a given time span (e.g. 10% in 50 years) or return periods in years (e.g. 475-year). To use this feature click [here](notebooks/plotting/hazard_outputs/plot_hazard_maps.ipynb).\n",
     "\n",
     "### Hazard curves\n",
-    "Seismic hazard curves express the relation between probability of exceedance (in a given time span) and a set of ground motion levels (e.g. peak ground acceleration, peak ground velocity, spectral acceleration at a given period of vibration). A seismic hazard curve is associated with a specific location. To use this feature click [here](rmtk/plotting/hazard_outputs/plot_hazard_curves.ipynb).\n",
+    "Seismic hazard curves express the relation between probability of exceedance (in a given time span) and a set of ground motion levels (e.g. peak ground acceleration, peak ground velocity, spectral acceleration at a given period of vibration). A seismic hazard curve is associated with a specific location. To use this feature click [here](notebooks/plotting/hazard_outputs/plot_hazard_curves.ipynb).\n",
     "\n",
     "### Uniform hazard spectra\n",
-    "A uniform hazard spectrum (UHS) calculated at a specific location describes the spectral acceleration values at different periods of vibration which correspond to a particular \"uniform\" probability of exceedance (in a given time span). This feature enables a user to plot the UHS results obtained from an OpenQuake probabilistic hazard calculation. To use this feature click [here](rmtk/plotting/hazard_outputs/plot_hazard_curves.ipynb).\n",
+    "A uniform hazard spectrum (UHS) calculated at a specific location describes the spectral acceleration values at different periods of vibration which correspond to a particular \"uniform\" probability of exceedance (in a given time span). This feature enables a user to plot the UHS results obtained from an OpenQuake probabilistic hazard calculation. To use this feature click [here](notebooks/plotting/hazard_outputs/plot_hazard_curves.ipynb).\n",
     "\n",
     "### Loss curves\n",
-    "Loss exceedance curves provide the probability of exceedance (in a given time span) for a set of loss levels. A seismic loss exceedance curve is associated with a specific asset. Aggregate loss exceedance curves describing the probability of exceedance of loss values for a portfolio of assets can also be calculated using the OpenQuake-engine and plotted using this notebook. To use this feature click [here](rmtk/plotting/loss_curves/plot_loss_curves.ipynb).\n"
+    "Loss exceedance curves provide the probability of exceedance (in a given time span) for a set of loss levels. A seismic loss exceedance curve is associated with a specific asset. Aggregate loss exceedance curves describing the probability of exceedance of loss values for a portfolio of assets can also be calculated using the OpenQuake-engine and plotted using this notebook. To use this feature click [here](notebooks/plotting/loss_curves/plot_loss_curves.ipynb).\n"
    ]
   },
   {
@@ -72,10 +72,10 @@
     "<img src=\"figures/pml_example.png\" width=\"400\" align=\"middle\">\n",
     "\n",
     "### Probable maximum loss curve\n",
-    "This functionality of the Risk Modeller's Toolkit allows users to generate probable maximum loss curves, establishing the return period of exceedance for a set of loss levels. To use this feature click here [here](rmtk/risk/event_loss_tables/loss_modelling.ipynb).\n",
+    "This functionality of the Risk Modeller's Toolkit allows users to generate probable maximum loss curves, establishing the return period of exceedance for a set of loss levels. To use this feature click here [here](notebooks/risk/event_loss_tables/loss_modelling.ipynb).\n",
     "\n",
     "### Logic tree branch selector\n",
-    "This feature of the Risk Modeller's Toolkit allows users to analyse sets of hazard curves derived using the Classical PSHA-based approach, and identify the branch of the logic tree that generated the hazard curve closest to the mean hazard curve, or a specific hazard curve fractile. This information can then be used to perform risk calculations for the identified logic tree branch. To use this feature click here [here](rmtk/risk/closest_curves/closest_curves.ipynb).\n"
+    "This feature of the Risk Modeller's Toolkit allows users to analyse sets of hazard curves derived using the Classical PSHA-based approach, and identify the branch of the logic tree that generated the hazard curve closest to the mean hazard curve, or a specific hazard curve fractile. This information can then be used to perform risk calculations for the identified logic tree branch. To use this feature click here [here](notebooks/risk/closest_curves/closest_curves.ipynb).\n"
    ]
   },
   {
@@ -88,13 +88,13 @@
     "<img src=\"figures/fragility_example.png\" width=\"400\" align=\"middle\">\n",
     "\n",
     "### Capacity model generator\n",
-    "This module enables users to generate a large number of numerical models that can be used in the derivation of fragility models. This feature allows the inclusion of the building-to-building variability necessary for the derivation of fragility functions for building classes. To use this feature click [here](rmtk/vulnerability/model_generator/model_generator.ipynb).\n",
+    "This module enables users to generate a large number of numerical models that can be used in the derivation of fragility models. This feature allows the inclusion of the building-to-building variability necessary for the derivation of fragility functions for building classes. To use this feature click [here](notebooks/vulnerability/model_generator/model_generator.ipynb).\n",
     "\n",
     "### Conversion from MDOF to SDOF\n",
-    "Several structural analysis packages allow the derivation of pushover curves (base shear versus top displacement) for multiple degree of freedom systems (MDOF). This module allows the conversion of results from MDOF analyses into equivalent single degree of freedom (SDOF) models, thus making them compatible with a wide range of non-linear static procedures. To use this feature click [here](rmtk/vulnerability/mdof_to_sdof/mdof_to_sdof.ipynb).\n",
+    "Several structural analysis packages allow the derivation of pushover curves (base shear versus top displacement) for multiple degree of freedom systems (MDOF). This module allows the conversion of results from MDOF analyses into equivalent single degree of freedom (SDOF) models, thus making them compatible with a wide range of non-linear static procedures. To use this feature click [here](notebooks/vulnerability/mdof_to_sdof/mdof_to_sdof.ipynb).\n",
     "\n",
     "### Derivation of fragility and vulnerability models\n",
-    "This module comprises a wide spectrum methdologies to assess the nonlinear response of one, or multiple, structures using nonlinear static procedures. One of the main outputs of this module are fragility functions. Fragility functions obtained using this module can be further transformed into vulnerability functions using appropriate damage-to-loss (i.e. consequence) models. To use this feature click [here](rmtk/vulnerability/derivation_fragility/derivation_fragility.ipynb).\n"
+    "This module comprises a wide spectrum methdologies to assess the nonlinear response of one, or multiple, structures using nonlinear static procedures. One of the main outputs of this module are fragility functions. Fragility functions obtained using this module can be further transformed into vulnerability functions using appropriate damage-to-loss (i.e. consequence) models. To use this feature click [here](notebooks/vulnerability/derivation_fragility/derivation_fragility.ipynb).\n"
    ]
   },
   {