sync changes from addons since r70655

ncsu-landscape-dynamics · Apr 8, 2019 · 6c56e18 · 6c56e18
1 parent be64d56
commit 6c56e18
Show file tree

Hide file tree

Showing 11 changed files with 141 additions and 74 deletions.
diff --git a/r.futures/r.futures.calib/r.futures.calib.html b/r.futures/r.futures.calib/r.futures.calib.html
@@ -58,17 +58,17 @@ <h3>Calibration input and output</h3>
 Calibration results are saved in a CSV file specified in <b>calibration_results</b>:
 
 <pre>
-input_discount_factor area_distance input_compactness_mean input_compactness_range compactness_distance
-0.1 1.01541178435 0.1 0.02 3.00000005937
-0.2 1.26578803108 0.1 0.02 4.12442780529
-0.3 1.17631210026 0.1 0.02 3.86904462396
-0.4 2.31700278644 0.1 0.02 15.0569602795
-0.5 1.08655152036 0.1 0.02 3.72484862687
-0.6 2.97628078734 0.1 0.02 21.6358616001
-0.7 3.61632549044 0.1 0.02 25.4492265706
-0.8 2.72789958233 0.1 0.02 18.1083820007
-0.9 2.45915297845 0.1 0.02 18.4500322711
-0.1 1.05473877995 0.1 0.04 3.09321560218
+input_discount_factor,area_distance,input_compactness_mean,input_compactness_range,compactness_distance
+0.1,1.01541178435,0.1,0.02,3.00000005937
+0.2,1.26578803108,0.1,0.02,4.12442780529
+0.3,1.17631210026,0.1,0.02,3.86904462396
+0.4,2.31700278644,0.1,0.02,15.0569602795
+0.5,1.08655152036,0.1,0.02,3.72484862687
+0.6,2.97628078734,0.1,0.02,21.6358616001
+0.7,3.61632549044,0.1,0.02,25.4492265706
+0.8,2.72789958233,0.1,0.02,18.1083820007
+0.9,2.45915297845,0.1,0.02,18.4500322711
+0.1,1.05473877995,0.1,0.04,3.09321560218
 ...
 </pre>
 
@@ -103,14 +103,20 @@ <h2>REFERENCES</h2>
     <a href="http://dx.doi.org/10.1080/00045608.2012.707591">FUTURES: Multilevel Simulations of Emerging
     Urban-Rural Landscape Structure Using a Stochastic Patch-Growing Algorithm</a>.
     Annals of the Association of American Geographers, 103(4), 785-807.
+    DOI: 10.1080/00045608.2012.707591
 <li>Dorning, M. A., Koch, J., Shoemaker, D. A., &amp; Meentemeyer, R. K. (2015).
    <a href="http://dx.doi.org/10.1016/j.landurbplan.2014.11.011">Simulating urbanization scenarios reveals
     tradeoffs between conservation planning strategies</a>.
-    Landscape and Urban Planning, 136, 28-39.</li>
+    Landscape and Urban Planning, 136, 28-39.
+    DOI: 10.1016/j.landurbplan.2014.11.011</li>
+<li>Petrasova, A., Petras, V., Van Berkel, D., Harmon, B. A., Mitasova, H.,  &amp; Meentemeyer, R. K. (2016).
+   <a href="https://www.int-arch-photogramm-remote-sens-spatial-inf-sci.net/XLI-B7/953/2016/isprs-archives-XLI-B7-953-2016.pdf">Open Source Approach to Urban Growth Simulation</a>.
+   Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLI-B7, 953-959.
+   DOI: 10.5194/isprsarchives-XLI-B7-953-2016</li>
 </ul>
 
 <h2>AUTHOR</h2>
 
-Anna Petrasova, <a href="http://geospatial.ncsu.edu/osgeorel/">NCSU OSGeoREL</a><br>
+Anna Petrasova, <a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll</a><br>
 
-<p><i>Last changed: $Date: 2015-02-12 14:32:45 -0500 (Thu, 12 Feb 2015) $</i>
+<p><i>Last changed: $Date: 2018-09-14 21:49:22 -0400 (Fri, 14 Sep 2018) $</i>
diff --git a/r.futures/r.futures.calib/r.futures.calib.py b/r.futures/r.futures.calib/r.futures.calib.py
@@ -39,7 +39,6 @@
 #% key: repeat
 #% description: How many times is the simulation repeated
 #% required: no
-#% answer: 10
 #% guisection: Calibration
 #%end
 #%option
@@ -147,7 +146,6 @@
 #% required: no
 #% multiple: no
 #% options: 4,8
-#% answer: 4
 #% description: The number of neighbors to be used for patch generation (4 or 8)
 #% guisection: PGA
 #%end
@@ -157,7 +155,6 @@
 #% required: no
 #% multiple: no
 #% options: 1,2
-#% answer: 2
 #% description: The way location of a seed is determined (1: uniform distribution 2: development probability)
 #% guisection: PGA
 #%end
@@ -167,7 +164,6 @@
 #% required: no
 #% multiple: no
 #% options: occurrence,gravity,kernel
-#% answer: gravity
 #% description: Approaches to derive development pressure
 #% guisection: PGA
 #%end
@@ -300,7 +296,7 @@ def run_one_combination(repeat, development_start, compactness_mean, compactness
             run_simulation(development_start=development_start, development_end=simulation_dev_end,
                            compactness_mean=compactness_mean, compactness_range=compactness_range,
                            discount_factor=discount_factor, patches_file=patches_file, fut_options=fut_options)
-        except CalledModuleError, e:
+        except CalledModuleError as e:
             queue.put(None)
             cleanup(tmp=TMP_PROCESS)
             gcore.error(_("Running r.futures.pga failed. Details: {e}").format(e=e))
@@ -344,8 +340,8 @@ def run_simulation(development_start, development_end, compactness_mean, compact
                               output=development_end)
     parameters.update(futures_parameters)
     for not_required in ('constrain_weight', 'num_steps', 'incentive_power'):
-        if options[not_required]:
-            parameters.update({not_required: options[not_required]})
+        if fut_options[not_required]:
+            parameters.update({not_required: fut_options[not_required]})
 
     gcore.run_command('r.futures.pga', flags='s', overwrite=True, **parameters)
 
@@ -475,7 +471,7 @@ def main():
     proc_list = []
     num_all = len(compactness_means) * len(compactness_ranges) * len(discount_factors)
     with open(options['calibration_results'], 'a') as f:
-        f.write(' '.join(['input_discount_factor', 'area_distance',
+        f.write(','.join(['input_discount_factor', 'area_distance',
                           'input_compactness_mean', 'input_compactness_range',
                           'compactness_distance']))
         f.write('\n')
@@ -500,7 +496,7 @@ def main():
                             data = queue_list[i].get()
                             if not data:
                                 continue
-                            f.write(' '.join([str(data['input_discount_factor']), str(data['area_distance']),
+                            f.write(','.join([str(data['input_discount_factor']), str(data['area_distance']),
                                               str(data['input_compactness_mean']), str(data['input_compactness_range']),
                                               str(data['compactness_distance'])]))
                             f.write('\n')

diff --git a/r.futures/r.futures.demand/r.futures.demand.html b/r.futures/r.futures.demand/r.futures.demand.html
@@ -120,14 +120,20 @@ <h2>REFERENCES</h2>
     <a href="http://dx.doi.org/10.1080/00045608.2012.707591">FUTURES: Multilevel Simulations of Emerging
     Urban-Rural Landscape Structure Using a Stochastic Patch-Growing Algorithm</a>.
     Annals of the Association of American Geographers, 103(4), 785-807.
+    DOI: 10.1080/00045608.2012.707591
 <li>Dorning, M. A., Koch, J., Shoemaker, D. A., &amp; Meentemeyer, R. K. (2015).
    <a href="http://dx.doi.org/10.1016/j.landurbplan.2014.11.011">Simulating urbanization scenarios reveals
     tradeoffs between conservation planning strategies</a>.
-    Landscape and Urban Planning, 136, 28-39.</li>
+    Landscape and Urban Planning, 136, 28-39.
+    DOI: 10.1016/j.landurbplan.2014.11.011</li>
+<li>Petrasova, A., Petras, V., Van Berkel, D., Harmon, B. A., Mitasova, H.,  &amp; Meentemeyer, R. K. (2016).
+   <a href="https://www.int-arch-photogramm-remote-sens-spatial-inf-sci.net/XLI-B7/953/2016/isprs-archives-XLI-B7-953-2016.pdf">Open Source Approach to Urban Growth Simulation</a>.
+   Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLI-B7, 953-959.
+   DOI: 10.5194/isprsarchives-XLI-B7-953-2016</li>
 </ul>
 
 <h2>AUTHOR</h2>
 
-Anna Petrasova, <a href="http://geospatial.ncsu.edu/osgeorel/">NCSU OSGeoREL</a><br>
+Anna Petrasova, <a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll</a><br>
 
-<p><i>Last changed: $Date: 2015-02-12 14:32:45 -0500 (Thu, 12 Feb 2015) $</i>
+<p><i>Last changed: $Date: 2018-09-14 21:49:22 -0400 (Fri, 14 Sep 2018) $</i>
diff --git a/r.futures/r.futures.devpressure/r.futures.devpressure.html b/r.futures/r.futures.devpressure/r.futures.devpressure.html
@@ -65,18 +65,24 @@ <h2>SEE ALSO</h2>
 <h2>REFERENCES</h2>
 <ul>
 <li>
-    Meentemeyer, R. K., Tang, W., Dorning, M. A., Vogler, J. B., Cunniffe, N. J., & Shoemaker, D. A. (2013).
+    Meentemeyer, R. K., Tang, W., Dorning, M. A., Vogler, J. B., Cunniffe, N. J., &amp; Shoemaker, D. A. (2013).
     <a href="http://dx.doi.org/10.1080/00045608.2012.707591">FUTURES: Multilevel Simulations of Emerging
     Urban-Rural Landscape Structure Using a Stochastic Patch-Growing Algorithm</a>.
     Annals of the Association of American Geographers, 103(4), 785-807.
-<li>Dorning, M. A., Koch, J., Shoemaker, D. A., & Meentemeyer, R. K. (2015).
+    DOI: 10.1080/00045608.2012.707591
+<li>Dorning, M. A., Koch, J., Shoemaker, D. A., &amp; Meentemeyer, R. K. (2015).
    <a href="http://dx.doi.org/10.1016/j.landurbplan.2014.11.011">Simulating urbanization scenarios reveals
     tradeoffs between conservation planning strategies</a>.
-    Landscape and Urban Planning, 136, 28-39.</li>
+    Landscape and Urban Planning, 136, 28-39.
+    DOI: 10.1016/j.landurbplan.2014.11.011</li>
+<li>Petrasova, A., Petras, V., Van Berkel, D., Harmon, B. A., Mitasova, H.,  &amp; Meentemeyer, R. K. (2016).
+   <a href="https://www.int-arch-photogramm-remote-sens-spatial-inf-sci.net/XLI-B7/953/2016/isprs-archives-XLI-B7-953-2016.pdf">Open Source Approach to Urban Growth Simulation</a>.
+   Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLI-B7, 953-959.
+   DOI: 10.5194/isprsarchives-XLI-B7-953-2016</li>
 </ul>
 
 <h2>AUTHOR</h2>
 
-Anna Petrasova, <a href="http://geospatial.ncsu.edu/osgeorel/">NCSU OSGeoREL</a><br>
+Anna Petrasova, <a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll</a><br>
 
-<p><i>Last changed: $Date: 2015-02-12 14:32:45 -0500 (Thu, 12 Feb 2015) $</i>
+<p><i>Last changed: $Date: 2018-09-14 21:49:22 -0400 (Fri, 14 Sep 2018) $</i>
diff --git a/r.futures/r.futures.html b/r.futures/r.futures.html
@@ -110,16 +110,16 @@ <h2>REFERENCES</h2>
     <a href="http://dx.doi.org/10.1080/00045608.2012.707591">FUTURES: Multilevel Simulations of Emerging
     Urban-Rural Landscape Structure Using a Stochastic Patch-Growing Algorithm</a>.
     Annals of the Association of American Geographers, 103(4), 785-807.
+    DOI: 10.1080/00045608.2012.707591
 <li>Dorning, M. A., Koch, J., Shoemaker, D. A., &amp; Meentemeyer, R. K. (2015).
    <a href="http://dx.doi.org/10.1016/j.landurbplan.2014.11.011">Simulating urbanization scenarios reveals
     tradeoffs between conservation planning strategies</a>.
-    Landscape and Urban Planning, 136, 28-39.</li>
-<li>
-    Petrasova, A., Petras, V., Shoemaker, D. A., Dorning, M. A., &amp; Meentemeyer, R. K. (2015).
-    <a href="http://geomatica.como.polimi.it/workbooks/n12/FOSS4G-eu15_submission_72.pdf">
-        The integration of land change modeling framework FUTURES into GRASS GIS 7</a>.
-    Geomatics Workbooks. Volume 12. FOSS4G Europe: Como 2015.
-    Politecnico di Milano. Italy.
+    Landscape and Urban Planning, 136, 28-39.
+    DOI: 10.1016/j.landurbplan.2014.11.011</li>
+<li>Petrasova, A., Petras, V., Van Berkel, D., Harmon, B. A., Mitasova, H.,  &amp; Meentemeyer, R. K. (2016).
+   <a href="https://www.int-arch-photogramm-remote-sens-spatial-inf-sci.net/XLI-B7/953/2016/isprs-archives-XLI-B7-953-2016.pdf">Open Source Approach to Urban Growth Simulation</a>.
+   Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLI-B7, 953-959.
+   DOI: 10.5194/isprsarchives-XLI-B7-953-2016</li>
 </ul>
 
 
@@ -138,7 +138,7 @@ <h2>AUTHORS</h2>
 <p>
 <em>Corresponding author:</em><br>
 Ross K. Meentemeyer, rkmeente ncsu edu,
-<a href="http://geospatial.ncsu.edu/">Center for Geospatial Analytics, NCSU</a>
+<a href="https://geospatial.ncsu.edu/">Center for Geospatial Analytics, NCSU</a>
 
 <p>
 <em>Original standalone version:</em><br>
@@ -153,17 +153,17 @@ <h2>AUTHORS</h2>
 
 <br>
 * Department of Geography and Earth Sciences, UNC Charlotte<br>
-** <a href="http://geospatial.ncsu.edu/">Center for Geospatial Analytics, NCSU</a><br>
+** <a href="https://geospatial.ncsu.edu/">Center for Geospatial Analytics, NCSU</a><br>
 
 <p>
 <em>Port to GRASS GIS and GRASS-specific additions:</em><br>
 
-Vaclav Petras, <a href="http://geospatial.ncsu.edu/osgeorel/">NCSU OSGeoREL</a><br>
+Vaclav Petras, <a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll</a><br>
 
 <p>
 <em>Developement pressure, demand and calibration and preprocessing modules:</em><br>
 
-Anna Petrasova, <a href="http://geospatial.ncsu.edu/osgeorel/">NCSU OSGeoREL</a><br>
+Anna Petrasova, <a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll</a><br>
 
 <p>
-<i>Last changed: $Date: 2014-03-25 20:16:47 -0400 (Tue, 25 Mar 2014) $</i>
+<i>Last changed: $Date: 2018-09-14 21:49:22 -0400 (Fri, 14 Sep 2018) $</i>
diff --git a/r.futures/r.futures.parallelpga/r.futures.parallelpga.html b/r.futures/r.futures.parallelpga/r.futures.parallelpga.html
@@ -37,14 +37,20 @@ <h2>REFERENCES</h2>
     <a href="http://dx.doi.org/10.1080/00045608.2012.707591">FUTURES: Multilevel Simulations of Emerging
     Urban-Rural Landscape Structure Using a Stochastic Patch-Growing Algorithm</a>.
     Annals of the Association of American Geographers, 103(4), 785-807.
+    DOI: 10.1080/00045608.2012.707591
 <li>Dorning, M. A., Koch, J., Shoemaker, D. A., &amp; Meentemeyer, R. K. (2015).
    <a href="http://dx.doi.org/10.1016/j.landurbplan.2014.11.011">Simulating urbanization scenarios reveals
     tradeoffs between conservation planning strategies</a>.
-    Landscape and Urban Planning, 136, 28-39.</li>
+    Landscape and Urban Planning, 136, 28-39.
+    DOI: 10.1016/j.landurbplan.2014.11.011</li>
+<li>Petrasova, A., Petras, V., Van Berkel, D., Harmon, B. A., Mitasova, H.,  &amp; Meentemeyer, R. K. (2016).
+   <a href="https://www.int-arch-photogramm-remote-sens-spatial-inf-sci.net/XLI-B7/953/2016/isprs-archives-XLI-B7-953-2016.pdf">Open Source Approach to Urban Growth Simulation</a>.
+   Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLI-B7, 953-959.
+   DOI: 10.5194/isprsarchives-XLI-B7-953-2016</li>
 </ul>
 
 <h2>AUTHOR</h2>
 
-Anna Petrasova, <a href="http://geospatial.ncsu.edu/osgeorel/">NCSU OSGeoREL</a><br>
+Anna Petrasova, <a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll</a><br>
 
-<p><i>Last changed: $Date: 2015-02-12 14:32:45 -0500 (Thu, 12 Feb 2015) $</i>
+<p><i>Last changed: $Date: 2018-09-14 21:49:22 -0400 (Fri, 14 Sep 2018) $</i>
diff --git a/r.futures/r.futures.pga/main.c b/r.futures/r.futures.pga/main.c
@@ -1319,13 +1319,15 @@ void updateMap1(t_Landscape * pLandscape, t_Params * pParams, int step,
     }
     G_debug(1, "After accounting for extra cells, attempt %d cells", nToConvert);
     /* if have cells to convert this step */
+    bool forceConvertEverything = false;
     if (nToConvert > 0) {
         /* if not enough cells to convert then alter number required */
         if (nToConvert > pLandscape->num_undevSites[regionID]) {
             G_warning("Not enough undeveloped sites (requested: %d,"
                       " available: %d). Converting all available.",
                        nToConvert, pLandscape->num_undevSites[regionID]);
             nToConvert = pLandscape->num_undevSites[regionID];
+            forceConvertEverything = true;
         }
         /* update in stochastic fashion */
         nDone = 0;
@@ -1364,7 +1366,7 @@ void updateMap1(t_Landscape * pLandscape, t_Params * pParams, int step,
                     /* Doug's "back to front" logit */
                     //  dProb = 1.0/(1.0 + exp(pLandscape->asUndev[i].logitVal));
                     dProb = pLandscape->asUndevs[regionID][i].logitVal;
-                    if (uniformRandom() < dProb) {
+                    if (forceConvertEverything || (uniformRandom() < dProb)) {
                         nDone +=
                                 convertCells(pLandscape, pParams,
                                              pLandscape->asUndevs[regionID]
@@ -1904,7 +1906,6 @@ int getUnDevIndex1(t_Landscape * pLandscape, int regionID)
     if (p >= pLandscape->asUndevs[regionID][last].cumulProb)
         return last;
     while (first <= last) {
-        // TODO: these might not me initialized (says also valgrind)
         if (pLandscape->asUndevs[regionID][middle].cumulProb < p)
             first = middle + 1;
         else if (pLandscape->asUndevs[regionID][middle - 1].cumulProb < p &&
@@ -2007,9 +2008,8 @@ void findAndSortProbsAll(t_Landscape * pLandscape, t_Params * pParams,
     int j;
 
     for (j = 0; j < pParams->num_Regions; j++) {
-        // TODO: value of pLandscape->asUndevs[j][0].cumulProb is what?
         double sum = pLandscape->asUndevs[j][0].logitVal;
-
+        pLandscape->asUndevs[j][0].cumulProb = pLandscape->asUndevs[j][0].logitVal;
         for (i = 1; i < pLandscape->num_undevSites[j]; i++) {
             pLandscape->asUndevs[j][i].cumulProb =
                 pLandscape->asUndevs[j][i - 1].cumulProb +

diff --git a/r.futures/r.futures.potential/r.futures.potential.html b/r.futures/r.futures.potential/r.futures.potential.html
@@ -26,7 +26,8 @@ <h3>Format</h3>
 The header contains the names of the predictor maps and the first column
 contains the identifiers of the subregions. The order of columns is important,
 the second column represents intercept, the third development pressure and
-then the predictors.
+then the predictors. Therefore the development pressure column must be specified
+as the first column in option <b>columns</b>.
 
 <pre>
 ID	Intercept	devpressure_0_5	slope	road_dens_perc	forest_smooth_perc ...
@@ -41,6 +42,8 @@ <h3>Format</h3>
 <h2>NOTES</h2>
 Note that this module is designed to automate the FUTURES workflow by brute-force
 selection of model, which has numerous caveats.
+<p>
+In case there is only one subregion, R function glm is used instead of glmer.
 
 <h2>EXAMPLES</h2>
 
@@ -61,14 +64,20 @@ <h2>REFERENCES</h2>
     <a href="http://dx.doi.org/10.1080/00045608.2012.707591">FUTURES: Multilevel Simulations of Emerging
     Urban-Rural Landscape Structure Using a Stochastic Patch-Growing Algorithm</a>.
     Annals of the Association of American Geographers, 103(4), 785-807.
+    DOI: 10.1080/00045608.2012.707591
 <li>Dorning, M. A., Koch, J., Shoemaker, D. A., &amp; Meentemeyer, R. K. (2015).
    <a href="http://dx.doi.org/10.1016/j.landurbplan.2014.11.011">Simulating urbanization scenarios reveals
     tradeoffs between conservation planning strategies</a>.
-    Landscape and Urban Planning, 136, 28-39.</li>
+    Landscape and Urban Planning, 136, 28-39.
+    DOI: 10.1016/j.landurbplan.2014.11.011</li>
+<li>Petrasova, A., Petras, V., Van Berkel, D., Harmon, B. A., Mitasova, H.,  &amp; Meentemeyer, R. K. (2016).
+   <a href="https://www.int-arch-photogramm-remote-sens-spatial-inf-sci.net/XLI-B7/953/2016/isprs-archives-XLI-B7-953-2016.pdf">Open Source Approach to Urban Growth Simulation</a>.
+   Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLI-B7, 953-959.
+   DOI: 10.5194/isprsarchives-XLI-B7-953-2016</li>
 </ul>
 
 <h2>AUTHOR</h2>
 
-Anna Petrasova, <a href="http://geospatial.ncsu.edu/osgeorel/">NCSU OSGeoREL</a><br>
+Anna Petrasova, <a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll</a><br>
 
-<p><i>Last changed: $Date: 2015-02-12 14:32:45 -0500 (Thu, 12 Feb 2015) $</i>
+<p><i>Last changed: $Date: 2018-09-14 21:49:22 -0400 (Fri, 14 Sep 2018) $</i>