Update documentation for release v1.1.1

docs/getting_started.md

@@ -16,7 +16,7 @@ To get started working with **omniscape** SyncroSim, begin by:
 ## **Installing SyncroSim and Julia**
 
 Running **omniscape** SyncroSim requires that SyncroSim and Julia be installed on your computer. 
-1. Download SyncroSim version 2.4.42 or higher [here](https://syncrosim.com/download/){:target="_blank"} and follow the installation prompts. 
+1. Download SyncroSim version 2.5.3 or higher [here](https://syncrosim.com/download/){:target="_blank"} and follow the installation prompts. 
 2. Download Julia version 1.5.4 or higher [here](https://julialang.org/downloads/){:target="_blank"} and follow the installation prompts.
 
 <br>
@@ -35,15 +35,15 @@ Running **omniscape** SyncroSim requires that SyncroSim and Julia be installed o
 
 4\. A new window will open listing the packages available for install from the Package Server. To install **omniscape** SyncroSim, mark the checkbox beside the package name and click **OK**. 
 
-<img align="center" style="padding: 13px" width="600" src="assets/images/screenshot3.png">
+<img align="center" style="padding: 13px" width="600" src="assets/images/screenshot3-new.png">
 
 5\.	The **omniscape** SyncroSim package uses Conda to manage the package dependencies. Upon installing the package, you will be prompted to install Conda if it is not already installed in your computer. Then, you will be prompted to create or update the Conda environment for **omniscape** SyncroSim. Click **Yes**.  
 
 <img align="center" style="padding: 13px" width="600" src="assets/images/screenshot4.png">
 
 6\.	Return to the *Packages* window, **omniscape** will now be listed along with the other installed packages, and the Conda checkbox will be marked.
 
-<img align="center" style="padding: 13px" width="600" src="assets/images/screenshot5.png">
+<img align="center" style="padding: 13px" width="600" src="assets/images/screenshot5-new.png">
 
 ## **Next steps**
 

docs/index.md

@@ -22,8 +22,8 @@ In addition, **omniscape** SyncroSim has an accompanying package: **omniscapeImp
 
 ## Requirements
 
-**omniscape** SyncroSim has two requirements:
-* SyncroSim [version 2.4.42](https://syncrosim.com/download/){:target="_blank"} or higher
+The latest version of **omniscape** SyncroSim has two requirements:
+* SyncroSim [version 2.5.3](https://syncrosim.com/download/){:target="_blank"} or higher
 * Julia [version 1.5.4](https://julialang.org/downloads/){:target="_blank"} or higher
 
 > Instructions for installing the above requirements for **omniscape** SyncroSim are provided on the [Getting Started](https://apexrms.github.io/omniscape/getting_started.html) page.

docs/omniscapeImpact_tutorial.md

@@ -24,7 +24,7 @@ This tutorial guides you through using the **omniscapeImpact** add-on package to
 
 ### **Requirements**
 
-Before you begin, make sure that the **omniscape** SyncroSim package version 1.1.0 is installed. For more information, see <A href="https://apexrms.github.io/omniscape/getting_started#installing-the-omniscape-syncrosim-package">Installing the **omniscape** SyncroSim package</A>.
+Before you begin, make sure that the **omniscape** SyncroSim package version 1.1.1 is installed. For more information, see <A href="https://apexrms.github.io/omniscape/getting_started#installing-the-omniscape-syncrosim-package">Installing the **omniscape** SyncroSim package</A>.
 
 <br>
 
@@ -38,19 +38,19 @@ Before you begin, make sure that the **omniscape** SyncroSim package version 1.1
 
 3\.	The *Packages* window will open, listing all the SyncroSim packages installed in your computer. To install a new package from the Package Server, click **Install**.
 
-<img align="center" style="padding: 13px" width="550" src="./images/screenshot44.png">
+<img align="center" style="padding: 13px" width="550" src="./images/screenshot44-new.png">
 
 4\.	A new window will open listing the packages available for install from the Package Server. To install **omniscapeImpact**, mark the checkbox beside the package name and click **OK**. 
 
-<img align="center" style="padding: 13px" width="550" src="./images/screenshot45.png">
+<img align="center" style="padding: 13px" width="550" src="./images/screenshot45-new.png">
 
 5\.	The **omniscapeImpact** package uses Conda to manage the package dependencies. Upon installing the package, you will be prompted to create or update the Conda environment for **omniscapeImpact**. Click **Yes**.
 
 <img align="center" style="padding: 13px" width="550" src="./images/screenshot46.png">
 
 6\.	Return to the *Packages* window. **omniscapeImpact** will now be listed along with the other installed packages, and the Conda checkbox will be marked.
 
-<img align="center" style="padding: 13px" width="550" src="./images/screenshot47.png">
+<img align="center" style="padding: 13px" width="550" src="./images/screenshot47-new.png">
 
 <br>
 
@@ -68,7 +68,7 @@ Before you begin, make sure that the **omniscape** SyncroSim package version 1.1
   b.	Select the <b>Omniscape Impact</b> template library. If desired, you may edit the <i>File name</i>, and change the <i>Folder</i> by clicking on the <i>Browse</i> button. Click <b>OK</b>.
 </div>
 
-<img align="center" style="padding: 13px" width="550" src="./images/screenshot49.png">
+<img align="center" style="padding: 13px" width="550" src="./images/screenshot49-new.png">
 
 <br>
 
@@ -159,14 +159,14 @@ The **omniscapeImpact** package generates spatial and tabular outputs.
 5\.	Under the *Tabular* node are the following outputs:
 
 <div class=indentation>
-  a.	<i>Differences Summary</i> – represents the change in area and percent cover between the baseline and alternative scenarios for each connectivity category.
+  a.	<i>Differences Summary</i> – represents the change in area and proportion between the baseline and alternative scenarios for each connectivity category.
   <br><br>
-  b.	<i>Transitions Summary</i> – represents the change in area and percent cover between the baseline and alternative scenarios for all possible transitions between connectivity categories.
+  b.	<i>Transitions Summary</i> – represents the change in area and proportion between the baseline and alternative scenarios for all possible transitions between connectivity categories.
   <br><br>
   c.	<i>Jaccard Dissimilarity</i> – represents the dissimilarity between the baseline and alternative scenarios for each connectivity category. For each connectivity category, the Jaccard Dissimilarity is calculated as 1 minus the ratio between the number of shared pixels across scenarios and the total number of pixels across scenarios.
 </div>
 
-<img align="center" style="padding: 13px" width="600" src="./images/screenshot58.png">
+<img align="center" style="padding: 13px" width="600" src="./images/screenshot58-new.png">
 
 6\.	Close the scenario properties and collapse the results and scenario folder.
 
@@ -176,11 +176,11 @@ You will now visualize the tabular outputs of <b>omniscapeImpact</b>
 
 7\.	In the Library Explorer window, select the scenarios **Impact of increased resistance** and **Impact of decreased resistance**, right-click, and select **Add to Results** from the context menu. 
 
-<img align="center" style="padding: 13px" width="400" src="./images/screenshot59.png">
+<img align="center" style="padding: 13px" width="400" src="./images/screenshot59-new.png">
 
 8\.	Navigate to the **Charts** tab and double-click to view the **Area difference** chart. 
 
-<img align="center" style="padding: 13px" width="600" src="./images/screenshot60.png">
+<img align="center" style="padding: 13px" width="600" src="./images/screenshot60-new.png">
 
 <div class=indentation>
 Note that the two scenarios had opposite effects on connectivity. 
@@ -194,7 +194,7 @@ Note also that the magnitude of change in area was larger under the Decreased re
 
 9\.	Close the *Area difference* chart and open the **Jaccard dissimilarity** chart.
 
-<img align="center" style="padding: 13px" width="600" src="./images/screenshot61.png">
+<img align="center" style="padding: 13px" width="600" src="./images/screenshot61-new.png">
 
 <div class=indentation>
 Note that a similar pattern is reflected here, with <i>Impact of decreased resistance</i> showing greater dissimilarity to the baseline scenario compared to <i>Impact of increased resistance</i>.

docs/omniscape_tutorial.md

@@ -39,7 +39,7 @@ a. From the list of packages, select <b>omniscape</b>. Three template library op
 b. Select the <b>Omniscape Example</b> template library. If desired, you may edit the <i>File name</i>, and change the <i>Folder</i> by clicking on the <i>Browse</i> button. Click <b>OK</b>.
 </div>
 
-<img align="center" style="padding: 13px" width="500" src="./images/screenshot7.png">
+<img align="center" style="padding: 13px" width="500" src="./images/screenshot7-new.png">
 
 <br>
 
@@ -51,15 +51,15 @@ A new library has been created based on the selected template. SyncroSim will au
 
 4\.	The *Summary* datasheet contains the metadata for the library.
 
-<img align="center" style="padding: 13px" width="600" src="./images/screenshot9.png">
+<img align="center" style="padding: 13px" width="600" src="./images/screenshot9-new.png">
 
 5\.	Navigate to the **Julia Configuration tab**.
 
 <div class=indentation> 
 The path to the <b>Julia executable</b> file must be specified to run <b>omniscape</b> SyncroSim. To do so, click on the folder icon and navigate to where Julia is installed in your computer. Its default location is <b>C:\Users\[User_Name]\AppData\Local\Programs\Julia-[version]\bin\julia.exe</b>. 
 </div>
 
-<img align="center" style="padding: 13px" width="500" src="./images/screenshot10.png">
+<img align="center" style="padding: 13px" width="500" src="./images/screenshot10-new.png">
 
 > **Note:** The AppData folder is sometimes hidden. To see it, in File Explorer, select View > Show > Hidden items.
 
@@ -209,7 +209,7 @@ You can export the tabular output by right-clicking on the data and selecting <i
 </div>
 </div>
 
-<img align="center" style="padding: 13px" width="600" src="./images/screenshot24.png">
+<img align="center" style="padding: 13px" width="600" src="./images/screenshot24-new.png">
 
 3\.	Close the results scenario properties.
 
@@ -259,14 +259,14 @@ Next, you will visualize the outputs of the second transformer, which takes the
 
 8\.	Keep the map open for comparison and from the Library Explorer window, navigate to the **Charts** tab and view the **Area** chart. 
 
-<img align="center" style="padding: 13px" width="600" src="./images/screenshot30.png">
+<img align="center" style="padding: 13px" width="600" src="./images/screenshot30-new.png">
 
 <div class=indentation>
 Note that it summarized the amount of area per connectivity category.
-Alternatively, a <b>Percent cover</b> summary is also available.
+Alternatively, a <b>Proportion</b> summary is also available.
 </div>
 
-<img align="center" style="padding: 13px" width="600" src="./images/screenshot31.png">
+<img align="center" style="padding: 13px" width="600" src="./images/screenshot31-new.png">
 
 9\.	Close all plot windows.
 
@@ -361,7 +361,7 @@ If required, right-click on the scenario(s) and select <b>Add to Results</b> fro
 
 2\.	First, view the **Area** chart.
 
-<img align="center" style="padding: 13px" width="600" src="./images/screenshot41.png">
+<img align="center" style="padding: 13px" width="600" src="./images/screenshot41-new.png">
 
 <div class=indentation>
 Note that the increase in resistance resulted in a small increase in the amount of <i>Impeded</i> and <i>Channelized</i> areas, and a decrease in the amount of <i>Diffuse</i> and <i>Intensified</i> areas.