From d9acb08d139baaddc8025587c783ba44c8c8cd44 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Mon, 24 Apr 2023 09:56:41 -0400
Subject: [PATCH 01/37] Adding a Software section

---
 docs/source/index.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/docs/source/index.md b/docs/source/index.md
index 66fe9709..553d36af 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -63,6 +63,13 @@ format/target-data.md
 format/model-abstracts.md
 ```
 
+```{toctree}
+:maxdepth: 2
+:caption: Software
+:hidden:
+software/overview.md
+```
+
 ```{toctree}
 :maxdepth: 2
 :caption: Data validation

From afe32b7980fd22caba8acb2bd34df3985dd5d66b Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Mon, 24 Apr 2023 10:10:37 -0400
Subject: [PATCH 02/37] Software page

---
 docs/source/software/overview.md | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 docs/source/software/overview.md

diff --git a/docs/source/software/overview.md b/docs/source/software/overview.md
new file mode 100644
index 00000000..97db9579
--- /dev/null
+++ b/docs/source/software/overview.md
@@ -0,0 +1,3 @@
+## Software Overview
+
+Software available for Hubs

From 28ce15a30d6701437a6534e84c3b61f825057cc1 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Mon, 24 Apr 2023 10:30:16 -0400
Subject: [PATCH 03/37] small name change

---
 docs/source/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 553d36af..0409da4b 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -67,7 +67,7 @@ format/model-abstracts.md
 :maxdepth: 2
 :caption: Software
 :hidden:
-software/overview.md
+software/software.md
 ```
 
 ```{toctree}

From f4d621c2797593bcedeec714bc5afcf2d104c336 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Mon, 24 Apr 2023 10:40:03 -0400
Subject: [PATCH 04/37] Fix skeleton of software page

---
 docs/source/software/overview.md |  3 ---
 docs/source/software/software.md | 15 +++++++++++++++
 2 files changed, 15 insertions(+), 3 deletions(-)
 delete mode 100644 docs/source/software/overview.md
 create mode 100644 docs/source/software/software.md

diff --git a/docs/source/software/overview.md b/docs/source/software/overview.md
deleted file mode 100644
index 97db9579..00000000
--- a/docs/source/software/overview.md
+++ /dev/null
@@ -1,3 +0,0 @@
-## Software Overview
-
-Software available for Hubs
diff --git a/docs/source/software/software.md b/docs/source/software/software.md
new file mode 100644
index 00000000..511de112
--- /dev/null
+++ b/docs/source/software/software.md
@@ -0,0 +1,15 @@
+# Software
+
+To assist users in building a Hub, we have developed a software suite with specific functions and uses outlined below, and explained in more detail in their documentation pages.
+
+## hubUtils
+
+Here is a brief explanation and a [link](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils) to the documentation page.
+
+## hubEnsembles
+
+Here is a brief explanation and a [link](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) to the documentation page.
+
+## hubValidations
+
+Here is a brief explanation and a [link](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations) to the documentation page.

From 9b661770b8993776b820a5d481b992604365f80d Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 12:50:56 -0400
Subject: [PATCH 05/37] Complete software page update

---
 docs/source/software/software.md | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/docs/source/software/software.md b/docs/source/software/software.md
index 511de112..27d16003 100644
--- a/docs/source/software/software.md
+++ b/docs/source/software/software.md
@@ -1,15 +1,20 @@
-# Software
+# Software  
 
-To assist users in building a Hub, we have developed a software suite with specific functions and uses outlined below, and explained in more detail in their documentation pages.
+To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 
-## hubUtils
+## `hubUtils`  
 
-Here is a brief explanation and a [link](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils) to the documentation page.
+The goal of [`hubUtils`](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils) is to provide a set of utility functions for downloading, plotting, and scoring forecast and truth data from Infectious Disease Modeling Hubs. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils).  
 
-## hubEnsembles
+## hubEnsembles  
 
-Here is a brief explanation and a [link](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) to the documentation page.
+[`hubEnsembles`](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) is an R package with functionality to build simple ensembles of data from modeling hubs. Different ensembles can be built using for instance the mean, median, and mode. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles).  
 
-## hubValidations
+## hubValidations  
+
+The [`hubValidations`](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations) repository facilitates the implementation of general validation rules that are enforced on submissions in the form of pull requests to hub repositories. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations).  
+
+## hubTemplate
+
+The [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository provides a template for groups wishing to build and maintain a new modeling hub, in the style of the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub), the [US Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub) or the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe). You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).  
 
-Here is a brief explanation and a [link](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations) to the documentation page.

From e58a476813ed0aef101146c268a0206d8c706d2a Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 12:59:53 -0400
Subject: [PATCH 06/37] Change in text formatting

---
 docs/source/software/software.md | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/docs/source/software/software.md b/docs/source/software/software.md
index 27d16003..74b5f02d 100644
--- a/docs/source/software/software.md
+++ b/docs/source/software/software.md
@@ -2,19 +2,19 @@
 
 To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 
-## `hubUtils`  
+## [`hubUtils`](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils)  
 
-The goal of [`hubUtils`](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils) is to provide a set of utility functions for downloading, plotting, and scoring forecast and truth data from Infectious Disease Modeling Hubs. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils).  
+The goal of `hubUtils` is to provide a set of utility functions for downloading, plotting, and scoring forecast and truth data from Infectious Disease Modeling Hubs. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils).  
 
-## hubEnsembles  
+## [`hubEnsembles`](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles)  
 
-[`hubEnsembles`](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) is an R package with functionality to build simple ensembles of data from modeling hubs. Different ensembles can be built using for instance the mean, median, and mode. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles).  
+`hubEnsembles` is an R package with functionality to build simple ensembles of data from modeling hubs. Different ensembles can be built using for instance the mean, median, and mode. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles).  
 
-## hubValidations  
+## [`hubValidations`](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations)  
 
-The [`hubValidations`](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations) repository facilitates the implementation of general validation rules that are enforced on submissions in the form of pull requests to hub repositories. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations).  
+The `hubValidations` repository facilitates the implementation of general validation rules that are enforced on submissions in the form of pull requests to hub repositories. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations).  
 
-## hubTemplate
+## [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate)
 
-The [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository provides a template for groups wishing to build and maintain a new modeling hub, in the style of the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub), the [US Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub) or the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe). You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).  
+The `hubTemplate` repository provides a template for groups wishing to build and maintain a new modeling hub, in the style of the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub), the [US Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub) or the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe). You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).  
 

From b6904f66f1b9c85ec63f6892545c3caff49e363a Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:03:18 -0400
Subject: [PATCH 07/37] Rename to Software overview

---
 docs/source/software/software.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/software/software.md b/docs/source/software/software.md
index 74b5f02d..c2868bfb 100644
--- a/docs/source/software/software.md
+++ b/docs/source/software/software.md
@@ -1,4 +1,4 @@
-# Software  
+# Software overview
 
 To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 

From d00d8bbef14d6c62b1c026fcb20cc59de4bee058 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:10:23 -0400
Subject: [PATCH 08/37] Rename to software-overview.md

---
 docs/source/software/{software.md => software-overview.md} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename docs/source/software/{software.md => software-overview.md} (100%)

diff --git a/docs/source/software/software.md b/docs/source/software/software-overview.md
similarity index 100%
rename from docs/source/software/software.md
rename to docs/source/software/software-overview.md

From 814f88c7fc91db8baca2f924e05c07f9bd806155 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:10:28 -0400
Subject: [PATCH 09/37] Rename to software-overview

---
 docs/source/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 62457e1d..0938239b 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -68,7 +68,7 @@ format/model-abstracts.md
 :maxdepth: 2
 :caption: Software
 :hidden:
-software/software.md
+software/software-overview.md
 ```
 
 ```{toctree}

From d39f1995ca314c241c26a6adbe5c4ca28770cb6f Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:21:10 -0400
Subject: [PATCH 10/37] Testing submenu edit

---
 docs/source/index.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/index.md b/docs/source/index.md
index 0938239b..3b90f18d 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -69,6 +69,7 @@ format/model-abstracts.md
 :caption: Software
 :hidden:
 software/software-overview.md
+software/software-overview.md#hubtemplate
 ```
 
 ```{toctree}

From 9c6e73ad3c5d8f580c06de33019fd045d3d9284f Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:25:22 -0400
Subject: [PATCH 11/37] Trying again

---
 docs/source/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 3b90f18d..c65228a9 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -65,7 +65,7 @@ format/model-abstracts.md
 ```
 
 ```{toctree}
-:maxdepth: 2
+:maxdepth: 3
 :caption: Software
 :hidden:
 software/software-overview.md

From 93b6521216262379dddddb211ac4c0c4d60939bb Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:27:39 -0400
Subject: [PATCH 12/37] will it work?

---
 docs/source/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index c65228a9..f7d576c9 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -69,7 +69,7 @@ format/model-abstracts.md
 :caption: Software
 :hidden:
 software/software-overview.md
-software/software-overview.md#hubtemplate
+software/software-overview/hubtemplate
 ```
 
 ```{toctree}

From 89bd4fb9edb52002ff991c6871636838e95cbb16 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:30:10 -0400
Subject: [PATCH 13/37] last try

---
 docs/source/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index f7d576c9..a9aedce8 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -69,7 +69,7 @@ format/model-abstracts.md
 :caption: Software
 :hidden:
 software/software-overview.md
-software/software-overview/hubtemplate
+software/software-overview/#hubtemplate
 ```
 
 ```{toctree}

From 51631c4435a7af9417822e964732aa6253c79f74 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:34:38 -0400
Subject: [PATCH 14/37] Back to how things were and a rename

---
 docs/source/index.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index a9aedce8..0bf8fc10 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -65,11 +65,10 @@ format/model-abstracts.md
 ```
 
 ```{toctree}
-:maxdepth: 3
+:maxdepth: 2
 :caption: Software
 :hidden:
-software/software-overview.md
-software/software-overview/#hubtemplate
+software/software-available.md
 ```
 
 ```{toctree}

From 88db3ef605b4ade597ff35bc8cf2a6b40545bc27 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:35:30 -0400
Subject: [PATCH 15/37] Renaming subheader

---
 .../software/{software-overview.md => software-available.md}    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename docs/source/software/{software-overview.md => software-available.md} (99%)

diff --git a/docs/source/software/software-overview.md b/docs/source/software/software-available.md
similarity index 99%
rename from docs/source/software/software-overview.md
rename to docs/source/software/software-available.md
index c2868bfb..03a13567 100644
--- a/docs/source/software/software-overview.md
+++ b/docs/source/software/software-available.md
@@ -1,4 +1,4 @@
-# Software overview
+# Software available
 
 To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 

From 19b22c0b8c6b292295cb89e36736e9b01c6188a2 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:38:00 -0400
Subject: [PATCH 16/37] Last rename

---
 docs/source/software/software-available.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/software/software-available.md b/docs/source/software/software-available.md
index 03a13567..d1a856e5 100644
--- a/docs/source/software/software-available.md
+++ b/docs/source/software/software-available.md
@@ -1,4 +1,4 @@
-# Software available
+# Software
 
 To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 

From 28835286cae7064b66ee5a870537aa39cfb83c8e Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:46:27 -0400
Subject: [PATCH 17/37] Last rename (I hope)

---
 docs/source/software/software-available.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/software/software-available.md b/docs/source/software/software-available.md
index d1a856e5..03a13567 100644
--- a/docs/source/software/software-available.md
+++ b/docs/source/software/software-available.md
@@ -1,4 +1,4 @@
-# Software
+# Software available
 
 To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 

From eea83115a65c03a91be53ee4ac4cfff290e377b3 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 3 May 2023 13:51:29 -0400
Subject: [PATCH 18/37] Add other software packages to list

---
 docs/source/index.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 0bf8fc10..8ed6787b 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -32,8 +32,10 @@ To take advantage of the infrastructure designed by the Consortium, a hub must c
 
 The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models. 
 
-- [hubUtils](https://infectious-disease-modeling-hubs.github.io/hubUtils/) is an R package with utility functions for working with data from modelings hubs.
-- [hubEnsembles](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) is an R package with functionality to build simple ensembles of data from modeling hubs.
+- [`hubUtils`](https://infectious-disease-modeling-hubs.github.io/hubUtils/) is an R package with utility functions for working with data from modelings hubs.  
+- [`hubEnsembles`](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) is an R package with functionality to build simple ensembles of data from modeling hubs.  
+- [`hubValidations`](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations) is an R package that facilitates the implementation of general validation rules to enforce on submissions to modeling hubs.  
+- [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) is a repository that provides a template for groups wishing to build and maintain a new modeling hub.  
 
 
 

From 36db69ba5df8ef60e32c608bbeae899611546439 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 10 May 2023 10:34:26 -0400
Subject: [PATCH 19/37] Update software-available.md

---
 docs/source/software/software-available.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/software/software-available.md b/docs/source/software/software-available.md
index 03a13567..fd7afe51 100644
--- a/docs/source/software/software-available.md
+++ b/docs/source/software/software-available.md
@@ -2,9 +2,9 @@
 
 To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 
-## [`hubUtils`](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils)  
+## [`hubUtils`](https://infectious-disease-modeling-hubs.github.io/hubUtils/)  
 
-The goal of `hubUtils` is to provide a set of utility functions for downloading, plotting, and scoring forecast and truth data from Infectious Disease Modeling Hubs. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils).  
+The goal of `hubUtils` is to provide a set of utility functions for downloading, plotting, and scoring forecast and truth data from Infectious Disease Modeling Hubs. You can find instructions to download and use the package [here](https://infectious-disease-modeling-hubs.github.io/hubUtils/).  
 
 ## [`hubEnsembles`](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles)  
 

From c82b2b24a38102356947cdeeeaa8b67e2899c65b Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 10 May 2023 10:42:22 -0400
Subject: [PATCH 20/37] Delete hubTemplate reference

---
 docs/source/index.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 8ed6787b..7727b8a7 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -34,8 +34,7 @@ The main benefit of setting up a hub using the structure outlined in this docume
 
 - [`hubUtils`](https://infectious-disease-modeling-hubs.github.io/hubUtils/) is an R package with utility functions for working with data from modelings hubs.  
 - [`hubEnsembles`](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) is an R package with functionality to build simple ensembles of data from modeling hubs.  
-- [`hubValidations`](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations) is an R package that facilitates the implementation of general validation rules to enforce on submissions to modeling hubs.  
-- [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) is a repository that provides a template for groups wishing to build and maintain a new modeling hub.  
+- [`hubValidations`](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations) is an R package that facilitates the implementation of general validation rules to enforce on submissions to modeling hubs.   
 
 
 

From c99825b5e1155404a0bd5e7660c2afc0a4447ce5 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 10 May 2023 10:45:05 -0400
Subject: [PATCH 21/37] Getting started section

---
 docs/source/index.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/index.md b/docs/source/index.md
index 7727b8a7..7fcab73e 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -46,6 +46,7 @@ The main benefit of setting up a hub using the structure outlined in this docume
 :maxdepth: 2
 :caption: Overview
 :hidden:
+overview/getting-started.md
 overview/who-we-are.md
 overview/scope.md
 overview/definitions.md

From 18843f87e3e608bd4c4723aa777aa5c07d8ea27a Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 10 May 2023 11:19:44 -0400
Subject: [PATCH 22/37] Create getting-started.md section

---
 docs/source/overview/getting-started.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 docs/source/overview/getting-started.md

diff --git a/docs/source/overview/getting-started.md b/docs/source/overview/getting-started.md
new file mode 100644
index 00000000..de0cd680
--- /dev/null
+++ b/docs/source/overview/getting-started.md
@@ -0,0 +1,21 @@
+# Getting started  
+
+The simplest way to set up a modeling hub is to use one of the [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) listed below, which are based on prior use cases. These repositories provide minimal working examples of hubs and could be used for ideas of how to set up configuration files for new projects. Additionally, we are devloping a [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository that provides the skeletal structure of a modeling hub.  
+
+## Examples  
+
+### 1. [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub)  
+The [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub) is designed to be similar to the [US CDC FluSight Hospitalization Forecasting exercise](https://github.com/cdcepi/Flusight-forecast-data) from 2022-2023.  
+
+### 2. [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub)  
+The [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub) is designed to be similar to the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub) and the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe).  
+
+### 3. [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub)  
+The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub) is designed to be similar to the [US COVID-19 Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub)  
+
+
+## [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate)  
+
+[`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) is a repository (under development) that provides a template for groups wishing to build and maintain a new modeling hub. This repository may be cloned to start a new repository for a modeling hub.  
+
+

From c837d3cb4aa370454f70b0286ccc0976a2f844bb Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 10 May 2023 11:30:22 -0400
Subject: [PATCH 23/37] Remove hubTemplate info

---
 docs/source/software/software-available.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docs/source/software/software-available.md b/docs/source/software/software-available.md
index fd7afe51..bedd0701 100644
--- a/docs/source/software/software-available.md
+++ b/docs/source/software/software-available.md
@@ -14,7 +14,5 @@ The goal of `hubUtils` is to provide a set of utility functions for downloading,
 
 The `hubValidations` repository facilitates the implementation of general validation rules that are enforced on submissions in the form of pull requests to hub repositories. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations).  
 
-## [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate)
 
-The `hubTemplate` repository provides a template for groups wishing to build and maintain a new modeling hub, in the style of the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub), the [US Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub) or the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe). You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).  
 

From 25c38907f1c97cf512d56167b7d261577c2d2747 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 10 May 2023 11:33:20 -0400
Subject: [PATCH 24/37] edit hubTemplate section

---
 docs/source/overview/getting-started.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/getting-started.md b/docs/source/overview/getting-started.md
index de0cd680..4b59001b 100644
--- a/docs/source/overview/getting-started.md
+++ b/docs/source/overview/getting-started.md
@@ -16,6 +16,6 @@ The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modelin
 
 ## [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate)  
 
-[`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) is a repository (under development) that provides a template for groups wishing to build and maintain a new modeling hub. This repository may be cloned to start a new repository for a modeling hub.  
+The [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository (under development) provides a skeleton structure for groups wishing to build and maintain a new modeling hub. This repository may be cloned to start a new repository for a modeling hub.  
 
 

From e17d231fa120fa44fcc55eb3adc210b4caac8610 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Wed, 10 May 2023 11:34:28 -0400
Subject: [PATCH 25/37] Link added to examples

---
 docs/source/overview/getting-started.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/getting-started.md b/docs/source/overview/getting-started.md
index 4b59001b..7de59117 100644
--- a/docs/source/overview/getting-started.md
+++ b/docs/source/overview/getting-started.md
@@ -2,7 +2,7 @@
 
 The simplest way to set up a modeling hub is to use one of the [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) listed below, which are based on prior use cases. These repositories provide minimal working examples of hubs and could be used for ideas of how to set up configuration files for new projects. Additionally, we are devloping a [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository that provides the skeletal structure of a modeling hub.  
 
-## Examples  
+## [Examples](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=)  
 
 ### 1. [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub)  
 The [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub) is designed to be similar to the [US CDC FluSight Hospitalization Forecasting exercise](https://github.com/cdcepi/Flusight-forecast-data) from 2022-2023.  

From b3c82ccec145080c52c38cbe5854a313e7dea0e4 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 12:07:01 -0400
Subject: [PATCH 26/37] Reorganizing menu

---
 docs/source/index.md | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 7fcab73e..f516967e 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -46,10 +46,11 @@ The main benefit of setting up a hub using the structure outlined in this docume
 :maxdepth: 2
 :caption: Overview
 :hidden:
-overview/getting-started.md
 overview/who-we-are.md
 overview/scope.md
 overview/definitions.md
+overview/getting-started.md
+overview/software.md
 ```
 
 ```{toctree}
@@ -66,13 +67,6 @@ format/target-data.md
 format/model-abstracts.md
 ```
 
-```{toctree}
-:maxdepth: 2
-:caption: Software
-:hidden:
-software/software-available.md
-```
-
 ```{toctree}
 :maxdepth: 2
 :caption: Data validation

From ca142e9b5ba584bae9192258800ffe5e0807840a Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 12:11:22 -0400
Subject: [PATCH 27/37] Moving and renaming software

---
 .../{software/software-available.md => overview/software.md}      | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename docs/source/{software/software-available.md => overview/software.md} (100%)

diff --git a/docs/source/software/software-available.md b/docs/source/overview/software.md
similarity index 100%
rename from docs/source/software/software-available.md
rename to docs/source/overview/software.md

From c9c86c696f9d760fbe99a27f80b6ecdce7c51eef Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 12:11:48 -0400
Subject: [PATCH 28/37] Renaming software

---
 docs/source/overview/software.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/software.md b/docs/source/overview/software.md
index bedd0701..5826955c 100644
--- a/docs/source/overview/software.md
+++ b/docs/source/overview/software.md
@@ -1,4 +1,4 @@
-# Software available
+# Software
 
 To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 

From 6df956284aff5bea869aaeeeb54323a165883ab2 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 12:55:09 -0400
Subject: [PATCH 29/37] space check

---
 docs/source/overview/software.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/software.md b/docs/source/overview/software.md
index 5826955c..5d96eaf5 100644
--- a/docs/source/overview/software.md
+++ b/docs/source/overview/software.md
@@ -1,4 +1,4 @@
-# Software
+# Software  
 
 To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 

From 98b1ba4509a7bac808d4f052ada7e75a274d67dd Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 12:55:35 -0400
Subject: [PATCH 30/37] Expanding and updating getting-started.md

---
 docs/source/overview/getting-started.md | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/docs/source/overview/getting-started.md b/docs/source/overview/getting-started.md
index 7de59117..25e32d2a 100644
--- a/docs/source/overview/getting-started.md
+++ b/docs/source/overview/getting-started.md
@@ -1,8 +1,14 @@
 # Getting started  
 
-The simplest way to set up a modeling hub is to use one of the [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) listed below, which are based on prior use cases. These repositories provide minimal working examples of hubs and could be used for ideas of how to set up configuration files for new projects. Additionally, we are devloping a [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository that provides the skeletal structure of a modeling hub.  
+The simplest way to set up a modeling hub is to directly clone one from the [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) or to use one of the [example hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=), which are based on prior use cases. The template hubs provide a skeletal structure of a hub without any data, whereas the example hubs provide minimal working examples of hubs and could be used for ideas of how to set up configuration files for new projects.    
 
-## [Examples](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=)  
+## Template hubs  
+
+The [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository (under development) provides a skeleton structure for groups wishing to build and maintain a new modeling hub. This repository may be cloned to start a new repository for a modeling hub.  
+
+## [Example hubs](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=)  
+
+The [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) provide minimal working examples of hubs that can be used for ideas of how to set up configuration files for new projects. They are also used as use-cases for testing the [software for modeling hubs](software.md). 
 
 ### 1. [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub)  
 The [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub) is designed to be similar to the [US CDC FluSight Hospitalization Forecasting exercise](https://github.com/cdcepi/Flusight-forecast-data) from 2022-2023.  
@@ -14,8 +20,11 @@ The [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modelin
 The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub) is designed to be similar to the [US COVID-19 Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub)  
 
 
-## [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate)  
+## Schema files  
 
-The [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository (under development) provides a skeleton structure for groups wishing to build and maintain a new modeling hub. This repository may be cloned to start a new repository for a modeling hub.  
+To take advantage of the infrastructure designed by the Consortium, a hub must contain JSON configuration files in a [specific location and format](hub-config). The schemas that define the structure and formats of the configuration files live in their own [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas). The schemas are versioned, and every hub must point to a specific version of the schemas that they are using.  
+
+## [Software for modeling hubs](software.md)  
 
+The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
 

From 52c0bca2486c48667ffb6c1c0401a795a2e8b8d4 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 12:57:07 -0400
Subject: [PATCH 31/37] Landing page link updates (and more)

---
 docs/source/index.md | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index f516967e..5e2c5256 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -12,11 +12,11 @@ The following sections of this page provide an outline of the different resource
 
 The following subsections provide pointers to resources developed by the Consortium to make designing, launching, and maintaining hubs easier.
 
-### Template hubs
+### [Template hubs](overview/getting-started.md/#template-hubs)  
 
-The [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) provided by the consortium may be cloned directly to start a new hub. Unlike the example hubs below, these repositories do not have any data in them, they just provide a skeletal structure of a hub. Currently, we only host a single [template hub](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).
+The [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) provided by the consortium may be cloned directly to start a new hub. Unlike the example hubs below, these repositories do not have any data in them, they just provide a skeletal structure of a hub. Currently, we only host a single [template hub](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).  
 
-### Example hubs
+### Example hubs(overview/getting-started.md/#example-hubs)  
 
 We have created some [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) that provide minimal working examples of hubs. These repositories could be used for ideas of how to set up configuration files for new projects. They are also used as use-cases for testing the software described below.
 
@@ -24,11 +24,11 @@ We have created some [example Hub repositories](https://github.com/Infectious-Di
 - The [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub) is designed to be similar to the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub) and the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe).
 - The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub) is designed to be similar to the [US COVID-19 Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub)
 
-### Schema files for hub configuration
+### Schema files for hub configuration(overview/getting-started.md/#schema-files)  
 
 To take advantage of the infrastructure designed by the Consortium, a hub must contain JSON configuration files in a [specific location and format](hub-config). The schemas that define the structure and formats of the configuration files live in their own [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas). The schemas are versioned, and every hub must point to a specific version of the schemas that they are using.
 
-## Software for modeling hubs
+## Software for modeling hubs(overview/software.md)  
 
 The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models. 
 
@@ -40,8 +40,6 @@ The main benefit of setting up a hub using the structure outlined in this docume
 
 
 
-
-
 ```{toctree}
 :maxdepth: 2
 :caption: Overview

From e51b9a1081ca1ab70660443e8540529fa02bac9f Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 12:58:04 -0400
Subject: [PATCH 32/37] fixing some links

---
 docs/source/index.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 5e2c5256..2212b52b 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -16,7 +16,7 @@ The following subsections provide pointers to resources developed by the Consort
 
 The [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) provided by the consortium may be cloned directly to start a new hub. Unlike the example hubs below, these repositories do not have any data in them, they just provide a skeletal structure of a hub. Currently, we only host a single [template hub](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).  
 
-### Example hubs(overview/getting-started.md/#example-hubs)  
+### [Example hubs](overview/getting-started.md/#example-hubs)  
 
 We have created some [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) that provide minimal working examples of hubs. These repositories could be used for ideas of how to set up configuration files for new projects. They are also used as use-cases for testing the software described below.
 
@@ -24,11 +24,11 @@ We have created some [example Hub repositories](https://github.com/Infectious-Di
 - The [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub) is designed to be similar to the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub) and the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe).
 - The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub) is designed to be similar to the [US COVID-19 Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub)
 
-### Schema files for hub configuration(overview/getting-started.md/#schema-files)  
+### [Schema files for hub configuration](overview/getting-started.md/#schema-files)  
 
 To take advantage of the infrastructure designed by the Consortium, a hub must contain JSON configuration files in a [specific location and format](hub-config). The schemas that define the structure and formats of the configuration files live in their own [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas). The schemas are versioned, and every hub must point to a specific version of the schemas that they are using.
 
-## Software for modeling hubs(overview/software.md)  
+## [Software for modeling hubs](overview/software.md)  
 
 The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models. 
 

From 6e4dd1a5713c804b8a31bc4c34c7aee6258ea05c Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 12:59:33 -0400
Subject: [PATCH 33/37] changing font size

---
 docs/source/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 2212b52b..7d7f0f80 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -28,7 +28,7 @@ We have created some [example Hub repositories](https://github.com/Infectious-Di
 
 To take advantage of the infrastructure designed by the Consortium, a hub must contain JSON configuration files in a [specific location and format](hub-config). The schemas that define the structure and formats of the configuration files live in their own [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas). The schemas are versioned, and every hub must point to a specific version of the schemas that they are using.
 
-## [Software for modeling hubs](overview/software.md)  
+### [Software for modeling hubs](overview/software.md)  
 
 The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models. 
 

From 67e75a1f3471996fd99e33ba9ea0b545b4eaf54e Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 13:19:04 -0400
Subject: [PATCH 34/37] homogenize titles (with links)

---
 docs/source/overview/getting-started.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/overview/getting-started.md b/docs/source/overview/getting-started.md
index 25e32d2a..7ce8e08b 100644
--- a/docs/source/overview/getting-started.md
+++ b/docs/source/overview/getting-started.md
@@ -2,7 +2,7 @@
 
 The simplest way to set up a modeling hub is to directly clone one from the [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) or to use one of the [example hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=), which are based on prior use cases. The template hubs provide a skeletal structure of a hub without any data, whereas the example hubs provide minimal working examples of hubs and could be used for ideas of how to set up configuration files for new projects.    
 
-## Template hubs  
+## [Template hubs](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=)  
 
 The [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository (under development) provides a skeleton structure for groups wishing to build and maintain a new modeling hub. This repository may be cloned to start a new repository for a modeling hub.  
 
@@ -20,7 +20,7 @@ The [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modelin
 The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub) is designed to be similar to the [US COVID-19 Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub)  
 
 
-## Schema files  
+## [Schema files](https://github.com/Infectious-Disease-Modeling-Hubs/schemas)  
 
 To take advantage of the infrastructure designed by the Consortium, a hub must contain JSON configuration files in a [specific location and format](hub-config). The schemas that define the structure and formats of the configuration files live in their own [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas). The schemas are versioned, and every hub must point to a specific version of the schemas that they are using.  
 

From b6995a8b7c6a0dce36eaeb1012742e2d77b09bda Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira" <acastrorivad@umass.edu>
Date: Thu, 11 May 2023 13:26:55 -0400
Subject: [PATCH 35/37] Cutting out redundant info on software.

---
 docs/source/index.md | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index 7d7f0f80..b1826c99 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -30,11 +30,7 @@ To take advantage of the infrastructure designed by the Consortium, a hub must c
 
 ### [Software for modeling hubs](overview/software.md)  
 
-The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models. 
-
-- [`hubUtils`](https://infectious-disease-modeling-hubs.github.io/hubUtils/) is an R package with utility functions for working with data from modelings hubs.  
-- [`hubEnsembles`](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) is an R package with functionality to build simple ensembles of data from modeling hubs.  
-- [`hubValidations`](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations) is an R package that facilitates the implementation of general validation rules to enforce on submissions to modeling hubs.   
+The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models. Details on the software available are provided [here](overview/software.md).  
 
 
 

From f44aea5971b6d7de21a52f08fb805c289547e202 Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 16:52:40 -0400
Subject: [PATCH 36/37] Deleting large chunks of redundant text

---
 docs/source/index.md | 26 +-------------------------
 1 file changed, 1 insertion(+), 25 deletions(-)

diff --git a/docs/source/index.md b/docs/source/index.md
index b1826c99..b6076943 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -6,31 +6,7 @@ This project is under active development.
 
 **The Consortium of Infectious Disease Modeling Hubs** is a collaboration of research teams that have built and maintained predictive modeling hubs for infectious disease applications. Working together, we have developed software for groups that are running collaborative modeling hub efforts. This website documents the requirements for using the infrastructure that the Consortium has set up.  
 
-The following sections of this page provide an outline of the different resources created by this project.
-
-## Tools for building and hosting modeling hubs
-
-The following subsections provide pointers to resources developed by the Consortium to make designing, launching, and maintaining hubs easier.
-
-### [Template hubs](overview/getting-started.md/#template-hubs)  
-
-The [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) provided by the consortium may be cloned directly to start a new hub. Unlike the example hubs below, these repositories do not have any data in them, they just provide a skeletal structure of a hub. Currently, we only host a single [template hub](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).  
-
-### [Example hubs](overview/getting-started.md/#example-hubs)  
-
-We have created some [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) that provide minimal working examples of hubs. These repositories could be used for ideas of how to set up configuration files for new projects. They are also used as use-cases for testing the software described below.
-
-- The [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub) is designed to be similar to the [US CDC FluSight Hospitalization Forecasting exercise](https://github.com/cdcepi/Flusight-forecast-data) from 2022-2023.
-- The [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub) is designed to be similar to the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub) and the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe).
-- The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub) is designed to be similar to the [US COVID-19 Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub)
-
-### [Schema files for hub configuration](overview/getting-started.md/#schema-files)  
-
-To take advantage of the infrastructure designed by the Consortium, a hub must contain JSON configuration files in a [specific location and format](hub-config). The schemas that define the structure and formats of the configuration files live in their own [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas). The schemas are versioned, and every hub must point to a specific version of the schemas that they are using.
-
-### [Software for modeling hubs](overview/software.md)  
-
-The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models. Details on the software available are provided [here](overview/software.md).  
+The [overview](overview/who-we-are.md) section provides an introduction to the project, and the [getting started](overview/getting-started.md) section outlines how to set up a working hub, as well as the different resources created by this project.  
 
 
 

From 0606c37fff862bf923435cb244a4f822fa73580e Mon Sep 17 00:00:00 2001
From: "Alvaro J. Castro Rivadeneira"
 <56451982+micokoch@users.noreply.github.com>
Date: Thu, 11 May 2023 16:53:04 -0400
Subject: [PATCH 37/37] Including some text that was on the landing page

---
 docs/source/overview/getting-started.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/source/overview/getting-started.md b/docs/source/overview/getting-started.md
index 7ce8e08b..92b343fd 100644
--- a/docs/source/overview/getting-started.md
+++ b/docs/source/overview/getting-started.md
@@ -1,6 +1,8 @@
 # Getting started  
 
-The simplest way to set up a modeling hub is to directly clone one from the [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) or to use one of the [example hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=), which are based on prior use cases. The template hubs provide a skeletal structure of a hub without any data, whereas the example hubs provide minimal working examples of hubs and could be used for ideas of how to set up configuration files for new projects.    
+The following subsections provide pointers to resources developed by the Consortium to make designing, launching, and maintaining hubs easier.  
+
+The simplest way to set up a modeling hub is to directly clone one from the [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) or to use one of the [example hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=), which are based on prior use cases. The template hubs provide a skeletal structure of a hub without any data in them, whereas the example hubs provide minimal working examples of hubs and could be used for ideas of how to set up configuration files for new projects.    
 
 ## [Template hubs](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=)