Reformat the structure of the document.

bookdown/01-intro.Rmd

@@ -1,13 +1,18 @@
 # Introduction
 
-The conservation and restoration of biodiversity is a global priority (Secretariat of the Convention on Biological
-Diversity, 2020), with the recent adoption of targets and goals through the 2022 Kunming-Montreal Global
-Biodiversity Framework (GBF) representing a global commitment to reverse the decline in biodiversity. Habitat loss is considered to be the primary cause of the global decline in biodiversity in recent decades (Millennium Ecosystem
-Assessment, 2005; Newbold et al., 2015; Semper-Pascual et al., 2021). The availability of high-quality habitat has
-been linked to species richness, species resilience and biodiversity (Rosenzweig, 1995; Klok and De Roos, 1998;
-Wilson et al., 2002; Ribic et al., 2009; Ramesh et al., 2016). Conversely, replacing native habitat (‘native cover’) with anthropogenic land uses (‘human footprints’) has been shown to reduce biodiversity (Vitousek et al., 1997; Crooks and Soulé, 1999; Laurance and Cochrane, 2001; Sanderson et al., 2002). A key aspect of the GBF is tracking
-progress of the targets and goals through the development and monitoring of indicators. Alberta Environment and
-Protected Areas, in partnership with the Alberta Biodiversity Monitoring Institute (ABMI), developed the Native Cover indicator to support biodiversity conservation and land-use management. ‘Native cover’ is defined as an area that is free of visible anthropogenic alteration (human footprint). ‘Human footprint’ is any area visibly altered for anthropogenic land use. The Native Cover indicator quantifies one facet of biodiversity loss by tracking the amount of native cover converted to human footprints, typically for settlement, agriculture, resource extraction, and transportation.
+## What is Native Cover?
 
+The conservation and restoration of biodiversity is a global priority (Secretariat of the Convention on Biological Diversity, 2020), with the recent adoption of targets and goals through the 2022 Kunming-Montreal Global Biodiversity Framework (GBF) representing a global commitment to reverse the decline in biodiversity. Habitat loss is considered to be the primary cause of the global decline in biodiversity in recent decades (Millennium Ecosystem Assessment, 2005; Newbold et al., 2015; Semper-Pascual et al., 2021). The availability of high-quality habitat has been linked to species richness, species resilience and biodiversity (Rosenzweig, 1995; Klok and De Roos, 1998;
+Wilson et al., 2002; Ribic et al., 2009; Ramesh et al., 2016). Conversely, replacing native habitat (‘native cover’) with anthropogenic land uses (‘human footprints’) has been shown to reduce biodiversity (Vitousek et al., 1997; Crooks and Soulé, 1999; Laurance and Cochrane, 2001; Sanderson et al., 2002). 
 
+A key aspect of the GBF is tracking progress of the targets and goals through the development and monitoring of indicators. Alberta Environment and Protected Areas, in partnership with the Alberta Biodiversity Monitoring Institute (ABMI), developed the Native Cover indicator to support biodiversity conservation and land-use management. ‘Native cover’ is defined as an area that is free of visible anthropogenic alteration (human footprint). ‘Human footprint’ is any area visibly altered for anthropogenic land use. The Native Cover indicator quantifies one facet of biodiversity loss by tracking the amount of native cover converted to human footprints, typically for settlement, agriculture, resource extraction, and transportation.
 
+## How can it be measured?
+
+This indicator measures two types of native cover:
+
+- **Aquatic native cover** represents the amount of aquatic habitat including bogs, fens, swamps, marshes, open water, and riparian areas.
+
+- **Terrestrial native cover** represents the amount of habitat not identified as aquatic habitat (i.e., upland).
+
+For each indicator, we delineated the areas of aquatic and terrestrial native cover and then overlaid human footprint to assess the **current** condition, while discounting for harvest area recovery. The **reference** condition was assessed as the total area of aquatic and terrestrial native cover without the presence of human footprint. This indicator is then presented as the percentage of current native cover (i.e., with footprint) relative to the reference state (i.e., without footprint).

bookdown/02-methods.Rmd

@@ -1,12 +1,4 @@
 # Native Cover Indicator
-
-There are two types of native cover:
-
-- **Aquatic native cover** represents the amount of aquatic habitat including bogs, fens, swamps, marshes, open water, and riparian areas.
-
-- **Terrestrial native cover** represents the amount of habitat not identified as aquatic habitat (i.e., upland).
-
-For each indicator, we delineated the areas of aquatic and terrestrial native cover and then overlaid human footprint to assess the **current** condition, while discounting for harvest area recovery. The **reference** condition was assessed as the total area of aquatic and terrestrial native cover without the presence of human footprint. This indicator is then presented as the percentage of current native cover (i.e., with footprint) relative to the reference state (i.e., without footprint).
 
 ## GIS Layers
 
@@ -21,15 +13,23 @@ The following GIS layers were used to delineate native habitat:
 4) **Hierarchical Watershed Boundaries of Alberta** The Hydrologic Unit Code Watersheds of Alberta layer allows us to aggregate the status of AWNC and TNC based on ecologically relevant boundaries ([Hydrologic Unit Code Watersheds of Alberta](https://open.alberta.ca/opendata/gda-7857b6fb-96c5-4bc5-ac3a-9017778fd183)). We chose to aggregate the information at the HUC-8 watershed scale. Each HUC-8 watershed contains both AWNC and TNC, with TNC ranging between 3.5% to 94% across watersheds. However, these indicators can be reported at alternative spatial scales.
 
 ## Reference condition
-The Native Cover indicator is expressed as a percentage based on a reference state. We defined the reference state
-as if there is a complete absence of human footprint. Under this reference condition, Alberta is composed
-of 66% TNC and 34% AWNC. By using this reference state, it can aid the interpretation of changes in native cover
-over time. Areas defined as aquatic and wetland native cover are based on when the source layers were derived.
-Areas which are now considered upland may have contained wetlands prior to anthropogenic disturbance and this
+The Native Cover indicator is expressed as a percentage based on a reference state. We defined the reference state as if there is a complete absence of human footprint. Under this reference condition, Alberta is composed of 66% TNC and 34% AWNC. By using this reference state, it can aid the interpretation of changes in native cover over time. Areas defined as aquatic and wetland native cover are based on when the source layers were derived. Areas which are now considered upland may have contained wetlands prior to anthropogenic disturbance and this
 loss is not reflected in this indicator.
 
 <center>
-![Areasa identified as aquatic and wetland (blue) and terrestrial (yellow) native cover based on the ABMI Wetland Inventory and Lotic Riparian layer.](NativeCover_files/figure-html/images/aquatic-riparian-upland-boundary.png){width=80%}
+![Areas identified as aquatic and wetland (blue) and terrestrial (yellow) native cover based on the ABMI Wetland Inventory and Lotic Riparian layer.](NativeCover_files/figure-html/images/aquatic-riparian-upland-boundary.png){width=80%}
+
+</center>
+
+## Recovery of forest harvest areas
+Applying recovery to harvest areas when calculating current conditions gives a more realistic representation of how
+harvest areas interact with the surrounding ecosystem. It is well known in the scientific literature that forest
+harvesting, particularly clearcut harvesting, differs from wildfire in their impacts on biodiversity (McRae et al., 2001). Although harvest areas provide habitat for some species, they are not equivalent to post-fire forest stands of the same age. However, forest harvest areas do recover over time, and recovery curves recommended by Huggard and
+Kremsater (2015) for deciduous and coniferous forest types were applied when calculating the conditions of the
+AWNC and TNC indicators. These recovery curves were simplified to a single recovery curve to allow the AWNC and TNC indicators to be calculated using only publicly available GIS layers.
+
+<center>
+![Forest recovery curves as described by Kremsater et al., 2015](NativeCover_files/figure-html/images/forest-recovery-curves.png){width=80%}
 
 </center>
 
@@ -53,18 +53,3 @@ $Terrestrial Native Cover  = \frac{Current Terrestrial Cover}{Reference Terrestr
 
 </center>
 
-## Recovery of forest harvest areas
-Applying recovery to harvest areas when calculating current conditions gives a more realistic representation of how
-harvest areas interact with the surrounding ecosystem. It is well known in the scientific literature that forest
-harvesting, particularly clearcut harvesting, differs from wildfire in their impacts on biodiversity (McRae et al., 2001). Although harvest areas provide habitat for some species, they are not equivalent to post-fire forest stands of the same age. However, forest harvest areas do recover over time, and recovery curves recommended by Huggard and
-Kremsater (2015) for deciduous and coniferous forest types were applied when calculating the conditions of the
-AWNC and TNC indicators. These recovery curves were simplified to a single recovery curve to allow the AWNC and TNC indicators to be calculated using only publicly available GIS layers.
-
-<center>
-![Forest recovery curves as described by Kremsater et al., 2015](NativeCover_files/figure-html/images/forest-recovery-curves.png){width=80%}
-
-</center>
-
-
-
-

bookdown/03-results.Rmd

@@ -1,4 +1,4 @@
-# Results
+# Measureing Native Cover
 
 ## Aquatic Native Cover
 Across all HUC-8 watersheds, AWNC values ranged from 10.6% to 100%, with provincial average values of 79.7%,
@@ -32,3 +32,17 @@ Across the province, TNC decreased by an average of 2.15% (SD = 2.69) from 2010
 
 </center>
 
+## Limitations and Future Improvements
+
+All indicators, as representations of a component of the environment, have limitations. A single indicator cannot
+measure all aspects of habitat quantity and quality. The Native Cover indicator is intended to serve as a general
+indicator of habitat quantity at the regional and sub-regional levels.
+
+Currently, clearcut harvest areas are the only type of footprint that is allowed to recover in the calculation of AWNC
+and TNC. Recovery for other footprint types (e.g., seismic lines, wellpads) will not be accounted for until sufficient
+supporting information becomes available. 
+
+Potential future improvements include:
+• incorporating recovery for other human footprint types and refining the recovery curves for forest harvest areas,
+• attributing changes in AWNC and TNC to relevant reporting sectors, and
+• acquiring new wetland inventories that better represent wetland loss over time.

bookdown/index.Rmd

@@ -13,7 +13,17 @@ description: "Technical documentation describing the methodology behind the Nati
 
 # Summary
 
-Alberta Environment and Parks (AEP), in partnership with the Alberta Biodiversity Monitoring Institute (ABMI), has developed an indicator to track the percentage of native cover in both terrestrial (i.e., upland) and aquatic (i.e., bogs, fens, swamps, marsh, open water) habitats.
+Alberta Environment and Protected Areas, in partnership with the Alberta Biodiversity Monitoring Institute (ABMI), developed the Native Cover indicator to support biodiversity conservation and land-use management. ‘Native cover’ is defined as an area that is free of visible anthropogenic alteration (human footprint). ‘Human footprint’ is any area visibly altered for anthropogenic land use. The Native Cover indicator quantifies one facet of biodiversity loss by tracking the amount of native cover converted to human footprints, typically for settlement, agriculture, resource extraction, and transportation.
+
+There are two types of native cover:
+- Aquatic and wetland native cover (**AWNC**), representing the amount of aquatic habitat free of visible human
+footprint, including bogs, fens, swamps, marshes, open water, and riparian areas;
+- Terrestrial native cover (**TNC**), representing the amount of upland (non-aquatic) habitat free of visible human
+footprint. 
+
+## Supporting Information
+
+This repository contains the R code (**src/**) required for reproducing the results presented on . The Native Cover Indicator for Alberta is a geospatial product that presents the status of **AWNC** and **TNC** for all HUC 8 watersheds in Alberta at five timesteps: 2010, 2018, 2019, 2020, and 2021. This data layer can be found on the Government of Alberta's [GeoDiscover Alberta](https://open.alberta.ca/opendata/gda-a582d6fe-b340-4f9b-9e7c-c7adeedbce7d) platform. Technical documentation describing the methodology and underlying data layers for this indicator can also be found on [GeoDiscover Alberta](https://open.alberta.ca/publications/native-cover-indicator-for-alberta).
 
 ## Acknowledgement