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diff --git a/modelling/winter-visitor/data/redwing_synthesised.png b/modelling/data/yil/winter/redwing_synthesised.png
similarity index 100%
rename from modelling/winter-visitor/data/redwing_synthesised.png
rename to modelling/data/yil/winter/redwing_synthesised.png
diff --git a/modelling/resident-detectability/README.md b/modelling/models/resident/README.md
similarity index 99%
rename from modelling/resident-detectability/README.md
rename to modelling/models/resident/README.md
index ae8c26c..6d197a6 100644
--- a/modelling/resident-detectability/README.md
+++ b/modelling/models/resident/README.md
@@ -254,7 +254,7 @@ The parameter fitting workflow is illustrated below:
 
 ![Parameter Fitting](https://github.com/davewalker5/OdeSolver/blob/main/docs/images/parameter-fitting.png?raw=true)
 
-The following summarises
+The following summarises the naming conventions and locations for the outputs from the modelling process:
 
 | File              | Naming                          | Type      | Location    |
 | ----------------- | ------------------------------- | --------- | ----------- |
diff --git a/modelling/resident-detectability/model/resident_detectability_generic.json b/modelling/models/resident/resident_detectability_generic.json
similarity index 100%
rename from modelling/resident-detectability/model/resident_detectability_generic.json
rename to modelling/models/resident/resident_detectability_generic.json
diff --git a/modelling/resident-detectability/model/resident_model.py b/modelling/models/resident/resident_model.py
similarity index 100%
rename from modelling/resident-detectability/model/resident_model.py
rename to modelling/models/resident/resident_model.py
diff --git a/modelling/seasonal-presence/README.md b/modelling/models/seasonal/README.md
similarity index 99%
rename from modelling/seasonal-presence/README.md
rename to modelling/models/seasonal/README.md
index 2ac9804..3da88d2 100644
--- a/modelling/seasonal-presence/README.md
+++ b/modelling/models/seasonal/README.md
@@ -226,7 +226,7 @@ The parameter fitting workflow is illustrated below:
 
 ![Parameter Fitting](https://github.com/davewalker5/OdeSolver/blob/main/docs/images/parameter-fitting.png?raw=true)
 
-The following summarises
+The following summarises the naming conventions and locations for the outputs from the modelling process:
 
 | File              | Naming                          | Type      | Location    |
 | ----------------- | ------------------------------- | --------- | ----------- |
diff --git a/modelling/seasonal-presence/model/seasonal_model.py b/modelling/models/seasonal/seasonal_model.py
similarity index 100%
rename from modelling/seasonal-presence/model/seasonal_model.py
rename to modelling/models/seasonal/seasonal_model.py
diff --git a/modelling/seasonal-presence/model/seasonal_presence_generic.json b/modelling/models/seasonal/seasonal_presence_generic.json
similarity index 100%
rename from modelling/seasonal-presence/model/seasonal_presence_generic.json
rename to modelling/models/seasonal/seasonal_presence_generic.json
diff --git a/modelling/winter-visitor/README.md b/modelling/models/winter/README.md
similarity index 99%
rename from modelling/winter-visitor/README.md
rename to modelling/models/winter/README.md
index 576cc88..47e1b90 100644
--- a/modelling/winter-visitor/README.md
+++ b/modelling/models/winter/README.md
@@ -196,7 +196,7 @@ The parameter fitting workflow is illustrated below:
 
 ![Parameter Fitting](https://github.com/davewalker5/OdeSolver/blob/main/docs/images/parameter-fitting.png?raw=true)
 
-The following summarises
+The following summarises the naming conventions and locations for the outputs from the modelling process:
 
 | File              | Naming                          | Type      | Location    |
 | ----------------- | ------------------------------- | --------- | ----------- |
diff --git a/modelling/winter-visitor/model/winter_model.py b/modelling/models/winter/winter_model.py
similarity index 100%
rename from modelling/winter-visitor/model/winter_model.py
rename to modelling/models/winter/winter_model.py
diff --git a/modelling/winter-visitor/model/winter_visitor_generic.json b/modelling/models/winter/winter_visitor_generic.json
similarity index 100%
rename from modelling/winter-visitor/model/winter_visitor_generic.json
rename to modelling/models/winter/winter_visitor_generic.json
diff --git a/modelling/scripts/clean-all.sh b/modelling/scripts/clean-all.sh
index ab77df8..8233c8e 100755
--- a/modelling/scripts/clean-all.sh
+++ b/modelling/scripts/clean-all.sh
@@ -1,35 +1,26 @@
 #!/usr/bin/env bash
 
-if (( $# != 1 )); then
+if (( $# != 2 )); then
     scriptname=$(basename -- "$0")
-    echo Usage: $scriptname MODEL
+    echo Usage: $scriptname PROJECT MODEL
     exit 1
 fi
 
 # Get the path to the modelling folder and the project root
 MODELLING_ROOT=$( cd "$( dirname "$0" )/.." && pwd )
 
-# Set the model=specific environment
-case "$1" in
-    resident)
-        MODEL_FOLDER="$MODELLING_ROOT/resident-detectability"
-        ;;
-    seasonal)
-        MODEL_FOLDER="$MODELLING_ROOT/seasonal-presence"
-        ;;
-    winter)
-        MODEL_FOLDER="$MODELLING_ROOT/winter-visitor"
-        ;;
-    *)
-        echo "Unrecognised model '$1'"
-        exit 1
-        ;;
-esac
+# Construct the path to the model-specific data folder for the specified project
+# and check the folder exists
+DATA_FOLDER="$MODELLING_ROOT/data/$1/$2"
+if [[ ! -d "$DATA_FOLDER" ]]; then
+    echo Data folder not found: $DATA_FOLDER
+    exit 1
+fi
 
-rm -f "$MODEL_FOLDER"/data/*_classification.json
-rm -f "$MODEL_FOLDER"/data/*_consensus.json
-rm -f "$MODEL_FOLDER"/data/*_parameters.csv
-rm -f "$MODEL_FOLDER"/data/*_simulated.csv
-rm -f "$MODEL_FOLDER"/data/*_simulated.png
-rm -f "$MODEL_FOLDER"/data/*_synthesised.csv
-rm -f "$MODEL_FOLDER"/data/*_synthesised.png
+rm -f "$DATA_FOLDER"/*_classification.json
+rm -f "$DATA_FOLDER"/*_consensus.json
+rm -f "$DATA_FOLDER"/*_parameters.csv
+rm -f "$DATA_FOLDER"/*_simulated.csv
+rm -f "$DATA_FOLDER"/*_simulated.png
+rm -f "$DATA_FOLDER"/*_synthesised.csv
+rm -f "$DATA_FOLDER"/*_synthesised.png
diff --git a/modelling/scripts/clean.sh b/modelling/scripts/clean.sh
index e42de25..cb41ca6 100755
--- a/modelling/scripts/clean.sh
+++ b/modelling/scripts/clean.sh
@@ -1,35 +1,26 @@
 #!/usr/bin/env bash
 
-if (( $# != 2 )); then
+if (( $# != 3 )); then
     scriptname=$(basename -- "$0")
-    echo Usage: $scriptname MODEL SPECIES
+    echo Usage: $scriptname PROJECT MODEL SPECIES
     exit 1
 fi
 
 # Get the path to the modelling folder and the project root
 MODELLING_ROOT=$( cd "$( dirname "$0" )/.." && pwd )
 
-# Set the model=specific environment
-case "$1" in
-    resident)
-        MODEL_FOLDER="$MODELLING_ROOT/resident-detectability"
-        ;;
-    seasonal)
-        MODEL_FOLDER="$MODELLING_ROOT/seasonal-presence"
-        ;;
-    winter)
-        MODEL_FOLDER="$MODELLING_ROOT/winter-visitor"
-        ;;
-    *)
-        echo "Unrecognised model '$1'"
-        exit 1
-        ;;
-esac
+# Construct the path to the model-specific data folder for the specified project
+# and check the folder exists
+DATA_FOLDER="$MODELLING_ROOT/data/$1/$2"
+if [[ ! -d "$DATA_FOLDER" ]]; then
+    echo Data folder not found: $DATA_FOLDER
+    exit 1
+fi
 
-rm -f "$MODEL_FOLDER/data/$2_classification.json"
-rm -f "$MODEL_FOLDER/data/$2_consensus.json"
-rm -f "$MODEL_FOLDER/data/$2_parameters.csv"
-rm -f "$MODEL_FOLDER/data/$2_simulated.csv"
-rm -f "$MODEL_FOLDER/data/$2_simulated.png"
-rm -f "$MODEL_FOLDER/data/$2_synthesised.csv"
-rm -f "$MODEL_FOLDER/data/$2_synthesised.png"
+rm -f "$DATA_FOLDER/$3_classification.json"
+rm -f "$DATA_FOLDER/$3_consensus.json"
+rm -f "$DATA_FOLDER/$3_parameters.csv"
+rm -f "$DATA_FOLDER/$3_simulated.csv"
+rm -f "$DATA_FOLDER/$3_simulated.png"
+rm -f "$DATA_FOLDER/$3_synthesised.csv"
+rm -f "$DATA_FOLDER/$3_synthesised.png"
diff --git a/modelling/scripts/process-pending.sh b/modelling/scripts/process-pending.sh
index 55e659f..8e8478a 100755
--- a/modelling/scripts/process-pending.sh
+++ b/modelling/scripts/process-pending.sh
@@ -1,40 +1,31 @@
 #!/usr/bin/env bash
 
-if (( $# != 1 )); then
+if (( $# != 2 )); then
     scriptname=$(basename -- "$0")
-    echo Usage: $scriptname MODEL
+    echo Usage: $scriptname PROJECT MODEL
     exit 1
 fi
 
 # Get the path to the modelling folder and the project root
 MODELLING_ROOT=$( cd "$( dirname "$0" )/.." && pwd )
 
-# Set the model=specific environment
-case "$1" in
-    resident)
-        MODEL_FOLDER="$MODELLING_ROOT/resident-detectability"
-        ;;
-    seasonal)
-        MODEL_FOLDER="$MODELLING_ROOT/seasonal-presence"
-        ;;
-    winter)
-        MODEL_FOLDER="$MODELLING_ROOT/winter-visitor"
-        ;;
-    *)
-        echo "Unrecognised model '$1'"
-        exit 1
-        ;;
-esac
+# Construct the path to the model-specific data folder for the specified project
+# and check the folder exists
+DATA_FOLDER="$MODELLING_ROOT/data/$1/$2"
+if [[ ! -d "$DATA_FOLDER" ]]; then
+    echo Data folder not found: $DATA_FOLDER
+    exit 1
+fi
 
 # Build the species list - a species needs to be modelled if it's "observed" data file is
 # present but the simulated output isn;t
 species_list=()
-for observed_file in "$MODEL_FOLDER"/data/*_observed.csv; do
+for observed_file in "$DATA_FOLDER"/*_observed.csv; do
     [[ -e "$observed_file" ]] || continue
 
     filename=$(basename "$observed_file")
     species=${filename%_observed.csv}
-    simulated_file="$MODEL_FOLDER/data/${species}_simulated.csv"
+    simulated_file="$DATA_FOLDER/${species}_simulated.csv"
 
     if [[ ! -f "$simulated_file" ]]; then
         species_list+=("$species")
@@ -49,5 +40,5 @@ fi
 
 # Iterate over the species that need processing
 for species in "${species_list[@]}"; do
-    "$MODELLING_ROOT/scripts/run-fit.sh" $1 "$species"
+    "$MODELLING_ROOT/scripts/run-fit.sh" "$1" "$2" "$species"
 done
diff --git a/modelling/scripts/retro-classify.sh b/modelling/scripts/retro-classify.sh
index 841901e..cb6675f 100755
--- a/modelling/scripts/retro-classify.sh
+++ b/modelling/scripts/retro-classify.sh
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-if (( $# < 1 )); then
+if (( $# < 2 )); then
     scriptname=$(basename -- "$0")
-    echo Usage: $scriptname MODEL [SPECIES]
+    echo Usage: $scriptname PROJECT MODEL [SPECIES]
     exit 1
 fi
 
@@ -10,8 +10,8 @@ fi
 MODELLING_ROOT=$( cd "$( dirname "$0" )/.." && pwd )
 
 # Run the classifier
-if (( $# == 1 )); then
-    python "$MODELLING_ROOT/src/retro-classify.py" --model "$1" --all
+if (( $# == 2 )); then
+    python "$MODELLING_ROOT/src/retro-classify.py" --project "$1" --model "$2" --all
 else
-    python "$MODELLING_ROOT/src/retro-classify.py" --model "$1" --species "$2"
+    python "$MODELLING_ROOT/src/retro-classify.py" --project "$1" --model "$2" --species "$3"
 fi
\ No newline at end of file
diff --git a/modelling/scripts/run-calendar.sh b/modelling/scripts/run-calendar.sh
index 82fd7ea..1faf23f 100755
--- a/modelling/scripts/run-calendar.sh
+++ b/modelling/scripts/run-calendar.sh
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-if (( $# > 1 )); then
+if (( $# != 1 )); then
     scriptname=$(basename -- "$0")
-    echo Usage: $scriptname [WRITE-CSV]
+    echo Usage: $scriptname PROJECT
     exit 1
 fi
 
@@ -13,15 +13,31 @@ MODELLING_ROOT=$( cd "$( dirname "$0" )/.." && pwd )
 PROJECT_FOLDER=$( cd "$MODELLING_ROOT/.." && pwd)
 source "$PROJECT_FOLDER/venv/bin/activate"
 
-# Build the paths to the per-model data folders
-RESIDENT_DATA="$MODELLING_ROOT/resident-detectability/data"
-SEASONAL_DATA="$MODELLING_ROOT/seasonal-presence/data"
-WINTER_DATA="$MODELLING_ROOT/winter-visitor/data"
+# Build the paths to the per-model data folders and the analysis output folder
+ANALYSIS_FOLDER="$MODELLING_ROOT/data/$1/analysis"
+RESIDENT_DATA="$MODELLING_ROOT/data/$1/resident"
+SEASONAL_DATA="$MODELLING_ROOT/data/$1/seasonal"
+WINTER_DATA="$MODELLING_ROOT/data/$1/winter"
+
+if [[ ! -d "$RESIDENT_DATA" ]]; then
+    echo Data folder not found: $RESIDENT_DATA
+    exit 1
+fi
+
+if [[ ! -d "$SEASONAL_DATA" ]]; then
+    echo Data folder not found: $SEASONAL_DATA
+    exit 1
+fi
+
+if [[ ! -d "$WINTER_DATA" ]]; then
+    echo Data folder not found: $WINTER_DATA
+    exit 1
+fi
 
 # Build the ecological calendar pipeline
 python "$MODELLING_ROOT/src/eco-calendar.py" \
     --input  "$RESIDENT_DATA" "$SEASONAL_DATA" "$WINTER_DATA" \
-    --clusters "$MODELLING_ROOT/data/cluster_analysis.json" \
-    --extracted "$MODELLING_ROOT/data/extracted_clusters.json" \
-    --activity "$MODELLING_ROOT/data/calendar_activity.json" \
-    --heatmap "$MODELLING_ROOT/data/activity_heatmap.png"
+    --clusters "$ANALYSIS_FOLDER/cluster_analysis.json" \
+    --extracted "$ANALYSIS_FOLDER/extracted_clusters.json" \
+    --activity "$ANALYSIS_FOLDER/calendar_activity.json" \
+    --heatmap "$ANALYSIS_FOLDER/activity_heatmap.png"
diff --git a/modelling/scripts/run-fit.sh b/modelling/scripts/run-fit.sh
index 4bf7e17..c844501 100755
--- a/modelling/scripts/run-fit.sh
+++ b/modelling/scripts/run-fit.sh
@@ -1,45 +1,43 @@
 #!/usr/bin/env bash
 
-if (( $# != 2 )); then
+if (( $# != 3 )); then
     scriptname=$(basename -- "$0")
-    echo Usage: $scriptname MODEL SPECIES
+    echo Usage: $scriptname PROJECT MODEL SPECIES
     exit 1
 fi
 
 # Get the path to the modelling folder and the project root
 MODELLING_ROOT=$( cd "$( dirname "$0" )/.." && pwd )
 PROJECT_FOLDER=$( cd "$MODELLING_ROOT/.." && pwd)
+DATA_FOLDER="$MODELLING_ROOT/data/$1/$2/"
 
 # Set the model=specific environment
-case "$1" in
+case "$2" in
     resident)
-        MODEL_FOLDER="$MODELLING_ROOT/resident-detectability"
-        MODEL="resident_detectability_generic.json"
+        MODEL="$MODELLING_ROOT/models/$2/resident_detectability_generic.json"
         ;;
     seasonal)
-        MODEL_FOLDER="$MODELLING_ROOT/seasonal-presence"
-        MODEL="seasonal_presence_generic.json"
+        MODEL="$MODELLING_ROOT/models/$2/seasonal_presence_generic.json"
         ;;
     winter)
-        MODEL_FOLDER="$MODELLING_ROOT/winter-visitor"
-        MODEL="winter_visitor_generic.json"
+        MODEL="$MODELLING_ROOT/models/$2/winter_visitor_generic.json"
         ;;
     *)
-        echo "Unrecognised model '$1'"
+        echo "Unrecognised model '$2'"
         exit 1
         ;;
 esac
 
 # Run the fit
-python "$MODELLING_ROOT/src/$1.py" \
-    --species "$2" \
-    --observed "$MODEL_FOLDER/data/$2_observed.csv" \
-    --simulation "$MODEL_FOLDER/model/$MODEL" \
+python "$MODELLING_ROOT/src/$2.py" \
+    --species "$3" \
+    --observed "$DATA_FOLDER/$3_observed.csv" \
+    --simulation "$MODEL" \
     --solver-command "$PROJECT_FOLDER/scripts/run-solver.sh" \
-    --csv "$MODEL_FOLDER/data/$2_parameters.csv" \
-    --consensus-json "$MODEL_FOLDER/data/$2_consensus.json" \
-    --classification-json "$MODEL_FOLDER/data/$2_classification.json" \
-    --export-simulated "$MODEL_FOLDER/data/$2_simulated.csv" \
-    --plot-simulated "$MODEL_FOLDER/data/$2_simulated.png" \
-    --export-synthesised "$MODEL_FOLDER/data/$2_synthesised.csv" \
-    --plot-synthesised "$MODEL_FOLDER/data/$2_synthesised.png"
+    --csv "$DATA_FOLDER/$3_parameters.csv" \
+    --consensus-json "$DATA_FOLDER/$3_consensus.json" \
+    --classification-json "$DATA_FOLDER/$3_classification.json" \
+    --export-simulated "$DATA_FOLDER/$3_simulated.csv" \
+    --plot-simulated "$DATA_FOLDER/$3_simulated.png" \
+    --export-synthesised "$DATA_FOLDER/$3_synthesised.csv" \
+    --plot-synthesised "$DATA_FOLDER/$3_synthesised.png"
diff --git a/modelling/scripts/run-similarity.sh b/modelling/scripts/run-similarity.sh
index 74b3ccd..3d91893 100755
--- a/modelling/scripts/run-similarity.sh
+++ b/modelling/scripts/run-similarity.sh
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-if (( $# > 1 )); then
+if (( $# < 1 )); then
     scriptname=$(basename -- "$0")
-    echo Usage: $scriptname [WRITE-CSV]
+    echo Usage: $scriptname PROJECT [WRITE-CSV]
     exit 1
 fi
 
@@ -13,27 +13,43 @@ MODELLING_ROOT=$( cd "$( dirname "$0" )/.." && pwd )
 PROJECT_FOLDER=$( cd "$MODELLING_ROOT/.." && pwd)
 source "$PROJECT_FOLDER/venv/bin/activate"
 
-# Build the paths to the per-model data folders
-RESIDENT_DATA="$MODELLING_ROOT/resident-detectability/data"
-SEASONAL_DATA="$MODELLING_ROOT/seasonal-presence/data"
-WINTER_DATA="$MODELLING_ROOT/winter-visitor/data"
+# Build the paths to the per-model data folders and the analysis output folder
+ANALYSIS_FOLDER="$MODELLING_ROOT/data/$1/analysis"
+RESIDENT_DATA="$MODELLING_ROOT/data/$1/resident"
+SEASONAL_DATA="$MODELLING_ROOT/data/$1/seasonal"
+WINTER_DATA="$MODELLING_ROOT/data/$1/winter"
+
+if [[ ! -d "$RESIDENT_DATA" ]]; then
+    echo Data folder not found: $RESIDENT_DATA
+    exit 1
+fi
+
+if [[ ! -d "$SEASONAL_DATA" ]]; then
+    echo Data folder not found: $SEASONAL_DATA
+    exit 1
+fi
+
+if [[ ! -d "$WINTER_DATA" ]]; then
+    echo Data folder not found: $WINTER_DATA
+    exit 1
+fi
 
 # Set the arguments to write the CSV file
 WRITE_CSV=""
-if (( $# == 1 )); then
+if (( $# == 2 )); then
     # Get the first argument in lowercase
-    value=$(printf '%s' "$1" | tr '[:upper:]' '[:lower:]')
+    value=$(printf '%s' "$2" | tr '[:upper:]' '[:lower:]')
 
     # If it's truthy, set the CSV output arguments. Otherwise, make them blank
     case "$value" in
         true|yes|y|1)
-            WRITE_CSV="--output-csv $MODELLING_ROOT/data/feature_matrix.csv"
+            WRITE_CSV="--output-csv $ANALYSIS_FOLDER/feature_matrix.csv"
             ;;
         false|no|n|0)
             WRITE_CSV=""
             ;;
         *)
-            echo "'$1' is not a valid value for WRITE-CSV"
+            echo "'$2' is not a valid value for WRITE-CSV"
             exit 1
             ;;
     esac
@@ -42,10 +58,10 @@ fi
 # Build the feature matrix, similarity and clustering pipeline
 python "$MODELLING_ROOT/src/feature-matrix.py" \
     --input  "$RESIDENT_DATA" "$SEASONAL_DATA" "$WINTER_DATA" \
-    --json "$MODELLING_ROOT/data/feature_matrix.json" \
-    --similarity "$MODELLING_ROOT/data/species_similarity.json" \
-    --similarity-summary "$MODELLING_ROOT/data/species_similarity.txt" \
-    --heatmap "$MODELLING_ROOT/data/species_similarity_heatmap.png" \
-    --clusters "$MODELLING_ROOT/data/cluster_analysis.json" \
-    --cluster-summary "$MODELLING_ROOT/data/cluster_summary.txt" \
-    --dendrogram "$MODELLING_ROOT/data/cluster_dendrogram.png"$WRITE_CSV
+    --json "$ANALYSIS_FOLDER/feature_matrix.json" \
+    --similarity "$ANALYSIS_FOLDER/species_similarity.json" \
+    --similarity-summary "$ANALYSIS_FOLDER/species_similarity.txt" \
+    --heatmap "$ANALYSIS_FOLDER/species_similarity_heatmap.png" \
+    --clusters "$ANALYSIS_FOLDER/cluster_analysis.json" \
+    --cluster-summary "$ANALYSIS_FOLDER/cluster_summary.txt" \
+    --dendrogram "$ANALYSIS_FOLDER/cluster_dendrogram.png"$WRITE_CSV
diff --git a/modelling/src/retro-classify.py b/modelling/src/retro-classify.py
index 18215d6..e15602e 100644
--- a/modelling/src/retro-classify.py
+++ b/modelling/src/retro-classify.py
@@ -10,13 +10,6 @@
 RESIDENT = "resident"
 SEASONAL = "seasonal"
 WINTER = "winter"
-
-MODEL_FOLDERS = {
-    RESIDENT: "resident-detectability",
-    SEASONAL: "seasonal-presence",
-    WINTER: "winter-visitor"
-}
-
 CONSENSUS_SUFFIX = "_consensus.json"
 
 
@@ -84,13 +77,14 @@ def main():
     """
     parser = argparse.ArgumentParser()
 
+    parser.add_argument("-p", "--project", required=True, help="Project name")
     parser.add_argument("-m", "--model", choices=[RESIDENT, SEASONAL, WINTER], required=True, help="Model name")
     parser.add_argument("-s", "--species", help="Species name")
     parser.add_argument("-a", "--all", action="store_true", help="Classify all species for the specied model")
     args = parser.parse_args()
 
     # Calculate the path to the models data folder
-    data_folder = Path(__file__).parent.parent / MODEL_FOLDERS[args.model] / "data"
+    data_folder = Path(__file__).parent.parent / "data" / args.project / args.model
 
     if args.all:
         classify_all_species(data_folder, args.model)