∆ diagrams

_quarto.yml

@@ -13,8 +13,7 @@ format:
     mermaid:
       theme: neutral
     theme:
-      dark: darkly
       light: flatly
-
+      dark: darkly
 
 search: false

diagrams/mosaic-hierarchy.mmd

@@ -0,0 +1,15 @@
+gantt
+        dateFormat  YYYY-MM-DD
+        title Adding GANTT diagram functionality to mermaid
+        section A section
+        Completed task            :done,    des1, 2014-01-06,2014-01-08
+        Active task               :active,  des2, 2014-01-09, 3d
+        Future task               :         des3, after des2, 5d
+        Future task2               :         des4, after des3, 5d
+        section Critical tasks
+        Completed task in the critical line :crit, done, 2014-01-06,24h
+        Implement parser and jison          :crit, done, after des1, 2d
+        Create tests for parser             :crit, active, 3d
+        Future task in critical line        :crit, 5d
+        Create tests for renderer           :2d
+        Add to mermaid                      :1d

figures/sdm-model.mmd → diagrams/sdm-model.mmd

@@ -1,6 +1,7 @@
 flowchart LR
 
-  tbl[[tbl]]:::in
+  %% nodes
+  D[[data]]:::in
   S[/split/]:::fxn
   t1[[train]]:::out
   t2[[test]]:::out
@@ -13,20 +14,24 @@ flowchart LR
   prd(prediction):::out
   prf(performance):::out
 
-  tbl --> S
-  S   --> t1
-  S   --> t2
-  t1  --> F
-  F   --> M
-  t2  --> E
-  M   --> C
-  C   --> F
-  M   --> P
-  N   --> P
-  M   --> E
-  P   --> prd
-  E   --> prf
+  %% edges
+  D  --> S
+  S  --> t1
+  S  --> t2
+  t1 --> F
+  F  --> M
+  t2 --> E
+  M  --> C
+  C  --> F
+  M  --> P
+  N  --> P
+  M  --> E
+  P  --> prd
+  E  --> prf
 
+  %% styles
   classDef in  fill:lightblue
   classDef out fill:lightgreen
   classDef fxn fill:yellow
+
+%% source: https://bbest.github.io/eds232-ml/lab1d_sdm-evaluate.html

figures/sdm-prep.mmd → diagrams/sdm-prep.mmd

@@ -1,30 +1,32 @@
 
 flowchart LR
 
+  %% nodes
   P(presence):::in
-
-  A(absence):::in
-
+  A("pseudo-absence"):::in
   pts(obs):::out
-
   X[/extract/]:::fxn
-
   env(env):::in
+  D[[data]]:::out
 
-  tbl[[tbl]]:::out
-
+  %% edges
   P   --> pts
-
   A   --> pts
-
   pts --> X
-
   env --> X
-
-  X   --> tbl
-
+  X   --> D
+
+  %% Legend
+  in(input):::in
+  fxn[/process/]:::fxn
+  out(output):::out
+  subgraph Legend
+    in
+    fxn
+    out
+  end
+
+  %% styles
   classDef in  fill:lightblue
-
   classDef out fill:lightgreen
-
   classDef fxn fill:yellow

sdm-process.qmd

@@ -5,26 +5,9 @@ title: "SDM Process"
 ## Data Prep
 
 ```{mermaid}
-%%| label: fig-sdm-prep
-%%| fig-cap: "Diagram of SDM data preparation."
-flowchart LR
-
-  P(presence):::in
-  A(absence):::in
-  pts(obs):::out
-  X[/extract/]:::fxn
-  env(env):::in
-  tbl[[tbl]]:::out
-  
-  P   --> pts
-  A   --> pts
-  pts --> X
-  env --> X
-  X   --> tbl
-  
-  classDef in  fill:lightblue
-  classDef out fill:lightgreen
-  classDef fxn fill:yellow
+%%| label: fig-prep
+%%| fig-cap: "Diagram of SDM data preparation for model fitting."
+%%| file: diagrams/sdm-prep.mmd
 ```
 
 ## definitions
@@ -43,43 +26,9 @@ flowchart LR
 ## Model
 
 ```{mermaid}
-%%| label: fig-linux-kernel
+%%| label: fig-model
 %%| fig-cap: "Diagram of SDM Modeling processes."
-
-flowchart LR
-
-  tbl[[tbl]]:::in
-  S[/split/]:::fxn
-  t1[[train]]:::out
-  t2[[test]]:::out
-  F[/fit/]:::fxn
-  M{{model}}:::out
-  E[/evaluate/]:::fxn
-  C[/calibrate/]:::fxn
-  P[/predict/]:::fxn
-  N[["new data"]]:::in
-  prd(prediction):::out
-  prf(performance):::out
-  
-  tbl --> S
-  S   --> t1
-  S   --> t2
-  t1  --> F
-  F   --> M
-  t2  --> E
-  M   --> C
-  C   --> F
-  M   --> P
-  N   --> P
-  M   --> E
-  P   --> prd
-  E   --> prf
-  
-  classDef in  fill:lightblue
-  classDef out fill:lightgreen
-  classDef fxn fill:yellow
-  
-%% source: https://bbest.github.io/eds232-ml/lab1d_sdm-evaluate.html
+%%| file: diagrams/sdm-model.mmd
 ```
 
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