## 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
-```
-
-## definitions
-
-- **obs\
- **observations: occurrences from OBIS; masked by FAO regions defined by AquaMaps [@aquamapsdata]
- - **presence**\
- OBIS: species occurrence
- - **absence**\
- OBIS not-species, but same family
-- **env\
- **environment
-- **tbl**\
- table of observations (presence and absence) with environmental values
-
-## Model
-
-```{mermaid}
-%%| label: fig-linux-kernel
-%%| 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
-```
-
-\
+%%| label: fig-prep
+%%| fig-cap: "Diagram of SDM data preparation for model fitting."
+%%| file: diagrams/sdm-prep.mmd
+```
+
+## definitions
+
+- **obs\
+ **observations: occurrences from OBIS; masked by FAO regions defined by AquaMaps [@aquamapsdata]
+ - **presence**\
+ OBIS: species occurrence
+ - **absence**\
+ OBIS not-species, but same family
+- **env\
+ **environment
+- **tbl**\
+ table of observations (presence and absence) with environmental values
+
+## Model
+
+```{mermaid}
+%%| label: fig-model
+%%| fig-cap: "Diagram of SDM Modeling processes."
+%%| file: diagrams/sdm-model.mmd
+```
+
+\
diff --git a/_quarto.yml b/_quarto.yml
index 1478244..fcd083c 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -13,8 +13,7 @@ format:
mermaid:
theme: neutral
theme:
- dark: darkly
light: flatly
-
+ dark: darkly
search: false
diff --git a/figures/mermaid-test.mmd b/diagrams/mermaid-test.mmd
similarity index 100%
rename from figures/mermaid-test.mmd
rename to diagrams/mermaid-test.mmd
diff --git a/diagrams/mosaic-hierarchy.mmd b/diagrams/mosaic-hierarchy.mmd
new file mode 100644
index 0000000..2340990
--- /dev/null
+++ b/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
diff --git a/figures/sdm-model.mmd b/diagrams/sdm-model.mmd
similarity index 55%
rename from figures/sdm-model.mmd
rename to diagrams/sdm-model.mmd
index 5687e09..f23fd2b 100644
--- a/figures/sdm-model.mmd
+++ b/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
diff --git a/figures/sdm-prep.mmd b/diagrams/sdm-prep.mmd
similarity index 52%
rename from figures/sdm-prep.mmd
rename to diagrams/sdm-prep.mmd
index 36246da..80497e1 100644
--- a/figures/sdm-prep.mmd
+++ b/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
diff --git a/sdm-process.qmd b/sdm-process.qmd
index fcee3a8..2f7ea88 100644
--- a/sdm-process.qmd
+++ b/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
```
\