MINTverse/_quarto.yml at main · CosmoNaught/MINTverse · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
project:
  type: website
  output-dir: _book
  execute-dir: project
  render:
    - index.qmd
    - chapters/
  resources:
    - misc/icon-mint.svg
    - data/

website:
  title: "MINTverse"
  favicon: favicon.ico
  search:
    location: sidebar
    type: textbox
  page-navigation: true
  page-footer:
    border: false
    center: |
      &copy;&nbsp;2026 Cosmo Santoni and Anmol Thapar &middot; part of the [MINTverse](https://github.com/CosmoNaught).
  navbar:
    title: "MINTverse"
    pinned: true
    search: false
    right:
      - icon: github
        href: "https://github.com/CosmoNaught/MINTverse"
        aria-label: GitHub
  sidebar:
    style: docked
    logo: misc/icon-mint.svg
    title: "MINTverse"
    collapse-level: 1
    contents:
      - href: index.qmd
        text: "Home"
      - href: chapters/00-front/overview.qmd
        text: "Overview"
      - href: chapters/00-front/reader-guide.qmd
        text: "Orientation"
      - section: "Python for Malaria Modellers"
        href: chapters/01-python/index.qmd
        contents:
          - href: chapters/01-python/what-is-python.qmd
            text: "What is Python?"
          - href: chapters/01-python/toolchain.qmd
            text: "Python tools"
          - href: chapters/01-python/installing-python.qmd
            text: "Installing Python"
          - href: chapters/01-python/vscode.qmd
            text: "Working in VS Code"
          - href: chapters/01-python/environments.qmd
            text: "Environments and packages"
          - href: chapters/01-python/notebooks.qmd
            text: "Notebooks"
      - section: "Getting Started"
        href: chapters/02-getting-started/index.qmd
        contents:
          - href: chapters/02-getting-started/installation.qmd
            text: "Installation"
          - href: chapters/02-getting-started/quickstart.qmd
            text: "Quickstart"
          - href: chapters/02-getting-started/coming-from-r.qmd
            text: "Coming from R"
          - href: chapters/02-getting-started/notebook.qmd
            text: "Colab notebook"
      - section: "Core Concepts"
        href: chapters/03-concepts/index.qmd
        contents:
          - href: chapters/03-concepts/pipeline.qmd
            text: "The MINTverse pipeline"
          - href: chapters/03-concepts/equilibrium.qmd
            text: "EIR, HBR, prevalence, and cases"
          - href: chapters/03-concepts/interventions.qmd
            text: "Interventions and nets"
          - href: chapters/03-concepts/models.qmd
            text: "The models"
          - href: chapters/03-concepts/validation.qmd
            text: "Accuracy and speed"
      - section: "estiMINT: EIR and HBR"
        href: chapters/04-estimint/index.qmd
        contents:
          - href: chapters/04-estimint/nets-and-dn0.qmd
            text: "Nets and dn0"
          - href: chapters/04-estimint/estimating-eir.qmd
            text: "Estimating EIR from prevalence"
          - href: chapters/04-estimint/eir-and-hbr.qmd
            text: "EIR and HBR"
          - href: chapters/04-estimint/mosquito-density.qmd
            text: "Mosquito density and EIR"
          - href: chapters/04-estimint/api.qmd
            text: "estiMINT API"
      - section: "stateMINT: the Emulator"
        href: chapters/05-statemint/index.qmd
        contents:
          - href: chapters/05-statemint/covariates.qmd
            text: "Covariates and the time grid"
          - href: chapters/05-statemint/the-emulator.qmd
            text: "Calling the emulator"
          - href: chapters/05-statemint/plotting.qmd
            text: "Plotting trajectories"
          - href: chapters/05-statemint/performance.qmd
            text: "Performance and caching"
          - href: chapters/05-statemint/api.qmd
            text: "stateMINT API"
      - section: "Scenarios"
        href: chapters/06-scenarios/index.qmd
        contents:
          - href: chapters/06-scenarios/run-scenarios.qmd
            text: "Running scenarios"
          - href: chapters/06-scenarios/scenario-grid.qmd
            text: "A list of scenarios"
          - href: chapters/06-scenarios/comparing.qmd
            text: "Trajectories and cases"
          - href: chapters/06-scenarios/exporting.qmd
            text: "Exporting results"
      - href: chapters/troubleshooting.qmd
        text: "Troubleshooting"


jupyter: python3

execute:
  freeze: auto
  eval: true
  echo: true
  warning: false
  error: false

format:
  html:
    theme:
      dark: [darkly, styles/theme-dark.scss]
      light: [flatly, styles/theme-light.scss]
    highlight-style: atom-one
    html-math-method: mathjax
    include-after-body: _after-body.html
    link-external-newwindow: true
    link-external-icon: false
    toc: true
    toc-depth: 3
    toc-title: "On this page"
    number-sections: false
    code-copy: true
    code-overflow: scroll
    fig-align: left
    grid:
      sidebar-width: 300px