docs/packages.yaml at main · Pandora-IsoMemo/docs · 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
151
152
153
154
155
156
157
158
159
categories:
  apps:
    - name: "BMSCS"
      full_name: "Bayesian Model Selection under Constraints"
      info_text: |
        BMSC is a Bayesian model selection algorithm used for causal analysis
        and other applications.
      repo_url: "https://github.com/Pandora-IsoMemo/BMSCS"
      doc_url: "https://pandora-isomemo.github.io/BMSCS/"
      app_url: "https://pandoraapp.earth/app/bmscs"
      app_beta_url: "https://pandoraapp.earth/app/bmscs-beta"
      docker_image: "bmscs"
      img: "img/bmscs.jpg"

    - name: "BNR"
      info_text: |
        This project leverages graphical models to perform queries with
        constrained bayesian estimation. This work is developed as a Shiny app
        in order to provide an easy and clean interaction.
      repo_url: "https://github.com/Pandora-IsoMemo/BNR"
      #doc_url: "https://pandora-isomemo.github.io/BNR/"
      app_url: "https://pandoraapp.earth/app/bnr"
      #app_beta_url: "https://pandoraapp.earth/app/bnr-beta"
      docker_image: "bnr"
      is_renv: TRUE
      img: "img/bnr.png"

    - name: "Bpred"
      full_name: "Bayesian Prediction"
      info_text: |
        Bayesian multivariate regression application.
      repo_url: "https://github.com/Pandora-IsoMemo/Bpred"
      doc_url: "https://pandora-isomemo.github.io/Bpred/"
      app_url: "https://pandoraapp.earth/app/bpred"
      app_beta_url: "https://pandoraapp.earth/app/bpred-beta"
      docker_image: "bpred"
      img: "img/bpred.jpg"

    - name: "CausalR"
      info_text: |
        CausalR is an R-Shiny user-friendly interface for CausalImpact R
        package, which leverages the Bayesian modeling capabilities to estimate
        the causal effect of an intervention on a time series.
      repo_url: "https://github.com/Pandora-IsoMemo/CausalR"
      #doc_url: "https://pandora-isomemo.github.io/CausalR/"
      app_url: "https://pandoraapp.earth/app/causalr"
      app_beta_url: "https://pandoraapp.earth/app/causalr-beta"
      docker_image: "causalr"
      img: "img/causalr.png"
      video: "https://www.youtube.com/watch?v=jlT15oblKBE"

    - name: "ChangeR"
      info_text: |
        An App to display and identify isotopic change points in human tooth sections.
      repo_url: "https://github.com/Pandora-IsoMemo/ChangeR"
      doc_url: "https://pandora-isomemo.github.io/ChangeR/"
      app_url: "https://pandoraapp.earth/app/changer"
      app_beta_url: "https://pandoraapp.earth/app/changer-beta"
      docker_image: "changer"
      img: "img/changer.png"
      inst_notes: |
        ChangeR utilizes [JAGS MCMC library](https://mcmc-jags.sourceforge.io/).
        This has been tested only on Linux (Ubuntu). For Windows & Mac user, you
        can either use the dockerized Version of the App or refer to the offical
        [installation manual](https://sourceforge.net/projects/mcmc-jags/files/Manuals/4.x/jags_installation_manual.pdf)
        of JAGS.

    - name: "DSSM"
      full_name: "Data Search and Spatiotemporal Modelling"
      info_text: |
        In addition to allowing users to query Pandora data includes different
        types of Bayesian and non-Bayesian spatiotemporal models.
      repo_url: "https://github.com/Pandora-IsoMemo/DSSM"
      doc_url: "https://pandora-isomemo.github.io/DSSM/"
      app_url: "https://pandoraapp.earth/app/dssm"
      app_beta_url: "https://pandoraapp.earth/app/dssm-beta"
      docker_image: "dssm"
      img: "img/dssm.jpg"
      video: "https://www.youtube.com/watch?v=dQm-0rJeyzY"

    - name: "MapR"
      info_text: |
        MapR displays temporal and temperature graphical files for Isomemo.
      repo_url: "https://github.com/Pandora-IsoMemo/MapR"
      doc_url: "https://pandora-isomemo.github.io/MapR/"
      app_url: "https://pandoraapp.earth/app/mapr"
      app_beta_url: "https://pandoraapp.earth/app/mapr-beta"
      docker_image: "mapr"
      img: "img/mapr.png"

    - name: "OsteoBioR"
      info_text: |
        OsteoBioR is used to model sequential data where each measurement is
        known to cover a time interval (integration time). This can be used,
        among others, to model isotopic temporal trajectories from isotopic
        measurements taken in multiple living tissues.
      repo_url: "https://github.com/Pandora-IsoMemo/OsteoBioR"
      doc_url: "https://pandora-isomemo.github.io/OsteoBioR/"
      app_url: "https://pandoraapp.earth/app/osteobior"
      app_beta_url: "https://pandoraapp.earth/app/osteobior-beta"
      docker_image: "osteobior"
      is_stan: TRUE
      img: "img/osteobior.jpg"

    - name: "PlotR"
      info_text: "PlotR produces Bayesian smoothed plots."
      repo_url: "https://github.com/Pandora-IsoMemo/PlotR"
      doc_url: "https://pandora-isomemo.github.io/PlotR/"
      app_url: "https://pandoraapp.earth/app/plotr"
      app_beta_url: "https://pandoraapp.earth/app/plotr-beta"
      docker_image: "plotr"
      img: "img/plotr.jpg"

    - name: "ReSources"
      full_name: "Food Reconstruction Using Isotopic Transferred Signals"
      info_text: "Bayesian mixing model."
      repo_url: "https://github.com/Pandora-IsoMemo/ReSources"
      doc_url: "https://pandora-isomemo.github.io/ReSources/"
      app_url: "https://pandoraapp.earth/app/resources"
      app_beta_url: "https://pandoraapp.earth/app/resources-beta"
      docker_image: "resources"
      img: "img/resources.jpg"
      video: "https://www.youtube.com/watch?v=mOyjs0Uov8w"

    - name: "TraceR"
      info_text: |
        TraceR helps to generate a visual representation of a relational map.
      repo_url: "https://github.com/Pandora-IsoMemo/TraceR"
      doc_url: "https://pandora-isomemo.github.io/TraceR/"
      app_url: "https://pandoraapp.earth/app/tracer"
      app_beta_url: "https://pandoraapp.earth/app/tracer-beta"
      docker_image: "tracer"
      img: "img/tracer.png"

    # - name: "oxcAARS"
    # - name: "ABMS"
    # - name: "deBInferS"

  apis:
    - name: "Isomemo"
      repo_url: "https://github.com/Pandora-IsoMemo/isomemo-data"
      doc_url: "https://pandora-isomemo.github.io/isomemo-data/"

    - name: "Pandora"
      repo_url: "https://github.com/Pandora-IsoMemo/pandora-data"
      doc_url: "https://pandora-isomemo.github.io/pandora-data/"

    # - name: iso-api

  other:
    - name: "DataTools"
      repo_url: "https://github.com/Pandora-IsoMemo/data-tools"
      doc_url: "https://pandora-isomemo.github.io/data-tools/"

    - name: "shinyTools"
      repo_url: "https://github.com/Pandora-IsoMemo/shiny-tools"
      doc_url: "https://pandora-isomemo.github.io/shiny-tools/"

    # - name: bmsc