IASDT.R/_pkgdown.yml at main · BioDT/IASDT.R · 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
url: https://biodt.github.io/IASDT.R

template:
  bootstrap: 5
  light-switch: true

authors:
  Ahmed El-Gabbas:
    href: https://elgabbas.netlify.app/

home:
  title: IASDT.R
  links:
  - text: BioDT project
    href: https://biodt.eu/
  - text: Community ecology @ UFZ
    href: https://www.ufz.de/index.php?en=36737

development:
  mode: auto


navbar:
  title: IASDT.R
  type: default
  left:
  - text: Functions
    icon: fa-file-code-o
    href: reference/index.html
  - text: Modelling workflow
    icon: fas fa-book
    menu:
    - text: Overview
      href: articles/workflow_1_overview.html
    - text: Processing abiotic data
      href: articles/workflow_2_abiotic_data.html
    - text: Processing biotic data
      href: articles/workflow_3_biotic_data.html
    - text: Model fitting
      href: articles/workflow_4_model_fitting.html
    - text: Model post-processing
      href: articles/workflow_5_model_postprocess.html

reference:
- title: Package info
  contents:
  - IASDT.R-package

- title: Prepare species distribution data
  contents:
  - gbif_data
  - easin_data
  - elter_process
  - naps_data
  - get_species_name

- title: Prepare abiotic data
  contents:
  - clc_process
  - chelsa_variables
  - chelsa_data
  - efforts_data
  - railway_intensity
  - road_intensity
  - river_length
  - bioreg_process
  - wetness_index_process
  - soil_density_process

- title: Modelling functions
  desc: Functions for preparing data, running the models, and postprocessing of model outputs
- subtitle: Data preparation
  desc: Prepare input data and scripts for fitting Hmsc-HPC on GPU
  contents:
  - mod_cv_prepare
  - prepare_knots
  - mod_inputs
  - mod_slurm
  - mod_slurm_refit
  - mod_fit_windows
  - mod_cv_fit
  - install_hmsc_windows
  - cpp_functions
  - fit_sdm_models
- subtitle: Model postprocessing
  desc: Postprocessing model outputs, including checking for convergence, making spatial predictions, evaluation, and plotting.
  contents:
  - coda_to_tibble
  - trim_hmsc
  - mod_get_posteriors
  - mod_merge_chains
  - mod_summary
  - response_curves
  - predict_latent_factor
  - plot_latent_factor
  - predict_hmsc
  - predict_maps
  - predict_maps_cv
  - plot_prediction
  - mod_cv_evaluate
  - mod_cv_evaluate_plot
  - mod_cv_merge_predictions
  - mod_postprocessing
  - plot_evaluation
  - parameter_heatmap
  - convergence_plot
  - convergence_plot_all
  - variance_partitioning
  - plot_gelman