A julia package for representing and manipulating model semantics
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

289 lines
2.8 KiB

2 years ago
2 years ago
[WIP] Add a theory for modeling SEIRD diseases w/ primitive transmision model (covid?) (#241) * Add a theory for modeling SEIRD diseases primitive transmision model * update covid example with operadic composition and SEIRD model * Update catlab dependency * Fix typo * Updated dependency versions * Updated catlab syntax and petri net syntax throughout files * Updated packages * attempt to update malaria example. Fixes problems with OpenPetri.model.model * More fixes to malaria.ipynb * fix the mk_function calls in malaria.ipynb * update wd render to orientation from direction. update malaria example * Add some TODOs to the CT api * attempt to use the new CT API for petri composition. * add implementation of Covid model without CT interface. * figured out how to use the new API * introduce PetriCospan instance, tests pass * WIP saving state * fix test failure on Death Sq * fix compose_pushout attempt 1 * remove compose_pushout debug stmts * collecting tests at the bottom of the file * move covid example to bottom of file * remove unnecessarily tight type constraint * add tests for building SEI and SEIR models * comment out drawing to make testing easier * WIP building intercity flow model * add more PetriCospan tests * add covid model and parameter exploration * refactor covid odemodel * move covid images to a `img` folder * ignore images in covid example directory * add SEIRD case for COVID * fix plotting * add peakgap analysis of SEIRD multicity * delete unused test file for catlab * add Pseird city model to covid example * update project.toml and tests * add comments to odemodel.jl * integrate PetriCospans into SemanticModels add tests * ammend previous commit * add estimate delay to odemodel.jl * add SEIR vs SEIRD comparison based on gap * add validation data generation script Co-authored-by: Micah Halter <micah.halter@gtri.gatech.edu>
12 months ago
  1. Manifest.toml
  2. *.jl.cov
  3. *.jl.*.cov
  4. *.jl.mem
  5. deps/deps.jl
  6. .DS_Store
  7. .pynb_checkpoints
  8. ## LATEX ignores
  9. ## Core latex/pdflatex auxiliary files:
  10. *.aux
  11. *.lof
  12. *.log
  13. *.lot
  14. *.fls
  15. *.out
  16. *.toc
  17. *.fmt
  18. *.fot
  19. *.cb
  20. *.cb2
  21. .*.lb
  22. ## Intermediate documents:
  23. *.dvi
  24. *.xdv
  25. *-converted-to.*
  26. # these rules might exclude image files for figures etc.
  27. # *.ps
  28. # *.eps
  29. # *.pdf
  30. ## Generated if empty string is given at "Please type another file name for output:"
  31. .pdf
  32. ## Bibliography auxiliary files (bibtex/biblatex/biber):
  33. *.bbl
  34. *.bcf
  35. *.blg
  36. *-blx.aux
  37. *-blx.bib
  38. *.run.xml
  39. ## Build tool auxiliary files:
  40. *.fdb_latexmk
  41. *.synctex
  42. *.synctex(busy)
  43. *.synctex.gz
  44. *.synctex.gz(busy)
  45. *.pdfsync
  46. ## Build tool directories for auxiliary files
  47. # latexrun
  48. latex.out/
  49. ## Auxiliary and intermediate files from other packages:
  50. # algorithms
  51. *.alg
  52. *.loa
  53. # achemso
  54. acs-*.bib
  55. # amsthm
  56. *.thm
  57. # beamer
  58. *.nav
  59. *.pre
  60. *.snm
  61. *.vrb
  62. # changes
  63. *.soc
  64. # comment
  65. *.cut
  66. # cprotect
  67. *.cpt
  68. # elsarticle (documentclass of Elsevier journals)
  69. *.spl
  70. # endnotes
  71. *.ent
  72. # fixme
  73. *.lox
  74. # feynmf/feynmp
  75. *.mf
  76. *.mp
  77. *.t[1-9]
  78. *.t[1-9][0-9]
  79. *.tfm
  80. #(r)(e)ledmac/(r)(e)ledpar
  81. *.end
  82. *.?end
  83. *.[1-9]
  84. *.[1-9][0-9]
  85. *.[1-9][0-9][0-9]
  86. *.[1-9]R
  87. *.[1-9][0-9]R
  88. *.[1-9][0-9][0-9]R
  89. *.eledsec[1-9]
  90. *.eledsec[1-9]R
  91. *.eledsec[1-9][0-9]
  92. *.eledsec[1-9][0-9]R
  93. *.eledsec[1-9][0-9][0-9]
  94. *.eledsec[1-9][0-9][0-9]R
  95. # glossaries
  96. *.acn
  97. *.acr
  98. *.glg
  99. *.glo
  100. *.gls
  101. *.glsdefs
  102. # gnuplottex
  103. *-gnuplottex-*
  104. # gregoriotex
  105. *.gaux
  106. *.gtex
  107. # htlatex
  108. *.4ct
  109. *.4tc
  110. *.idv
  111. *.lg
  112. *.trc
  113. *.xref
  114. # hyperref
  115. *.brf
  116. # knitr
  117. *-concordance.tex
  118. # TODO Comment the next line if you want to keep your tikz graphics files
  119. *.tikz
  120. *-tikzDictionary
  121. # listings
  122. *.lol
  123. # makeidx
  124. *.idx
  125. *.ilg
  126. *.ind
  127. *.ist
  128. # minitoc
  129. *.maf
  130. *.mlf
  131. *.mlt
  132. *.mtc[0-9]*
  133. *.slf[0-9]*
  134. *.slt[0-9]*
  135. *.stc[0-9]*
  136. # minted
  137. _minted*
  138. *.pyg
  139. # morewrites
  140. *.mw
  141. # nomencl
  142. *.nlg
  143. *.nlo
  144. *.nls
  145. # pax
  146. *.pax
  147. # pdfpcnotes
  148. *.pdfpc
  149. # sagetex
  150. *.sagetex.sage
  151. *.sagetex.py
  152. *.sagetex.scmd
  153. # scrwfile
  154. *.wrt
  155. # sympy
  156. *.sout
  157. *.sympy
  158. sympy-plots-for-*.tex/
  159. # pdfcomment
  160. *.upa
  161. *.upb
  162. # pythontex
  163. *.pytxcode
  164. pythontex-files-*/
  165. # tcolorbox
  166. *.listing
  167. # thmtools
  168. *.loe
  169. # TikZ & PGF
  170. *.dpth
  171. *.md5
  172. *.auxlock
  173. # todonotes
  174. *.tdo
  175. # vhistory
  176. *.hst
  177. *.ver
  178. # easy-todo
  179. *.lod
  180. # xcolor
  181. *.xcp
  182. # xmpincl
  183. *.xmpi
  184. # xindy
  185. *.xdy
  186. # xypic precompiled matrices
  187. *.xyc
  188. # endfloat
  189. *.ttt
  190. *.fff
  191. # Latexian
  192. TSWLatexianTemp*
  193. ## Editors:
  194. # WinEdt
  195. *.bak
  196. *.sav
  197. # Texpad
  198. .texpadtmp
  199. # LyX
  200. *.lyx~
  201. # Kile
  202. *.backup
  203. # KBibTeX
  204. *~[0-9]*
  205. # auto folder when using emacs and auctex
  206. ./auto/*
  207. *.el
  208. # expex forward references with \gathertags
  209. *-tags.tex
  210. # standalone packages
  211. *.sta
  212. doc/src/img/*.dot.png
  213. /doc/src/img/*.dot.svg
  214. /.ipynb_checkpoints/*
  215. **/.ipynb_checkpoints
  216. /doc/build
  217. *__pycache__/
  218. examples/*.dot
  219. examples/*.dot.svg
  220. doc/src/img/petri/*.png
  221. /doc/workflow.slides.html
  222. /examples/petri/covid/img/
  223. # Environments
  224. .env
  225. .venv
  226. env/
  227. venv/
  228. ENV/
  229. env.bak/
  230. venv.bak/