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2. Tidy documentation and update reference #82

Merged
merged 66 commits into from
Aug 22, 2023
Merged

2. Tidy documentation and update reference #82

merged 66 commits into from
Aug 22, 2023

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gareth-j
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@gareth-j gareth-j commented Aug 9, 2023 •
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This updates the documentation to add the new shiny priors app vignette and adds all exposed functions to the reference. Closes #81.

#57 needs to go in first.

@gareth-j
WIP: First pass at a priors app
0867dec
@gareth-j
WIP: Priors vignette to work on Shiny priors interface
3586184
@gareth-j
Basic model running but crashes, looking at causes
3f9a1af
@gareth-j
Basic shiny app working and outputting model summary
4f10a63
@gareth-j
Improved layout of app, basic functionality working, added busy spinner
641614e
@gareth-j
Small subset of data working with new mesh
31120ca
@gareth-j
Added sliders for other priors, looking at SPDE error
bce9574
@gareth-j
Converted app to use tabset. New sliders working with (hopefully) sen…
e20a913 
…sible defaults, added more params to be passed into app
@gareth-j
Merge branch 'main' into Iss54/ShinyPriors
b1d1c50 
Merging in changes from main
@gareth-j
Added eval=FALSE to temporary vignette
ddec081
@gareth-j
Merge branch 'main' into Iss54/ShinyPriors
ee80c90 
Merging in main
@gareth-j
Merge branch 'Prior_Tut' into Iss54/ShinyPriors
71e133a 
Merging in Xueqing's priors tutorial
@gareth-j
WIP: Updating prior values, adding in storage of model_output for com…
5a0072a 
…parison plotting
@gareth-j
Merge branch 'main' into Iss54/ShinyPriors
87dddbd 
Merging in main
@gareth-j
Adding in storage of model out
6904b6d
@gareth-j
Model output save working
1f65a18
@gareth-j
Adding function to parse output of inlabru::bru
8fe7cae
@gareth-j
Adding functions to parse inlabru model output
d686c65
@gareth-j
Looking into cause of INLA crashes, currently running with alphaprior…
b9333a9 
… from inputs, spde fixed
@gareth-j
spde and alphaprior with input$ working
2e8c2ef
@gareth-j
Save each run
702866b
@gareth-j
WIP: Adding f-string customisation back in
6a16279
@gareth-j
Custom fstring working
409cdb8
@gareth-j
Adding in status text
a9b3f0f
@gareth-j
Models running correctly and their outputs parsed
618f95b
@gareth-j
Adding in documentation files
160a74d
@gareth-j
Plotting comparison boxplots working
7783dad
@gareth-j
Adding code output for code tab
f74e5e8
@gareth-j
Prior values shown correctly in code tab
8861598
@gareth-j
Adding the four plots to app, updating handling code
02b9e3c
@gareth-j
Added fdmr logo busy gif, added model summary output to model run window
b646b3c
@gareth-j
WIP: Adding writing of model summary and priors to logfile [skip ci]
885d67c
@gareth-j
Adding help tab to app
a4a88d1
@gareth-j
Split out plotting functions for priors app, update app to pass in ti…
af68477 
…me variable
@gareth-j
Adding async libraries to description
2f0c7dd
@gareth-j
WIP: Move to async promise for model run
60ff706
@gareth-j
WIP: Moving variables back to reactive components
8fcb7f4
@gareth-j
Check if model output is correct
973c84e
@gareth-j
Remove unused gif component
ab0b0c0
@gareth-j
Merge branch 'Iss54+/async' into Iss54/ShinyPriors
7f51c4f 
Merging in async branch
@gareth-j
Disable eval of final mesh build step
188874a
@gareth-j
Separate lines for packages
ac3ec41
@gareth-j
Does using loadNamespace work?
6b62a0a
@gareth-j
Move to require for INLA loads
d9d0ccd
@gareth-j
Remove INLA load calls
d270bc6
@gareth-j
Add require of INLA back in
d7383d9
@gareth-j
Install INLA first
df05517
@gareth-j
Correct caching steps
1657bdc
@gareth-j
Ensure docstrings are up to date and added INLA to imports and remote
5471490
@gareth-j
Reduce number of requires, updated logging to create cleaner files
277f59f
@gareth-j
Put back delete log folder path
6560d5c
@gareth-j
Add missing words for file explanation
3377a1c
@gareth-j
Update text to use alpha symbol instead of a as per Xueqing's suggestion
5eb3291
@gareth-j
Make sure vignette name is synced
f16b693
@gareth-j
Remove explicit INLA install
4bef5f5
@gareth-j
Merge branch 'Iss54/ShinyPriors' into Iss81/tidyDocs
65f6151 
Merging in changes from priors branch
@gareth-j
Ensure vignette titles are synced
cece648
@gareth-j gareth-j changed the title 2. Tidy documentation and update refrence 2. Tidy documentation and update reference Aug 22, 2023
@gareth-j gareth-j merged commit e9edc71 into main Aug 22, 2023
2 of 3 checks passed
@gareth-j gareth-j deleted the Iss81/tidyDocs branch October 18, 2023 10:31
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@XueqingYin XueqingYin XueqingYin approved these changes

@mnky9800n mnky9800n Awaiting requested review from mnky9800n

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Tidy documentation and update reference
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@gareth-j @XueqingYin