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Migrate to terra and sf. Partially migrate to fmesher #2

Merged
merged 174 commits into from
Jan 8, 2024
Merged

Migrate to terra and sf. Partially migrate to fmesher #2

merged 174 commits into from
Jan 8, 2024

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simon-smart88
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timcdlucas and others added 30 commits February 23, 2022 16:19
@timcdlucas
Try switching to actions.
d76d011
@timcdlucas
Try to force to trigger on this branch.
0683f49
@timcdlucas
empty to trigger.
ae32f13
@timcdlucas
Copy workflow from inlabru
7edee45
@timcdlucas
Try another workflow from inlabru
783749b
@timcdlucas
Trigger
3d93757
@timcdlucas
Readd actions branch as trigger.
4a29dec
@timcdlucas
Fix Jacobian correction for iid effect.
4ac6f20 
We were accidentally correcting by log sd rather than log tau.
Think this will be minr, but still important to correct.
Brought to our attention by Bowen He, Vanderbilt.
@timcdlucas
Change maintainor to tim lucas.
1987b09
@timcdlucas
Merge pull request aknandi#60 from aknandi/fix_jacob
dd114e3 
Fix jacob
Fix bad default intercept prior. Closes aknandi#61
96a214c
@timcdlucas
Document priors properly. Closes aknandi#59
6042b1c
@timcdlucas
Merge branch 'actions' into fix_jacob
78cce86
@timcdlucas
Trigger actions
7ada2e9
@timcdlucas
Actions on all branches.
d914c15
@timcdlucas
Run isinla block in vignette
04583de
@timcdlucas
Only run ci on one system for now.
32b9ff8
@timcdlucas
Move vignette to .txt to prevent it being built for now.
eab23d4
@timcdlucas
Delete unneeded extra .gitignore.
57381ee
@timcdlucas
Use actions badges.
f075536
@timcdlucas
Dont fit models with gaussian error and iid in tests to avoid warning.
a69e20c
@timcdlucas
Use inherits instead of if(class(object) == something)
728d1bc
@timcdlucas
Fix single covariate test.
d30371c
@timcdlucas
Version bump.
f9efd1c
@timcdlucas
Import some packages to namespace to avoid being told off?
0f2f744
@timcdlucas
Add imports.
a109df9
@timcdlucas
Fix some tests with iid removed.
f4fba4b
@timcdlucas
Remove vignette for now.
3f55f49
@timcdlucas
Readd vignette
4e43033
@timcdlucas
cut out most of vignette to work out how to get it to wwork.
f59a4ce
@simon-smart88
fix predict tests and remove some dependencies
4130016
@simon-smart88
move test data to helper_data
aca877b
@simon-smart88
update examples and docs. remove sp from imports
b412537
@simon-smart88
partially migrate plotting (not functional yet)
6ad196c
@simon-smart88
migrate summary
793077b
@simon-smart88
update prepare docs
268e7e0
@simon-smart88
fix id_var handling in prepare_data
3d2cc96
@simon-smart88
switch plotting to use tidyterra and update some docs
e6a0576
@simon-smart88
update docs after migration
b1874a5
@simon-smart88
Update prepare_data.R
225c866 
more robust removal of aggregation data
@simon-smart88
Update fit_model.R
5ff89dc 
fix cov_matrix column selection bug
@simon-smart88
migrate INLA::inla.mesh.project to fmesher::fm_evaluate
1db8d22
@simon-smart88
remove getamatrix function
9d66d11
@simon-smart88
tweaks to yesterdays changes
ad953fa
@simon-smart88
deprectate ncores
bedcb09
@simon-smart88
fix prepare bug
dc94f28
@simon-smart88
Update vignette
4df4c4d
@simon-smart88
update readme
ee0a1c0
@simon-smart88
update description
ca2a9d1
@simon-smart88
adjust test-extract
ffd1711
@simon-smart88
replace skip_if_not_installed('INLA')
7ef6593
@simon-smart88
add missing skip inla and update prepare docs
17aa2ca
@simon-smart88
another missing INLA skip
fa9f1d5
@simon-smart88
remove INLA requirement from prepare data
e867911
@simon-smart88
remove foreach dependency
0e2031c
@simon-smart88
fix long lines in docs
8e0e63a
@simon-smart88
improve vignette plot
166b085
@simon-smart88
add missing suggest
3b80068
@simon-smart88
tweak priors
d8a5e1b
@timcdlucas timcdlucas merged commit 3acb727 into timcdlucas:master Jan 8, 2024
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@simon-smart88 @timcdlucas