Skip to content

Devel validation #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
MayaGueguen wants to merge 181 commits into
base: master
Choose a base branch
from
Open

Devel validation #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
181 commits
Select commit Hold shift + click to select a range
1c372c4
Add files via upload
maximedelprat Feb 22, 2022
c56c839
Delete POST_FATE.validation_habitat.R
maximedelprat Feb 22, 2022
8d05b71
Delete UTILS.do_habitat_validation.R
maximedelprat Feb 22, 2022
74647c2
Delete UTILS.plot_predicted_habitat.R
maximedelprat Feb 22, 2022
848cab7
Delete UTILS.train_RF_habitat.R
maximedelprat Feb 22, 2022
d3d0ad6
Add files via upload
maximedelprat Feb 22, 2022
580822b
Update UTILS.plot_predicted_habitat.R
maximedelprat Feb 22, 2022
d54d0d8
Update POST_FATE.validation_habitat.R
maximedelprat Feb 22, 2022
71a2c93
Update UTILS.do_habitat_validation.R
maximedelprat Feb 22, 2022
7068728
Update UTILS.plot_predicted_habitat.R
maximedelprat Feb 22, 2022
02b95af
Update UTILS.train_RF_habitat.R
maximedelprat Feb 22, 2022
12d5032
Update POST_FATE.validation_habitat.R
maximedelprat Feb 22, 2022
ec413be
Update UTILS.do_habitat_validation.R
maximedelprat Feb 22, 2022
a61ec30
Update UTILS.do_habitat_validation.R
maximedelprat Feb 22, 2022
409fe3c
Update POST_FATE.validation_habitat.R
maximedelprat Feb 22, 2022
625e9d4
Update UTILS.do_habitat_validation.R
maximedelprat Feb 22, 2022
5c9149e
Update UTILS.plot_predicted_habitat.R
maximedelprat Feb 22, 2022
1b6896c
Update UTILS.train_RF_habitat.R
maximedelprat Feb 22, 2022
5df7fc7
Add files via upload
maximedelprat Feb 22, 2022
05d90b1
Add files via upload
maximedelprat Feb 22, 2022
d3d4a8b
Update _pkgdown.yml
maximedelprat Feb 22, 2022
910c345
Add files via upload
maximedelprat Feb 23, 2022
6cd3ef7
Update POST_FATE.validation.habitat.html
maximedelprat Feb 23, 2022
4375b59
Add files via upload
maximedelprat Feb 23, 2022
f5607bf
Update POST_FATE.validation.habitat.Rd
maximedelprat Feb 23, 2022
4d75823
Add files via upload
maximedelprat Feb 23, 2022
95b185a
Add files via upload
maximedelprat Feb 23, 2022
a68ff79
Add files via upload
maximedelprat Feb 23, 2022
de6cb9f
Add files via upload
maximedelprat Feb 23, 2022
1dba32b
Update POST_FATE.validation.habitat.html
maximedelprat Feb 23, 2022
a54bf0a
Update UTILS.train_RF_habitat.R
maximedelprat Feb 28, 2022
2f1681c
Update train.RF.habitat.Rd
maximedelprat Feb 28, 2022
2604496
Update train.RF.habitat.html
maximedelprat Feb 28, 2022
463a037
Add files via upload
maximedelprat Mar 1, 2022
50fc4de
Add files via upload
maximedelprat Mar 1, 2022
d4dd212
Add files via upload
maximedelprat Mar 1, 2022
54de808
Add files via upload
maximedelprat Mar 1, 2022
0b8a1d4
Delete POST_FATE.validation_habitat.R
maximedelprat Mar 4, 2022
65bf12a
Delete POST_FATE.validation.habitat.html
maximedelprat Mar 4, 2022
8d3898c
Delete POST_FATE.validation.habitat.Rd
maximedelprat Mar 4, 2022
3772cee
Add files via upload
maximedelprat Mar 4, 2022
c275cf8
Add files via upload
maximedelprat Mar 4, 2022
91f44dc
Add files via upload
maximedelprat Mar 4, 2022
7612aed
Add files via upload
maximedelprat Mar 4, 2022
fc92bae
Add files via upload
maximedelprat Mar 4, 2022
8a827f9
Add files via upload
maximedelprat Mar 4, 2022
4a5b3f2
Add files via upload
maximedelprat Mar 4, 2022
7f70f92
Add files via upload
maximedelprat Mar 4, 2022
9fc0704
Add files via upload
maximedelprat Mar 8, 2022
2925618
Add files via upload
maximedelprat Mar 8, 2022
5e9b5f6
Add files via upload
maximedelprat Mar 8, 2022
6043db9
Update POST_FATE.validation.html
maximedelprat Mar 9, 2022
7e051b5
Update POST_FATE.validation.R
maximedelprat Mar 9, 2022
77bc54e
Update POST_FATE.validation.Rd
maximedelprat Mar 9, 2022
fd81ce0
Update PRE_FATE.skeletonDirectory.R
maximedelprat Mar 9, 2022
abf55e2
Add files via upload
maximedelprat Mar 9, 2022
59459c3
Add files via upload
maximedelprat Mar 9, 2022
737f56c
Add files via upload
maximedelprat Mar 18, 2022
b38567f
Add files via upload
maximedelprat Mar 18, 2022
1277847
Add files via upload
maximedelprat Mar 18, 2022
94b74b8
Add files via upload
maximedelprat Mar 18, 2022
40cb47c
First corrections and remarks on UTILS.train_RF_habitat
MayaGueguen Mar 21, 2022
ba5289e
Corrections and adjustments
maximedelprat Mar 22, 2022
abfb871
correction in train.RF.habitat : preliminary checks, computing relati…
maximedelprat Mar 22, 2022
09a85c7
correction of train.RF.habitat
maximedelprat Mar 22, 2022
ba8772f
Premier check sur UTILS.do_habitat_validation
MayaGueguen Mar 22, 2022
5c282fc
small adjustments
maximedelprat Mar 22, 2022
d1a951d
first correction on do.habitat.validation
maximedelprat Mar 22, 2022
70ded50
Correction and adjustments in do.habitat.validation (maxime)
maximedelprat Mar 22, 2022
11cf905
small adjustments
maximedelprat Mar 22, 2022
a3b2c06
Corrections of validation functions (23/03)
maximedelprat Mar 23, 2022
827fe8a
Corrections in documentation of validation functions
maximedelprat Mar 23, 2022
dbf8f5a
small adjustments
maximedelprat Mar 23, 2022
c2caa9a
small adjustments
maximedelprat Mar 23, 2022
1db7b87
Small comment about what is redundant and could be merged
MayaGueguen Mar 24, 2022
e33e53f
aggregation of habitat & PFG composition validation in POST_FATE.vali…
maximedelprat Mar 25, 2022
cd337ba
corrections
maximedelprat Mar 25, 2022
44678d0
small correction
maximedelprat Mar 25, 2022
a5dd3ef
Corrections with foreach loops in order to take into account a set of…
maximedelprat Mar 25, 2022
6ed53a3
Corrections for POST_FATE.validation, all associated functions and do…
maximedelprat Mar 31, 2022
d4f4afd
Delete do.habitat.validation.html
maximedelprat Mar 31, 2022
8144c79
Delete do.PFG.composition.validation.html
maximedelprat Mar 31, 2022
36e7bc3
Delete do.habitat.validation.html
maximedelprat Mar 31, 2022
7d89501
Delete get.observed.distribution.html
maximedelprat Mar 31, 2022
3320e50
Delete plot.predicted.habitat.html
maximedelprat Mar 31, 2022
5f6d4b3
Delete train.RF.habitat.html
maximedelprat Mar 31, 2022
5bb9966
Update _pkgdown.yml
maximedelprat Mar 31, 2022
54c4a71
Minor corrections in documentation of the function
maximedelprat Apr 6, 2022
18cf0d8
Correction for checks of releves.PFG parameter
maximedelprat Apr 7, 2022
d0c1c03
Minor corrections in documentations of the functions
maximedelprat Apr 7, 2022
95c8ec5
Minor corrections of documentation
maximedelprat Apr 8, 2022
a044571
minor corrections & deletion of those corrections
maximedelprat Apr 28, 2022
d002b3f
Choice in validation mask (provide a map or using simulation mask) & …
maximedelprat Apr 28, 2022
62bd5c3
Add BinaryMaps function corrections to devel_validation
maximedelprat Apr 28, 2022
45409ff
corrections in validation functions & in BinaryMaps
maximedelprat Apr 28, 2022
5f8182d
Corrections in Graphics_PFG for devel_validation
maximedelprat Apr 28, 2022
173d450
minor correction
maximedelprat Apr 28, 2022
4062e1c
Display adjusments
maximedelprat Apr 28, 2022
0045b12
adding of unzip stage on validationStatistics
maximedelprat Apr 28, 2022
2a1b99b
Display adjustments
maximedelprat Apr 29, 2022
7021511
Add predict.all.map argument to let the user decide if the function m…
maximedelprat Apr 29, 2022
5aecce0
minor corrections
maximedelprat Apr 29, 2022
596ecb5
minor corrections
maximedelprat Apr 29, 2022
f764552
minor corrections
maximedelprat Apr 29, 2022
3471a3c
minor corrections
maximedelprat Apr 29, 2022
6a76a4c
Documentation corrections
maximedelprat May 2, 2022
3b88ab9
modification about colors in the final prediction map
maximedelprat May 2, 2022
9db0c75
small mistake correction
maximedelprat May 2, 2022
a9bcdd3
Using fread & fwrite function from data.table package instead of read…
maximedelprat May 18, 2022
fc94d83
corrections to improve function documentations
maximedelprat May 23, 2022
88a597d
example of validation function correction
maximedelprat May 23, 2022
50e3967
small corrections in example of the function
maximedelprat May 24, 2022
0db54db
corrections in results dispay
maximedelprat May 24, 2022
b1c82f7
corrections in display of habitat performance results
maximedelprat May 25, 2022
3bbd9f0
small corrections
maximedelprat May 25, 2022
43171b2
minor corrections
maximedelprat May 25, 2022
7d6e211
minor corrections
maximedelprat May 25, 2022
471ffb6
adding hab.obs.RF map with different resolution to fit more precisely…
maximedelprat Jun 1, 2022
319a56c
minor correction about display of results
maximedelprat Jun 1, 2022
111131d
minor correction in display of the results
maximedelprat Jun 3, 2022
0cf9e23
possibility to display the results of all the simulations if number o…
maximedelprat Jun 7, 2022
b5fdf1a
Possibility to set the proportion of the data used for the training o…
maximedelprat Jun 7, 2022
455a1ea
correction in documentation
maximedelprat Jun 7, 2022
8e591f3
new light parameters evaluation
maximedelprat Jun 8, 2022
39e4461
minor corrections
maximedelprat Jun 8, 2022
70f5e17
minor corrections
maximedelprat Jun 8, 2022
86f0cd6
correction in packages inmportation
maximedelprat Jun 8, 2022
79232eb
corrections in namesapce and documentation of validation functions
maximedelprat Jun 8, 2022
4f4b41e
minor corrections
maximedelprat Jun 8, 2022
01e5839
minor corrections
maximedelprat Jun 8, 2022
900e13d
corrections in documentation of POST_FATE.validation and in evolution…
maximedelprat Jun 9, 2022
1662556
minor changes in documentation
maximedelprat Jun 9, 2022
8026709
correction in documentation of the validation functions
maximedelprat Jun 10, 2022
ad434a0
Update _pkgdown.yml
maximedelprat Jun 10, 2022
e666e70
corrections in documentations and deletion of exportation of validati…
maximedelprat Jun 10, 2022
7ad5d5a
deletion of validation sub functions
maximedelprat Jun 10, 2022
e3f56a7
Merge branch 'devel_validation' of https://github.com/leca-dev/RFate …
maximedelprat Jun 10, 2022
e6a042f
deletion of documentation of validation sub functions
maximedelprat Jun 10, 2022
1a626dd
last corrections in documentation
maximedelprat Jun 13, 2022
9c79b89
add packages dependencies
maximedelprat Jun 13, 2022
346a4e4
small mistake correction in get_observed_distribution, about columns …
maximedelprat Jun 13, 2022
162b4a0
display of richness
maximedelprat Jun 13, 2022
48918e9
display of habtat performance
maximedelprat Jun 13, 2022
0bca130
final adjustments in documentation
maximedelprat Jun 13, 2022
066fcc4
final adjustments in documentation
maximedelprat Jun 14, 2022
4be9717
delete S3 method
maximedelprat Jun 14, 2022
59f5291
corrections
maximedelprat Jun 14, 2022
2bf3f43
corrections in documentation
maximedelprat Jun 15, 2022
45cf27a
corrections in display of results & deletion of the reproducibility o…
maximedelprat Jun 20, 2022
fb54d64
export of simu_PFG
maximedelprat Jun 20, 2022
f6e4e8f
final correction of duplicate simulated abundance loading for richnes…
maximedelprat Jun 21, 2022
ac2b871
display corrections
maximedelprat Jun 22, 2022
cd7d12c
diplay and documentation corrections
maximedelprat Jun 22, 2022
0f81b72
docs corrections
maximedelprat Jun 22, 2022
b778c11
richness validation for several simulations mistake corrected
maximedelprat Jun 23, 2022
4ff1c85
PFG richness validation corrections
maximedelprat Jun 23, 2022
bb10bce
cleaning for PFG richness computation
maximedelprat Jun 27, 2022
72cfc21
final cleaning for PFG richness computation
maximedelprat Jun 27, 2022
8aa6d69
UPDATE R files with files from master branch
MayaGueguen Jun 27, 2022
e838a32
UPDATE docs files with files from master branch
MayaGueguen Jun 27, 2022
17a99e3
Move all checks at the beginning of POST_FATE.validation
MayaGueguen Jun 28, 2022
d00f8eb
corrections in order to harmonize the POST_FATE.validation function w…
maximedelprat Jun 30, 2022
c3c968f
corrections in documentation
maximedelprat Jun 30, 2022
0834dda
corrections
maximedelprat Jul 1, 2022
bfcd24a
documentation updating for the validation function
maximedelprat Jul 1, 2022
8574307
correction for RF.training argument
maximedelprat Jul 5, 2022
a776a7c
corrections on the TSS formula
maximedelprat Jul 7, 2022
e6eb93e
Clean and reorganize validation functions (not fnished yet)
MayaGueguen Oct 12, 2022
9fd5bb3
Add small intern functions (.valid_[...])
MayaGueguen Oct 12, 2022
f4bccd7
Continue reorganization
MayaGueguen Oct 12, 2022
4eec69e
Remove unnecessary stuff
MayaGueguen Oct 12, 2022
a4c35f5
Add comments and save results properly
MayaGueguen Oct 13, 2022
8ae94ff
Correct documentation for param (still missing corrections for detail…
MayaGueguen Oct 14, 2022
d747c90
Start cleaning documentation of POST_FATE.validation
MayaGueguen Oct 25, 2022
2ebe37a
Update devel_validation branch with master branch
MayaGueguen Jun 27, 2023
c07b166
FATE : add SOIL_MASK parameter in simulParam file and SOIL_FILL_MAP p…
MayaGueguen Sep 4, 2023
0798be0
Add LIGHT_RECRUITMENT and SOIL_RECRUITMENT parameters
MayaGueguen Sep 8, 2023
5541088
Remove UTILS. functions linked to previous validation workflow (now i…
MayaGueguen Oct 23, 2023
ade8a2b
Update documentation for POST_FATE.validation
MayaGueguen Oct 23, 2023
42e902d
Update documentation for POST_FATE.validation function
MayaGueguen Oct 23, 2023
172c0d1
Merge with master branch to catch up
MayaGueguen Oct 23, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 16 additions & 0 deletions NAMESPACE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ export(POST_FATE.graphic_validationStatistics)
export(POST_FATE.graphics)
export(POST_FATE.relativeAbund)
export(POST_FATE.temporalEvolution)
export(POST_FATE.validation)
export(PRE_FATE.abundBraunBlanquet)
export(PRE_FATE.params_PFGdispersal)
export(PRE_FATE.params_PFGdisturbance)
Expand Down Expand Up @@ -71,6 +72,7 @@ importFrom(adehabitatHR,kernelUD)
importFrom(adehabitatMA,ascgen)
importFrom(ape,as.phylo)
importFrom(ape,plot.phylo)
importFrom(caret,confusionMatrix)
importFrom(cluster,silhouette)
importFrom(colorspace,heat_hcl)
importFrom(colorspace,sequential_hcl)
Expand Down Expand Up @@ -107,6 +109,9 @@ importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_alpha)
importFrom(ggplot2,scale_color_continuous)
Expand Down Expand Up @@ -142,28 +147,38 @@ importFrom(huge,huge.npn)
importFrom(methods,as)
importFrom(parallel,mclapply)
importFrom(phyloclim,niche.overlap)
importFrom(prettyR,Mode)
importFrom(randomForest,randomForest)
importFrom(randomForest,tuneRF)
importFrom(raster,as.data.frame)
importFrom(raster,as.matrix)
importFrom(raster,cellFromXY)
importFrom(raster,cellStats)
importFrom(raster,coordinates)
importFrom(raster,crop)
importFrom(raster,crs)
importFrom(raster,extension)
importFrom(raster,extent)
importFrom(raster,extract)
importFrom(raster,levels)
importFrom(raster,mask)
importFrom(raster,nlayers)
importFrom(raster,projectRaster)
importFrom(raster,projection)
importFrom(raster,raster)
importFrom(raster,rasterToPoints)
importFrom(raster,ratify)
importFrom(raster,res)
importFrom(raster,stack)
importFrom(raster,writeRaster)
importFrom(raster,xyFromCell)
importFrom(readr,write_rds)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(sp,SpatialPoints)
importFrom(stats,aggregate)
importFrom(stats,as.dist)
importFrom(stats,complete.cases)
importFrom(stats,cophenetic)
importFrom(stats,cor)
importFrom(stats,cutree)
Expand All @@ -182,6 +197,7 @@ importFrom(utils,combn)
importFrom(utils,download.file)
importFrom(utils,install.packages)
importFrom(utils,packageDescription)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
Expand Down
Loading