As dev, I'd like to know the effects of spatial resolution on outputs comparison

statnmap commented 1 year ago

As dev, I'd like to know the effects of spatial resolution on outputs comparison, so that I can decide if and how to set up unit tests for higher resolution

Client - Validation

[x] Outputs between devs and clients are compared, and potential differences are shown in the vignette "dev - check high resolution model reproducibility"

=> https://balglave.github.io/FishMap/articles/dev-check-model-reproducibility-highres.html

[x] Vous notez qu'il y a toujours des différences avec les sorties de Baptiste sur cette comparaison. Nous allons maintenant réaliser les tests avec la mise à jour des versions de INLA et TMB pour commencer à se rassurer: https://github.com/balglave/FishMap/issues/53
[x] Nous vous laissons interpréter les différences. Peut-être avez-vous une tolérance acceptable. Nous avons mis 10E-4, mais peut-être qu'il faut aller sur des valeurs plus faibles, selon les données que l'on regarde. Qu'est-ce qui a du sens pour vous ?

Dev - Tech

[x] Increase k=0.75 and months
[x] Send instructions to clients
[x] Re-run outputs
[ ] Re-run for the thinkr-compare
[x] Change header of the lowres Vignette => change title to lowres
[x] Change header of the Rmd (dev_check_model_reproducibility.Rmd) for a Vignette header
[x] Change title for "highres"
[x] Generate a new vignette, pre-compiled, specific to this "highres" usecase
- flat => knit("dev-highres-.....Rmd")

Blocked

We need to verify that the outputs on your machine are the same as ours, while using the same "seed" and with a higher spatial resolution, so that we can properly define the future unit tests.

=> The k value was updated to 0.75, and the number of months was increased to 10:12 in the main.R file, so that we can compare higher resolution outputs.

Actions:

[x] Please do not change your R or packages versions for this run. We will do it after the results of the comparison.
[x] Please follow instructions in this vignette: https://balglave.github.io/FishMap/articles/execute-main.html
- [x] Please change your Renviron to use FISHMAP_OUTPUT_DIR="~/shared/outputs_fishmap_highres" so that the directory is different from the previous one.
- [x] Restart R
- [ ] You'll find the source of this vignette in file "vignette/execute-main.Rmd"
[x] Please zip the output directory and upload it in a comment below
[x] Please generate the output of sessionInfo() after the run, and add it in your comment below

JCasemajor commented 1 year ago

outputs_fishmap_highres.zip

JCasemajor commented 1 year ago

R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=French_France.utf8 LC_CTYPE=French_France.utf8 LC_MONETARY=French_France.utf8 [4] LC_NUMERIC=C LC_TIME=French_France.utf8

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] TMB_1.9.2 tidyr_1.3.0 stringr_1.5.0 sf_1.0-9 raster_3.6-14 ggplot2_3.4.1 INLA_23.02.04 sp_1.6-0
[9] foreach_1.5.2 Matrix_1.5-3 dplyr_1.1.0 tictoc_1.1

loaded via a namespace (and not attached): [1] tidyselect_1.2.0 terra_1.7-3 purrr_1.0.1 splines_4.2.2 lattice_0.20-45 colorspace_2.1-0
[7] vctrs_0.5.2 generics_0.1.3 s2_1.1.2 utf8_1.2.3 rlang_1.0.6 e1071_1.7-13
[13] pillar_1.8.1 glue_1.6.2 withr_2.5.0 DBI_1.1.3 RColorBrewer_1.1-3 wk_0.7.1
[19] lifecycle_1.0.3 munsell_0.5.0 gtable_0.3.1 codetools_0.2-19 labeling_0.4.2 class_7.3-21
[25] fansi_1.0.4 Rcpp_1.0.10 KernSmooth_2.23-20 scales_1.2.1 classInt_0.4-8 farver_2.1.1
[31] stringi_1.7.12 splancs_2.01-43 grid_4.2.2 rprojroot_2.0.3 here_1.0.1 rgdal_1.6-4
[37] cli_3.6.0 tools_4.2.2 magrittr_2.0.3 proxy_0.4-27 tibble_3.1.8 pkgconfig_2.0.3
[43] rstudioapi_0.14 iterators_1.0.14 R6_2.5.1 units_0.8-1 compiler_4.2.2

balglave commented 1 year ago

outputs_fishmap_highres.zip

balglave commented 1 year ago

R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 [4] LC_NUMERIC=C LC_TIME=French_France.1252

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] TMB_1.7.20 tidyr_1.1.3 stringr_1.4.0 sf_0.9-8
[5] raster_3.4-10 ggplot2_3.3.3 INLA_20.03.17 foreach_1.5.1
[9] sp_1.4-5 Matrix_1.2-18 dplyr_1.0.6 tictoc_1.0
[13] RevoUtils_11.0.2 RevoUtilsMath_11.0.0

loaded via a namespace (and not attached): [1] tidyselect_1.1.1 purrr_0.3.4 splines_4.0.2 lattice_0.20-41 colorspace_2.0-1
[6] vctrs_0.3.8 generics_0.1.3 utf8_1.2.1 blob_1.2.3 rlang_0.4.11
[11] e1071_1.7-7 pillar_1.6.1 glue_1.4.2 withr_2.5.0 DBI_1.1.1
[16] RColorBrewer_1.1-2 lifecycle_1.0.0 munsell_0.5.0 gtable_0.3.0 codetools_0.2-16
[21] labeling_0.4.2 class_7.3-17 fansi_0.4.2 Rcpp_1.0.6 KernSmooth_2.23-17 [26] scales_1.1.1 backports_1.2.1 classInt_0.4-3 farver_2.1.0 digest_0.6.27
[31] stringi_1.6.2 splancs_2.01-42 grid_4.0.2 rprojroot_1.3-2 cli_3.2.0
[36] here_0.1 rgdal_1.5-23 tools_4.0.2 magrittr_2.0.1 proxy_0.4-25
[41] tibble_3.1.2 crayon_1.5.2 pkgconfig_2.0.3 ellipsis_0.3.2 rstudioapi_0.13
[46] assertthat_0.2.1 iterators_1.0.13 R6_2.5.0 units_0.7-1 compiler_4.0.2

balglave commented 1 year ago

je valide.

JCasemajor commented 1 year ago

Je valide.

balglave / FishMap