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R 4.3.3 (#140)
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* 移除 xgboost INLA 等包

* follow up

* 不编译生存分析

* add glmnet
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@XiangyunHuang
XiangyunHuang authored Mar 4, 2024
1 parent afb4196 commit 2bee57f
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2 changes: 1 addition & 1 deletion .github/workflows/quarto-book-macos.yaml
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Expand Up @@ -24,7 +24,7 @@ jobs:
- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
r-version: '4.3.2'
r-version: '4.3.3'
extra-repositories: 'https://grantmcdermott.r-universe.dev'

- uses: r-lib/actions/setup-r-dependencies@v2
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2 changes: 1 addition & 1 deletion .github/workflows/quarto-book-ubuntu.yaml
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Expand Up @@ -24,7 +24,7 @@ jobs:
- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
r-version: '4.3.2'
r-version: '4.3.3'
extra-repositories: 'https://grantmcdermott.r-universe.dev'

- uses: r-lib/actions/setup-r-dependencies@v2
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -50,6 +50,7 @@ Imports:
ggTimeSeries,
ggVennDiagram,
ggwordcloud,
glmnet,
gt (>= 0.10.1),
hexbin,
HistData,
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rsconnect (>= 1.1.0)
Enhances:
sp (>= 2.0-0)
SystemRequirements: pgf (>= 3.00), JAGS 4.x.y
SystemRequirements: pgf (>= 3.00)
Additional_repositories:
https://grantmcdermott.r-universe.dev
Encoding: UTF-8
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175 changes: 31 additions & 144 deletions README.md
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Expand Up @@ -100,155 +100,42 @@ xfun::session_info(packages = pkg_dep, dependencies = FALSE)
```

```
R version 4.3.2 (2023-10-31)
R version 4.3.3 (2024-02-29)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3, RStudio 2023.12.1.402
Running under: macOS Sonoma 14.3.1, RStudio 2023.12.1.402
Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8
Package version:
abess_0.4.8 abind_1.4.5 admisc_0.34
ape_5.7.1 aplot_0.2.2 AsioHeaders_1.22.1.2
askpass_1.2.0 backports_1.4.1 base64enc_0.1.3
bayesplot_1.11.0 BB_2019.10-1 beanplot_1.3.1
beeswarm_0.4.0 BH_1.84.0-0 bigD_0.2.0
bit_4.0.5 bit64_4.0.5 bitops_1.0.7
blme_1.0-5 blob_1.2.4 boot_1.3.28.1
bridgesampling_1.1.2 brio_1.1.4 brms_2.20.4
Brobdingnag_1.2.9 broom_1.0.5 broom.helpers_1.14.0
bslib_0.6.1 cachem_1.0.8 callr_3.7.3
car_3.1-2 carData_3.0.5 checkmate_2.3.1
chromote_0.1.2 class_7.3.22 classInt_0.4.10
cli_3.6.2 clipr_0.8.0 cluster_2.1.6
cmdstanr_0.7.1 coda_0.19.4.1 codetools_0.2.19
coin_1.4-3 colorspace_2.1.0 colourpicker_1.3.0
commonmark_1.9.1 compiler_4.3.2 config_0.3.2
corpcor_1.6.10 corrplot_0.92 cowplot_1.1.3
cpp11_0.4.7 crayon_1.5.2 crosstalk_1.2.1
cubature_2.1.0 curl_5.2.0 cvar_0.5
data.table_1.15.0 datasauRus_0.1.6 DBI_1.2.1
dbplyr_2.4.0 deldir_2.0.2 desc_1.4.3
diffobj_0.3.5 digest_0.6.34 distributional_0.3.2
dotCall64_1.1.1 downlit_0.4.3 dplyr_1.1.4
DT_0.31 dunn.test_1.3.5 dygraphs_1.1.1.6
e1071_1.7-14 ECOSolveR_0.5.5 ellipsis_0.3.2
evaluate_0.23 expm_0.999-9 fansi_1.0.6
farver_2.1.1 fastICA_1.2.4 fastmap_1.1.1
fastmatrix_0.5-772 fBasics_4032.96 fGarch_4031.90
filehash_2.4.5 float_0.3.2 fmesher_0.1.5
fontawesome_0.5.2 forcats_1.0.0 foreach_1.5.2
foreign_0.8.86 Formula_1.2.5 FRK_2.2.1
fs_1.6.3 future_1.33.1 GA_3.2.4
gamm4_0.2.6 gbutils_0.5 generics_0.1.3
geodata_0.5-9 geometry_0.4.7 ggalluvial_0.12.5
gganimate_1.0.8 ggbeeswarm_0.7.2 ggbump_0.1.99999
ggdensity_1.0.0 ggeffects_1.3.4 ggExtra_0.10.1
ggfittext_0.10.2 ggforce_0.4.1 ggfortify_0.4.16
ggfun_0.1.4 ggmosaic_0.3.3 ggnewscale_0.4.9
ggplot2_3.5.0 ggplotify_0.1.2 ggpubr_0.6.0
ggraph_2.1.0.9000 ggrepel_0.9.5 ggridges_0.5.6
ggsci_3.0.0 ggsignif_0.6.4 ggstats_0.5.1
ggstream_0.1.0 ggthemes_5.0.0 ggTimeSeries_1.0.2
ggVennDiagram_1.5.0 ggwordcloud_0.6.1 gifski_1.12.0-2
GLMMadaptive_0.9-1 glmmTMB_1.1.8 glmnet_4.1-8
globals_0.16.2 glue_1.7.0 gmp_0.7.4
goftest_1.2.3 graphics_4.3.2 graphlayouts_1.1.0
grDevices_4.3.2 grid_4.3.2 gridExtra_2.3
gridGraphics_0.5.1 gridtext_0.1.5 gss_2.2.7
gt_0.10.1 gtable_0.3.4 gtools_3.9.5
haven_2.5.4 here_1.0.1 hexbin_1.28.3
hglm_2.2-1 hglm.data_1.0.1 highr_0.10
HistData_0.9-1 Hmisc_5.1.1 hms_1.1.3
htmlTable_2.4.2 htmltools_0.5.7 htmlwidgets_1.6.4
httpuv_1.6.14 httr_1.4.7 igraph_2.0.1.1
INLA_24.01.20 inline_0.3.19 insight_0.19.8
interp_1.1.6 intervals_0.15.4 isoband_0.2.7
iterators_1.0.14 jiebaR_0.11 jiebaRD_0.1
jpeg_0.1.10 jquerylib_0.1.4 jsonlite_1.8.8
juicyjuice_0.1.0 keras_2.13.0 kernlab_0.9-32
KernSmooth_2.23.22 knitr_1.45 labeling_0.4.3
labelled_2.12.0 lars_1.3 later_1.3.2
lattice_0.22.5 latticeExtra_0.6-30 lavaan_0.6-17
lazyeval_0.2.2 lgr_0.4.4 libcoin_1.0.10
lifecycle_1.0.4 linprog_0.9.4 listenv_0.9.1
lme4_1.1-35.1 lmtest_0.9.40 loo_2.6.0
lpSolve_5.6.20 lvplot_0.2.1 magic_1.6.1
magick_2.8.2 magrittr_2.0.3 maps_3.4.2
markdown_1.12 MASS_7.3.60.0.1 Matrix_1.6.5
MatrixExtra_0.1.15 MatrixModels_0.5.3 matrixStats_1.2.0
mclogit_0.9.6 MCMCglmm_2.35 memisc_0.99.31.7
memoise_2.0.1 methods_4.3.2 mgcv_1.9.1
mime_0.12 miniUI_0.1.1.1 minqa_1.2.6
misc3d_0.9-1 mlapi_0.1.1 mnormt_2.1.1
modeltools_0.2.23 multcomp_1.4.25 munsell_0.5.0
mvtnorm_1.2.4 ncvreg_3.14.1 nleqslv_3.3.5
nlme_3.1.164 nloptr_2.0.3 nnet_7.3.19
nomnoml_0.3.0 numDeriv_2016.8.1.1 openssl_2.1.1
ordinal_2023.12.4 parallel_4.3.2 parallelly_1.36.0
patchwork_1.2.0 pbapply_1.7.2 pbivnorm_0.6.0
pbkrtest_0.5.2 pdftools_3.4.0 pillar_1.9.0
pkgbuild_1.4.3 pkgconfig_2.0.3 pkgload_1.3.4
plogr_0.2.0 plot2_0.0.4 plot3D_1.4
plotly_4.10.4 pls_2.8-3 plyr_1.8.9
png_0.1.8 polyclip_1.10.6 polynom_1.4.1
posterior_1.5.0 praise_1.0.0 prettyunits_1.2.0
pROC_1.18.5 processx_3.8.3 productplots_0.1.1
progress_1.2.3 projpred_2.8.0 promises_1.2.1
proxy_0.4.27 ps_1.7.6 purrr_1.0.2
pwr_1.3-0 qpdf_1.3.2 quadprog_1.5-8
quantmod_0.4.25 quantreg_5.97 QuickJSR_1.1.3
R6_2.5.1 ragg_1.2.7 randomForest_4.7-1.1
rappdirs_0.3.3 rbibutils_2.2.16 RColorBrewer_1.1.3
Rcpp_1.0.12 RcppArmadillo_0.12.6.6.1 RcppEigen_0.3.3.9.4
RcppParallel_5.1.7 RcppProgress_0.4.2 RcppTOML_0.2.2
Rdpack_2.6 reactable_0.4.4 reactR_0.5.0
readr_2.1.5 registry_0.5.1 rematch2_2.1.2
reshape2_1.4.4 reticulate_1.35.0 Rglpk_0.6.5.1
RhpcBLASctl_0.23.42 rjags_4-15 rlang_1.1.3
rmarkdown_2.25 ROI_1.0-1 ROI.plugin.ecos_1.0-2
ROI.plugin.glpk_1.0-0 ROI.plugin.nloptr_1.0-1 ROI.plugin.quadprog_1.0-1
ROI.plugin.scs_1.1-2 rootSolve_1.8.2.4 rpart_4.1.23
rpart.plot_3.1.1 rprojroot_2.0.4 rsparse_0.5.1
RSQLite_2.3.5 rstan_2.32.5 rstantools_2.4.0
rstatix_0.7.2 rstudioapi_0.15.0 rvest_1.0.3
s2_1.1.6 sandwich_3.1.0 sass_0.4.8
scales_1.3.0 scs_3.2.4 selectr_0.4.2
sf_1.0-15 shades_1.4.0 shape_1.4.6
shiny_1.8.0 shinyjs_2.1.0 shinystan_2.6.0
shinythemes_1.2.0 showtext_0.9-6 showtextdb_3.0
slam_0.1.50 sm_2.2.5.7.1 sourcetools_0.1.7.1
sp_2.1.3 spacetime_1.3.1 spacyr_1.3.0
spam_2.10.0 spaMM_4.4.16 sparseinv_0.1.3
SparseM_1.81 spatial_7.3.17 spatstat_3.0-7
spatstat.data_3.0.4 spatstat.explore_3.2.5 spatstat.geom_3.2.8
spatstat.linnet_3.1.3 spatstat.model_3.2.8 spatstat.random_3.2.2
spatstat.sparse_3.0.3 spatstat.utils_3.0.4 spData_2.3.0
spdep_1.3-1 splancs_2.01-44 splines_4.3.2
stabledist_0.7.1 StanHeaders_2.32.5 stars_0.6-4
statmod_1.5.0 stats_4.3.2 stats4_4.3.2
stringi_1.8.3 stringr_1.5.1 survival_3.5.7
sys_3.4.2 sysfonts_0.8.8 systemfonts_1.0.5
tcltk_4.3.2 tensor_1.5 tensorA_0.36.2.1
tensorflow_2.15.0 terra_1.7.71 testthat_3.2.1
text2vec_0.6.4 textshaping_0.3.7 tfautograph_0.3.2
tfruns_1.5.2 TH.data_1.1.2 threejs_0.3.3
tibble_3.2.1 tidycensus_1.6 tidygraph_1.3.1
tidyr_1.3.1 tidyselect_1.2.0 tigris_2.1
tikzDevice_0.12.6 timeDate_4032.109 timeSeries_4032.109
tinytex_0.49 titanic_0.1.0 TMB_1.9.10
tools_4.3.2 treemapify_2.5.6 TSP_1.2-4
TTR_0.24.4 tweenr_2.0.2 tzdb_0.4.0
ucminf_1.2.1 units_0.8.5 utf8_1.2.4
utils_4.3.2 uuid_1.2.0 V8_4.4.1
vcd_1.4-12 vctrs_0.6.5 venn_1.12
VGAM_1.1-9 vioplot_0.4.0 vipor_0.4.7
viridis_0.6.5 viridisLite_0.4.2 visNetwork_2.1.2
vroom_1.6.5 waldo_0.5.2 webshot2_0.1.1
websocket_1.4.1 whisker_0.4.1 withr_3.0.0
wk_0.9.1 xfun_0.41 xgboost_1.7.7.1
xml2_1.3.6 xtable_1.8.4 xts_0.13.2
yaml_2.3.8 yulab.utils_0.1.4 zeallot_0.1.0
zoo_1.8.13
BB_2019.10.1 beanplot_1.3.1 broom_1.0.5
car_3.1.2 coin_1.4.3 data.table_1.15.2
datasauRus_0.1.8 dbplyr_2.4.0 downlit_0.4.3
dplyr_1.1.4 DT_0.32 dunn.test_1.3.5
dygraphs_1.1.1.6 e1071_1.7.14 ECOSolveR_0.5.5
GA_3.2.4 ggalluvial_0.12.5 gganimate_1.0.9
ggbeeswarm_0.7.2 ggbump_0.1.99999 ggdensity_1.0.0
ggeffects_1.5.0 ggExtra_0.10.1 ggforce_0.4.2
ggfortify_0.4.16 ggmosaic_0.3.3 ggnewscale_0.4.10
ggplot2_3.5.0 ggraph_2.2.0 ggrepel_0.9.5
ggridges_0.5.6 ggsignif_0.6.4 ggstats_0.5.1
ggstream_0.1.0 ggthemes_5.1.0 ggTimeSeries_1.0.2
ggVennDiagram_1.5.2 ggwordcloud_0.6.1 gifski_1.12.0.2
gt_0.10.1 hexbin_1.28.3 HistData_0.9.1
jiebaR_0.11 kernlab_0.9.32 knitr_1.45
latticeExtra_0.6.30 lvplot_0.2.1 magick_2.8.3
maps_3.4.2 misc3d_0.9.1 nloptr_2.0.3
nomnoml_0.3.0 patchwork_1.2.0 pdftools_3.4.0
plot3D_1.4.1 plotly_4.10.4 pROC_1.18.5
purrr_1.0.2 pwr_1.3.0 quadprog_1.5.8
quantmod_0.4.26 ragg_1.2.7 ROI_1.0.1
ROI.plugin.ecos_1.0.2 ROI.plugin.glpk_1.0.0 ROI.plugin.nloptr_1.0.1
ROI.plugin.quadprog_1.0.1 ROI.plugin.scs_1.1.2 rootSolve_1.8.2.4
RSQLite_2.3.5 scs_3.2.4 showtext_0.9.7
spacyr_1.3.0 text2vec_0.6.4 tidygraph_1.3.1
tikzDevice_0.12.6 tinyplot_0.0.5.9000 titanic_0.1.0
treemapify_2.5.6 TSP_1.2.4 vcd_1.4.12
vioplot_0.4.0 visNetwork_2.1.2 webshot2_0.1.1
xml2_1.3.6 xts_0.13.2
```

</details>
2 changes: 1 addition & 1 deletion _quarto.yml
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Expand Up @@ -62,7 +62,7 @@ book:
chapters:
- analyze-network-data.qmd
- analyze-text-data.qmd
- analyze-survival-data.qmd
# - analyze-survival-data.qmd
- analyze-time-series-data.qmd
- part: "优化建模"
chapters:
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2 changes: 0 additions & 2 deletions index.qmd
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Expand Up @@ -35,8 +35,6 @@ xfun::session_info(packages = c(
"plotly", "lattice", "igraph", "tidygraph", "ggraph",
"dplyr", "purrr", "tidyr", "httr", "data.table",
"rsconnect", "knitr", "rmarkdown", "gt", "DT",
"mgcv", "glmnet", "lme4", "xgboost", "spaMM",
"sf", "stars", "terra", "INLA", "cmdstanr",
"showtext", "gifski", "tinytex", "magick"
), dependencies = FALSE)
```

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