From 2bee57fcd32bd9c4c8ee5f34036945be7533538b Mon Sep 17 00:00:00 2001 From: Xiangyun Huang Date: Mon, 4 Mar 2024 12:51:02 +0800 Subject: [PATCH] R 4.3.3 (#140) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 移除 xgboost INLA 等包 * follow up * 不编译生存分析 * add glmnet --- .github/workflows/quarto-book-macos.yaml | 2 +- .github/workflows/quarto-book-ubuntu.yaml | 2 +- DESCRIPTION | 3 +- README.md | 175 ++++------------------ _quarto.yml | 2 +- index.qmd | 2 - 6 files changed, 36 insertions(+), 150 deletions(-) diff --git a/.github/workflows/quarto-book-macos.yaml b/.github/workflows/quarto-book-macos.yaml index 9d09348d..4f6dad30 100644 --- a/.github/workflows/quarto-book-macos.yaml +++ b/.github/workflows/quarto-book-macos.yaml @@ -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 diff --git a/.github/workflows/quarto-book-ubuntu.yaml b/.github/workflows/quarto-book-ubuntu.yaml index c59656c4..faf139be 100644 --- a/.github/workflows/quarto-book-ubuntu.yaml +++ b/.github/workflows/quarto-book-ubuntu.yaml @@ -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 diff --git a/DESCRIPTION b/DESCRIPTION index 2bea9706..3ee21ce1 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -50,6 +50,7 @@ Imports: ggTimeSeries, ggVennDiagram, ggwordcloud, + glmnet, gt (>= 0.10.1), hexbin, HistData, @@ -104,7 +105,7 @@ Suggests: 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 diff --git a/README.md b/README.md index 35cc3c25..7fd6ae60 100755 --- a/README.md +++ b/README.md @@ -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 ``` diff --git a/_quarto.yml b/_quarto.yml index f688e606..80470ef1 100755 --- a/_quarto.yml +++ b/_quarto.yml @@ -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: diff --git a/index.qmd b/index.qmd index 38c0a2c1..33b21dd8 100755 --- a/index.qmd +++ b/index.qmd @@ -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) ```