From 35a2f9cb9b7dbb7ebcd7b0c66e2964ae566c62ca Mon Sep 17 00:00:00 2001 From: XiangyunHuang Date: Thu, 1 Feb 2024 13:33:49 +0800 Subject: [PATCH] =?UTF-8?q?=E9=87=8D=E6=96=B0=E7=BB=84=E7=BB=87=EF=BC=8C?= =?UTF-8?q?=E5=B0=86=E7=A9=BA=E9=97=B4=E5=88=86=E6=9E=90=E7=9A=84=E9=83=A8?= =?UTF-8?q?=E5=88=86=E7=8B=AC=E7=AB=8B=E5=87=BA=E6=9D=A5?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.md | 273 +++++++++++++++++------------------ _quarto.yml | 2 + analyze-areal-data.qmd | 2 +- analyze-network-data.qmd | 2 +- analyze-point-pattern.qmd | 2 +- analyze-spatial-data.qmd | 2 +- analyze-survival-data.qmd | 2 +- analyze-text-data.qmd | 2 +- analyze-time-series-data.qmd | 2 +- index.qmd | 10 +- 10 files changed, 147 insertions(+), 152 deletions(-) diff --git a/README.md b/README.md index 8d34027b..c83ec0d8 100755 --- a/README.md +++ b/README.md @@ -107,168 +107,161 @@ quarto render 点击获取 R 包信息 ``` r -xfun::session_info(packages = .packages(TRUE), dependencies = FALSE) +pkg_dep <- desc::desc_get_deps() +pkg_dep <- pkg_dep[pkg_dep$type == "Imports", "package"] +xfun::session_info(packages = pkg_dep, dependencies = FALSE) ``` ``` R version 4.3.2 (2023-10-31) -Platform: x86_64-redhat-linux-gnu (64-bit) -Running under: Fedora Linux 39 (Container Image), RStudio 2023.9.1.494 +Platform: x86_64-apple-darwin20 (64-bit) +Running under: macOS Sonoma 14.3, RStudio 2023.12.1.402 -Locale: - LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 - LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 - LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C - LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C +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 ape_5.7.1 - AsioHeaders_1.22.1.2 askpass_1.2.0 backports_1.4.1 - base_4.3.2 base64enc_0.1.3 bayesplot_1.10.0 - BB_2019.10.1 beanplot_1.3.1 beeswarm_0.4.0 - BH_1.81.0.1 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_1.1.3 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_3.6.1 - clipr_0.8.0 cluster_2.1.6 cmdstanr_0.6.1 - coda_0.19.4 codetools_0.2.19 coin_1.4.3 - colorspace_2.1.0 colourpicker_1.3.0 commonmark_1.9.0 - compiler_4.3.2 config_0.3.2 CoprManager_0.5.5 - corpcor_1.6.10 corrplot_0.92 cowplot_1.1.1 + 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_5.1.0 cvar_0.5 - data.table_1.14.8 datasauRus_0.1.6 datasets_4.3.2 - DBI_1.1.3 dbplyr_2.4.0 deldir_2.0.2 - desc_1.4.2 dichromat_2.0.0.1 diffobj_0.3.5 - digest_0.6.33 distributional_0.3.2 docopt_0.7.1 + 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_0.30 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_0.999.8 fansi_1.0.6 + 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_0.5.77 fBasics_4032.96 fGarch_4031.90 - filehash_2.4.5 fmesher_0.1.4 fontawesome_0.5.2 - forcats_1.0.0 foreach_1.5.2 foreign_0.8.86 - Formula_1.2.5 FRK_2.2.0 fs_1.6.3 - future_1.33.0 GA_3.2.3 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_1.3.2 ggExtra_0.10.1 ggfittext_0.10.1 - ggforce_0.4.1 ggfortify_0.4.16 ggmosaic_0.3.3 - ggnewscale_0.4.9 ggplot2_3.4.4 ggpubr_0.6.0 - ggraph_2.1.0 ggrepel_0.9.4 ggridges_0.5.4 + 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 ggsurvfit_1.0.0 ggthemes_5.0.0 - ggTimeSeries_1.0.2 ggVennDiagram_1.2.3 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_1.6.2 - gmp_0.7.3 goftest_1.2.3 graphics_4.3.2 - graphlayouts_1.0.2 grDevices_4.3.2 grid_4.3.2 - 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lattice_0.22.5 latticeExtra_0.6.30 lavaan_0.6.16 - lazyeval_0.2.2 libcoin_1.0.10 lifecycle_1.0.4 - linprog_0.9.4 listenv_0.9.0 littler_0.3.18 - lme4_1.1.35.1 lmtest_0.9.40 loo_2.6.0 - lpSolve_5.6.19 lvplot_0.2.1 magic_1.6.1 - magick_2.8.1 magrittr_2.0.3 mapproj_1.2.11 - maps_3.4.1.1 markdown_1.12 MASS_7.3.60 - Matrix_1.6.4 MatrixModels_0.5.3 matrixStats_1.1.0 - mclogit_0.9.6 MCMCglmm_2.35 memisc_0.99.31.6 - memoise_2.0.1 methods_4.3.2 mgcv_1.9.0 + 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 mnormt_2.1.1 modeltools_0.2.23 - multcomp_1.4.25 munsell_0.5.0 mvtnorm_1.2.4 - 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sass_0.4.8 scales_1.3.0 scs_3.2.4 - selectr_0.4.2 sf_1.0.14 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_2.1.2 spacetime_1.3.1 - spam_2.10.0 spaMM_4.4.0 sparseinv_0.1.3 - SparseM_1.81 spatial_7.3.17 spatstat_3.0.7 - spatstat.data_3.0.3 spatstat.explore_3.2.5 spatstat.geom_3.2.7 + 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_2.1.44 splines_4.3.2 - stabledist_0.7.1 StanHeaders_2.32.2 stars_0.6.4 + 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_1.8.2 stringr_1.5.1 survival_3.5.7 + 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 - tensorflow_2.14.0 terra_1.7.55 testthat_3.2.1 - textshaping_0.3.7 tfautograph_0.3.2 tfruns_1.5.1 - TH.data_1.1.2 threejs_0.3.3 tibble_3.2.1 - tidycensus_1.5 tidygraph_1.2.3 tidyr_1.3.0 - tidyselect_1.2.0 tigris_2.0.4 tikzDevice_0.12.6 - timeDate_4022.108 timeSeries_4031.107 tinytex_0.49 - titanic_0.1.0 TMB_1.9.9 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_1.2.0 - units_0.8.5 utf8_1.2.4 utils_4.3.2 - uuid_1.1.1 V8_4.4.1 vcd_1.4.11 - vctrs_0.6.5 vegan_2.6.4 VGAM_1.1.9 - vioplot_0.4.0 vipor_0.4.5 viridis_0.6.4 - viridisLite_0.4.2 vroom_1.6.5 waldo_0.5.2 - webshot2_0.1.1 websocket_1.4.1 whisker_0.4.1 - withr_2.5.2 wk_0.9.1 xfun_0.41 - xgboost_1.7.6.1 xml2_1.3.6 xtable_1.8.4 - xts_0.13.1 yaml_2.3.7 yulab.utils_0.1.0 - zoo_1.8.12 - -Pandoc version: 3.1.9 - -LaTeX version used: - TeX Live 2023 with tlmgr 2023-03-08 + 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 ``` diff --git a/_quarto.yml b/_quarto.yml index 45209a30..357c7a07 100755 --- a/_quarto.yml +++ b/_quarto.yml @@ -64,6 +64,8 @@ book: - analyze-text-data.qmd - analyze-survival-data.qmd - analyze-time-series-data.qmd + - part: "空间分析" + chapters: - analyze-point-pattern.qmd - analyze-spatial-data.qmd - analyze-areal-data.qmd diff --git a/analyze-areal-data.qmd b/analyze-areal-data.qmd index c2074fd0..028f4501 100644 --- a/analyze-areal-data.qmd +++ b/analyze-areal-data.qmd @@ -1,4 +1,4 @@ -# 空间区域数据分析 {#sec-analyze-areal-data} +# 区域数据分析 {#sec-analyze-areal-data} ## 苏格兰唇癌数据分析 {#sec-scotland-lip-cancer} diff --git a/analyze-network-data.qmd b/analyze-network-data.qmd index 9442f6f1..a658bcb0 100755 --- a/analyze-network-data.qmd +++ b/analyze-network-data.qmd @@ -1,4 +1,4 @@ -# 网络分析 {#sec-analysis-network-data} +# 网络数据分析 {#sec-analysis-network-data} ```{r} #| echo: false diff --git a/analyze-point-pattern.qmd b/analyze-point-pattern.qmd index 14bd1d26..8c4c4da8 100644 --- a/analyze-point-pattern.qmd +++ b/analyze-point-pattern.qmd @@ -1,4 +1,4 @@ -# 空间点模式分析 {#sec-analyze-point-pattern} +# 点模式数据分析 {#sec-analyze-point-pattern} ```{r} #| echo: false diff --git a/analyze-spatial-data.qmd b/analyze-spatial-data.qmd index be31fef4..7d38fb37 100755 --- a/analyze-spatial-data.qmd +++ b/analyze-spatial-data.qmd @@ -1,4 +1,4 @@ -# 空间点参考数据分析 {#sec-nuclear-pollution-concentration} +# 点参考数据分析 {#sec-nuclear-pollution-concentration} ```{r} #| echo: false diff --git a/analyze-survival-data.qmd b/analyze-survival-data.qmd index 0c091b48..2bade1f6 100755 --- a/analyze-survival-data.qmd +++ b/analyze-survival-data.qmd @@ -1,4 +1,4 @@ -# 生存分析 {#sec-survival-analysis} +# 生存数据分析 {#sec-survival-analysis} > The fact that some people murder doesn't mean we should copy them. And murdering data, though not as serious, should also be avoided. > diff --git a/analyze-text-data.qmd b/analyze-text-data.qmd index e16c2abb..f95b63b1 100755 --- a/analyze-text-data.qmd +++ b/analyze-text-data.qmd @@ -1,4 +1,4 @@ -# 文本分析 {#sec-analysis-text-data} +# 文本数据分析 {#sec-analysis-text-data} ```{r} #| echo: false diff --git a/analyze-time-series-data.qmd b/analyze-time-series-data.qmd index 4e9e6c2c..d8a3dee6 100755 --- a/analyze-time-series-data.qmd +++ b/analyze-time-series-data.qmd @@ -1,4 +1,4 @@ -# 时序分析 {#sec-analyze-time-series-data} +# 时序数据分析 {#sec-analyze-time-series-data} 预测是非常古老的话题，几乎人人都想拥有预测未来的能力，唐朝袁天罡和李淳风的故事至今还广为流传。事实上，古时候只有至高无上的皇帝才可以去问钦天监了解星辰大海和国运命脉。时间序列数据的分析，以及根据分析得到的一般规律进行预测是经久不衰的命题。预测既包含一般规律指向的确定性，又有无法预知的不确定性，且**同时**包含认知局限带来的不确定性，后者往往更大。无休止地渴求往往伴随着巨大的挑战，而更大的挑战则是预测效果常常不能满足期待。 diff --git a/index.qmd b/index.qmd index 9312394d..38c0a2c1 100755 --- a/index.qmd +++ b/index.qmd @@ -29,11 +29,11 @@ CI <- identical(Sys.getenv("CI"), "true") #| message: false xfun::session_info(packages = c( - "ggplot2", "gganimate", "ggrepel", "ggraph", - "ggridges", "ggsignif", "ggforce", "ggdensity", - "ggbeeswarm", "ggeffects", "ggnewscale", - "patchwork", "shiny", "plotly", "lattice", - "dplyr", "purrr", "tidyr", "data.table", + "ggplot2", "gganimate", "ggrepel", "ggdensity", + "ggridges", "ggsignif", "ggforce", "ggbeeswarm", + "ggeffects", "ggnewscale", "patchwork", "shiny", + "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",