diff --git a/README.Rmd b/README.Rmd index 2d84b6c..e6881bd 100644 --- a/README.Rmd +++ b/README.Rmd @@ -37,6 +37,12 @@ a mindfulness intervention study. ## Installation +You can install the stable [CRAN version](https://cran.r-project.org/package=multimedia) with: + +``` r +install.packages("multimedia") +``` + You can install the development version from [GitHub](https://github.com/krisrs1128/multimedia) with: diff --git a/README.md b/README.md index 8d15dc1..664b16d 100644 --- a/README.md +++ b/README.md @@ -31,6 +31,11 @@ and survey responses in a mindfulness intervention study. ## Installation +You can install the stable [CRAN +version](https://cran.r-project.org/package=multimedia) with: + + install.packages("multimedia") + You can install the development version from [GitHub](https://github.com/krisrs1128/multimedia) with: @@ -106,22 +111,16 @@ are identical for the two indirect settings. direct_effect(model, exper) -
##   outcome indirect_setting
-## 1     PHQ          Control
-## 2     PHQ        Treatment
-##              contrast direct_effect
-## 1 Control - Treatment    0.09314376
-## 2 Control - Treatment    0.09314376
+
##   outcome indirect_setting            contrast direct_effect
+## 1     PHQ          Control Control - Treatment    0.09314376
+## 2     PHQ        Treatment Control - Treatment    0.09314376
 

 
     indirect_overall(model, exper)
 
-
##   outcome direct_setting            contrast
-## 1     PHQ        Control Control - Treatment
-## 2     PHQ      Treatment Control - Treatment
-##   indirect_effect
-## 1      0.02256029
-## 2      0.02256029
+
##   outcome direct_setting            contrast indirect_effect
+## 1     PHQ        Control Control - Treatment      0.02256029
+## 2     PHQ      Treatment Control - Treatment      0.02256029
 

 
 The package also includes helpers to visualize and perform inference on
@@ -146,12 +145,9 @@ model, which correctly recovers that the direct effects are 0.
         estimate(exper) |>
         direct_effect()
 
-
##   outcome indirect_setting
-## 1     PHQ          Control
-## 2     PHQ        Treatment
-##              contrast direct_effect
-## 1 Control - Treatment             0
-## 2 Control - Treatment             0
+
##   outcome indirect_setting            contrast direct_effect
+## 1     PHQ          Control Control - Treatment             0
+## 2     PHQ        Treatment Control - Treatment             0
 

 
 ## Help
@@ -177,137 +173,28 @@ We welcome questions and comments about the package either through
 ## tzcode source: internal
 ## 
 ## attached base packages:
-## [1] stats     graphics  grDevices utils    
-## [5] datasets  methods   base     
+## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] ggplot2_3.5.1     multimedia_0.2.0 
-## [3] tidyselect_1.2.1  ranger_0.16.0    
-## [5] glmnetUtils_1.1.9 brms_2.21.0      
-## [7] Rcpp_1.0.13      
+## [1] ggplot2_3.5.1     multimedia_0.2.0  tidyselect_1.2.1  ranger_0.16.0     glmnetUtils_1.1.9 brms_2.21.0       Rcpp_1.0.13      
 ## 
 ## loaded via a namespace (and not attached):
-##   [1] gridExtra_2.3              
-##   [2] inline_0.3.19              
-##   [3] permute_0.9-7              
-##   [4] sandwich_3.1-0             
-##   [5] rlang_1.1.4                
-##   [6] magrittr_2.0.3             
-##   [7] multcomp_1.4-26            
-##   [8] ade4_1.7-22                
-##   [9] matrixStats_1.4.1          
-##  [10] compiler_4.4.1             
-##  [11] mgcv_1.9-1                 
-##  [12] loo_2.8.0                  
-##  [13] vctrs_0.6.5                
-##  [14] reshape2_1.4.4             
-##  [15] stringr_1.5.1              
-##  [16] pkgconfig_2.0.3            
-##  [17] shape_1.4.6.1              
-##  [18] crayon_1.5.3               
-##  [19] fastmap_1.2.0              
-##  [20] backports_1.5.0            
-##  [21] XVector_0.45.0             
-##  [22] labeling_0.4.3             
-##  [23] utf8_1.2.4                 
-##  [24] rmarkdown_2.28             
-##  [25] UCSC.utils_1.1.0           
-##  [26] purrr_1.0.2                
-##  [27] xfun_0.47                  
-##  [28] glmnet_4.1-8               
-##  [29] zlibbioc_1.51.1            
-##  [30] GenomeInfoDb_1.41.1        
-##  [31] jsonlite_1.8.8             
-##  [32] progress_1.2.3             
-##  [33] biomformat_1.33.0          
-##  [34] highr_0.11                 
-##  [35] rhdf5filters_1.17.0        
-##  [36] DelayedArray_0.31.11       
-##  [37] Rhdf5lib_1.27.0            
-##  [38] prettyunits_1.2.0          
-##  [39] cluster_2.1.6              
-##  [40] parallel_4.4.1             
-##  [41] R6_2.5.1                   
-##  [42] stringi_1.8.4              
-##  [43] StanHeaders_2.32.10        
-##  [44] GenomicRanges_1.57.1       
-##  [45] estimability_1.5.1         
-##  [46] rstan_2.32.6               
-##  [47] SummarizedExperiment_1.35.1
-##  [48] iterators_1.0.14           
-##  [49] knitr_1.48                 
-##  [50] zoo_1.8-12                 
-##  [51] IRanges_2.39.2             
-##  [52] bayesplot_1.11.1           
-##  [53] igraph_2.0.3               
-##  [54] Matrix_1.7-0               
-##  [55] splines_4.4.1              
-##  [56] abind_1.4-5                
-##  [57] yaml_2.3.10                
-##  [58] vegan_2.6-8                
-##  [59] codetools_0.2-20           
-##  [60] curl_5.2.2                 
-##  [61] pkgbuild_1.4.4             
-##  [62] lattice_0.22-6             
-##  [63] tibble_3.2.1               
-##  [64] plyr_1.8.9                 
-##  [65] withr_3.0.1                
-##  [66] Biobase_2.65.1             
-##  [67] bridgesampling_1.1-2       
-##  [68] posterior_1.6.0            
-##  [69] coda_0.19-4.1              
-##  [70] evaluate_0.24.0            
-##  [71] survival_3.7-0             
-##  [72] RcppParallel_5.1.9         
-##  [73] Biostrings_2.73.1          
-##  [74] pillar_1.9.0               
-##  [75] phyloseq_1.49.0            
-##  [76] MatrixGenerics_1.17.0      
-##  [77] tensorA_0.36.2.1           
-##  [78] checkmate_2.3.2            
-##  [79] foreach_1.5.2              
-##  [80] stats4_4.4.1               
-##  [81] distributional_0.4.0       
-##  [82] generics_0.1.3             
-##  [83] hms_1.1.3                  
-##  [84] S4Vectors_0.43.2           
-##  [85] rstantools_2.4.0           
-##  [86] munsell_0.5.1              
-##  [87] scales_1.3.0               
-##  [88] xtable_1.8-4               
-##  [89] glue_1.7.0                 
-##  [90] emmeans_1.10.4             
-##  [91] tools_4.4.1                
-##  [92] data.table_1.16.0          
-##  [93] mvtnorm_1.3-1              
-##  [94] tidygraph_1.3.1            
-##  [95] rhdf5_2.49.0               
-##  [96] grid_4.4.1                 
-##  [97] tidyr_1.3.1                
-##  [98] ape_5.8                    
-##  [99] QuickJSR_1.3.1             
-## [100] miniLNM_0.1.0              
-## [101] colorspace_2.1-1           
-## [102] nlme_3.1-166               
-## [103] formula.tools_1.7.1        
-## [104] GenomeInfoDbData_1.2.12    
-## [105] patchwork_1.2.0            
-## [106] cli_3.6.3                  
-## [107] fansi_1.0.6                
-## [108] S4Arrays_1.5.7             
-## [109] Brobdingnag_1.2-9          
-## [110] dplyr_1.1.4                
-## [111] V8_5.0.0                   
-## [112] gtable_0.3.5               
-## [113] digest_0.6.37              
-## [114] operator.tools_1.6.3       
-## [115] BiocGenerics_0.51.1        
-## [116] SparseArray_1.5.31         
-## [117] TH.data_1.1-2              
-## [118] farver_2.1.2               
-## [119] multtest_2.61.0            
-## [120] htmltools_0.5.8.1          
-## [121] lifecycle_1.0.4            
-## [122] httr_1.4.7                 
-## [123] MASS_7.3-61
+##   [1] tensorA_0.36.2.1            jsonlite_1.8.8              shape_1.4.6.1               magrittr_2.0.3              TH.data_1.1-2               estimability_1.5.1          farver_2.1.2                rmarkdown_2.28             
+##   [9] fs_1.6.4                    zlibbioc_1.51.1             vctrs_0.6.5                 multtest_2.61.0             memoise_2.0.1               progress_1.2.3              htmltools_0.5.8.1           S4Arrays_1.5.7             
+##  [17] usethis_3.0.0               distributional_0.5.0        curl_5.2.2                  Rhdf5lib_1.27.0             SparseArray_1.5.31          rhdf5_2.49.0                StanHeaders_2.32.10         htmlwidgets_1.6.4          
+##  [25] plyr_1.8.9                  sandwich_3.1-0              emmeans_1.10.4              zoo_1.8-12                  cachem_1.1.0                igraph_2.0.3                mime_0.12                   lifecycle_1.0.4            
+##  [33] iterators_1.0.14            pkgconfig_2.0.3             Matrix_1.7-0                R6_2.5.1                    fastmap_1.2.0               GenomeInfoDbData_1.2.12     MatrixGenerics_1.17.0       shiny_1.9.1                
+##  [41] digest_0.6.37               colorspace_2.1-1            patchwork_1.3.0             S4Vectors_0.43.2            pkgload_1.4.0               miniLNM_0.1.0               GenomicRanges_1.57.1        vegan_2.6-8                
+##  [49] labeling_0.4.3              fansi_1.0.6                 mgcv_1.9-1                  httr_1.4.7                  abind_1.4-8                 compiler_4.4.1              remotes_2.5.0               withr_3.0.1                
+##  [57] backports_1.5.0             inline_0.3.19               highr_0.11                  QuickJSR_1.3.1              pkgbuild_1.4.4              MASS_7.3-61                 DelayedArray_0.31.11        sessioninfo_1.2.2          
+##  [65] biomformat_1.33.0           permute_0.9-7               loo_2.8.0                   tools_4.4.1                 ape_5.8                     httpuv_1.6.15               glue_1.7.0                  rhdf5filters_1.17.0        
+##  [73] nlme_3.1-166                promises_1.3.0              grid_4.4.1                  checkmate_2.3.2             cluster_2.1.6               reshape2_1.4.4              ade4_1.7-22                 generics_0.1.3             
+##  [81] operator.tools_1.6.3        gtable_0.3.5                formula.tools_1.7.1         tidyr_1.3.1                 hms_1.1.3                   data.table_1.16.0           tidygraph_1.3.1             utf8_1.2.4                 
+##  [89] XVector_0.45.0              BiocGenerics_0.51.1         foreach_1.5.2               pillar_1.9.0                stringr_1.5.1               posterior_1.6.0             later_1.3.2                 splines_4.4.1              
+##  [97] dplyr_1.1.4                 lattice_0.22-6              survival_3.7-0              Biostrings_2.73.1           miniUI_0.1.1.1              knitr_1.48                  gridExtra_2.3               V8_5.0.0                   
+## [105] phyloseq_1.49.0             IRanges_2.39.2              SummarizedExperiment_1.35.1 stats4_4.4.1                xfun_0.47                   bridgesampling_1.1-2        Biobase_2.65.1              devtools_2.4.5             
+## [113] matrixStats_1.4.1           rstan_2.32.6                stringi_1.8.4               UCSC.utils_1.1.0            yaml_2.3.10                 evaluate_0.24.0             codetools_0.2-20            tibble_3.2.1               
+## [121] cli_3.6.3                   RcppParallel_5.1.9          xtable_1.8-4                munsell_0.5.1               GenomeInfoDb_1.41.1         coda_0.19-4.1               parallel_4.4.1              rstantools_2.4.0           
+## [129] ellipsis_0.3.2              prettyunits_1.2.0           profvis_0.3.8               urlchecker_1.0.1            bayesplot_1.11.1            Brobdingnag_1.2-9           glmnet_4.1-8                mvtnorm_1.3-1              
+## [137] scales_1.3.0                purrr_1.0.2                 crayon_1.5.3                rlang_1.1.4                 multcomp_1.4-26