ready for Melanie check

CODE/SM.Rmd

@@ -1,13 +1,13 @@
 ---
 title: Supplementary Materials to Establishing the reliability and validity of measures extracted from long-form recordings
 output:
+  pdf_document:
+    toc: yes
+    toc_depth: 3
   html_document:
     toc: yes
     toc_depth: '3'
     df_print: paged
-  pdf_document:
-    toc: yes
-    toc_depth: 3
 ---
 
 ```{r setup, include=FALSE, eval=TRUE}
@@ -608,11 +608,19 @@ f_labels$age_bin<-factor(f_labels$age_bin,levels=age_levels)
 
 fig6 <- ggplot(df.icc.age, aes(y = icc_child_id, x = toupper(data_set))) +
   geom_violin(alpha = 0.5) +
-    stat_summary(fun = mean, geom = "point", aes(x = as.numeric(factor(toupper(data_set))) - 0.5), shape = 23, size = 3, fill = "white", color = "black", position = position_dodge(width = 0.75)) +
+#    stat_summary(fun = mean, geom = "point", aes(x = as.numeric(factor(toupper(data_set))) - 0.5), shape = 23, size = 3, fill = "white", color = "black", position = position_dodge(width = 0.75)) +
   geom_quasirandom(aes(colour = Type,shape = Type)) +  
   theme(legend.position="none") +labs( y = "r",x="Pipeline") + facet_wrap(~age_bin, ncol = 3) +
   geom_text(x=1.5,y=max(df.icc.age$icc_child_id,na.rm=T),aes(label=facet_labels_chi),data=f_labels,size=3) +
   geom_text(x=1.5,y=max(df.icc.age$icc_child_id,na.rm=T)*.95,aes(label=facet_labels_cor),data=f_labels,size=3) + 
+    stat_summary(fun = mean, geom = "point", aes(group = Type,x = as.numeric(factor(toupper(data_set))) + 0.5), shape = 1, size = 3, fill = "white", color = "black") +
+  stat_summary(
+    aes(group = Type, x = as.numeric(factor(toupper(data_set))) + 0.5, y = icc_child_id,color = Type, shape = Type), 
+    fun = mean, 
+    geom = "point", 
+    show.legend = FALSE,
+    inherit.aes = FALSE
+  ) +
   theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
 panel.background = element_blank(), legend.key=element_blank(), axis.line = element_line(colour = "black")) 
 

CODE/sessionInfo.txt

@@ -23,21 +23,20 @@ other attached packages:
 [13] lme4_1.1-33           Matrix_1.5-4         
 
 loaded via a namespace (and not attached):
- [1] beeswarm_0.4.0    gtable_0.3.3      xfun_0.39         bslib_0.5.0      
- [5] insight_0.19.7    rstatix_0.7.2     lattice_0.21-8    vctrs_0.6.4      
- [9] tools_4.3.0       generics_0.1.3    parallel_4.3.0    tibble_3.2.1     
-[13] fansi_1.0.4       highr_0.10        pkgconfig_2.0.3   webshot_0.5.5    
-[17] lifecycle_1.0.3   farver_2.1.1      compiler_4.3.0    textshaping_0.3.6
-[21] mnormt_2.1.1      munsell_0.5.0     vipor_0.4.7       htmltools_0.5.5  
-[25] sass_0.4.6        yaml_2.3.7        pillar_1.9.0      nloptr_2.0.3     
-[29] jquerylib_0.1.4   MASS_7.3-58.4     cachem_1.0.8      boot_1.3-28.1    
-[33] abind_1.4-5       nlme_3.1-162      tidyselect_1.2.0  rvest_1.0.3      
-[37] digest_0.6.31     stringi_1.7.12    purrr_1.0.2       labeling_0.4.2   
-[41] splines_4.3.0     cowplot_1.1.1     fastmap_1.1.1     grid_4.3.0       
-[45] colorspace_2.1-0  cli_3.6.1         magrittr_2.0.3    utf8_1.2.3       
-[49] broom_1.0.5       withr_2.5.0       scales_1.2.1      backports_1.4.1  
-[53] rmarkdown_2.23    httr_1.4.6        gridExtra_2.3     ggsignif_0.6.4   
-[57] ragg_1.2.5        evaluate_0.21     knitr_1.43        viridisLite_0.4.2
-[61] mgcv_1.8-42       rlang_1.1.1       Rcpp_1.0.11       glue_1.6.2       
-[65] xml2_1.3.5        svglite_2.1.1     rstudioapi_0.14   minqa_1.2.5      
-[69] jsonlite_1.8.7    R6_2.5.1          systemfonts_1.0.4
+ [1] beeswarm_0.4.0    gtable_0.3.3      xfun_0.39         insight_0.19.7   
+ [5] rstatix_0.7.2     lattice_0.21-8    vctrs_0.6.4       tools_4.3.0      
+ [9] generics_0.1.3    parallel_4.3.0    tibble_3.2.1      fansi_1.0.4      
+[13] highr_0.10        pkgconfig_2.0.3   webshot_0.5.5     lifecycle_1.0.3  
+[17] farver_2.1.1      compiler_4.3.0    textshaping_0.3.6 munsell_0.5.0    
+[21] mnormt_2.1.1      vipor_0.4.7       htmltools_0.5.5   yaml_2.3.7       
+[25] pillar_1.9.0      nloptr_2.0.3      MASS_7.3-58.4     boot_1.3-28.1    
+[29] abind_1.4-5       nlme_3.1-162      tidyselect_1.2.0  rvest_1.0.3      
+[33] digest_0.6.31     stringi_1.7.12    purrr_1.0.2       labeling_0.4.2   
+[37] splines_4.3.0     cowplot_1.1.1     fastmap_1.1.1     grid_4.3.0       
+[41] colorspace_2.1-0  cli_3.6.1         magrittr_2.0.3    utf8_1.2.3       
+[45] broom_1.0.5       withr_2.5.0       scales_1.2.1      backports_1.4.1  
+[49] rmarkdown_2.23    httr_1.4.6        gridExtra_2.3     ggsignif_0.6.4   
+[53] ragg_1.2.5        evaluate_0.21     knitr_1.43        viridisLite_0.4.2
+[57] mgcv_1.8-42       rlang_1.1.1       Rcpp_1.0.11       glue_1.6.2       
+[61] xml2_1.3.5        svglite_2.1.1     rstudioapi_0.14   minqa_1.2.5      
+[65] R6_2.5.1          systemfonts_1.0.4