final analyses

CODE/SM.Rmd

@@ -172,10 +172,10 @@ age_max_per_corpus = aggregate(data = mydat_aclew, age ~ experiment, function(ag
 
 age_r_per_corpus = paste(age_min_per_corpus,age_max_per_corpus,sep="-")
 
-experiments=c("bergelson", "cougar", "fausey-trio", "lucid","lyon", "quechua",  "warlaumont", "winnipeg")
-locations=c("Northeast US", "Northwest US", "Western US", "Northwest England", "Central France", "Highlands Bolivia", "Western US", "Western Canada")
+corpus=c("bergelson", "cougar", "fausey-trio", "lucid","lyon", "quechua",  "warlaumont", "winnipeg")
+location=c("Northeast US", "Northwest US", "Western US", "Northwest England", "Central France", "Highlands Bolivia", "Western US", "Western Canada")
 
-corpus_description=cbind(experiments,chi_per_corpus, rec_r_per_child, rec_per_corpus, dur_per_corpus, age_mean_per_corpus,age_r_per_corpus)
+corpus_description=cbind(corpus,location,chi_per_corpus, rec_r_per_child, rec_per_corpus, dur_per_corpus, age_mean_per_corpus,age_r_per_corpus)
 
 write.table(corpus_description, "../output/corpus_description.csv", sep='\t')
 
@@ -655,8 +655,36 @@ ggplot(r_X_corpus, aes(y = cor, x = corpusA)) +
   theme() +labs( y = "r",x="Corpus")
 ```
 
+## SM W: Code to reproduce text in the Discussion section
 
 
+```{r bias}
+
+urban<-rep(T,length(location))
+urban[grep("Bolivia",location)]<-F
+
+english<-rep(T,length(location))
+english[grep("Bolivia",location)]<-F
+english[grep("France",location)]<-F
+
+northam<-rep(T,length(location))
+northam[grep("Bolivia",location)]<-F
+northam[grep("France",location)]<-F
+northam[grep("England",location)]<-F
+
+bias_tab<-data.frame(cbind(chi_per_corpus, rec_per_corpus))
+bias_tab$chi_per_corpus<-bias_tab$chi_per_corpus/sum(bias_tab$chi_per_corpus)
+bias_tab$rec_per_corpus<-bias_tab$rec_per_corpus/sum(bias_tab$rec_per_corpus)
+
+
+```
+
+Our data draws mainly from urban (`r round(sum(bias_tab$rec_per_corpus[urban])*100)`% of recordings, `r round(sum(bias_tab$chi_per_corpus[urban])*100)`% of the children, `r round(sum(urban)/length(urban)*100)`% of the corpora), English-speaking settings (`r round(sum(bias_tab$rec_per_corpus[english])*100)`% of recordings, `r round(sum(bias_tab$chi_per_corpus[english])*100)`% of the children, `r round(sum(english)/length(english)*100)`% of the corpora), and almost exclusively from North America (`r round(sum(bias_tab$rec_per_corpus[northam])*100)`% of recordings, `r round(sum(bias_tab$chi_per_corpus[northam])*100)`% of the children, `r round(sum(northam)/length(northam)*100)`% of the corpora). 
+
+## SM X: Variability as a function of hardware
+
+Another potential negative contribution to reliability that is currently not discussed is variability in the experimental setup. In a corpus collected in the Solomon Islands, children were wearing two recorders simultaneously. These were USB devices, sourced from two different providers. In this dataset, the duration of the recordings could be very different within the same pair (a ~10% difference was not atypical), which means that what is actually recorded is somewhat random in itself. Even comparing identical audio ranges covered by both recordings of each pair, the corresponding ACLEW metrics differed slightly; they were strongly correlated (R^2 was close to 0.95) but not perfectly correlated. This suggests that randomness in the recorders properties and their placement may also contribute to a decrease reliability. This reliability is importantly not at all due to changing underlying conditions, as both recorders picked up on the exact same day, so it is not due to variability in underlying behaviors. It is also not due to algorithmic variation because ACLEW algorithms are deterministic. Thus, this variability is only due to hardware differences and potentially also differences in e.g. USB placement.
+
 ## Save information about packages used
 
 ```{r}

CODE/SM.log

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CODE/sessionInfo.txt

@@ -1,43 +1,39 @@
-R version 4.3.1 (2023-06-16)
-Platform: x86_64-apple-darwin20 (64-bit)
-Running under: macOS Ventura 13.3.1
+R version 4.2.0 (2022-04-22)
+Platform: x86_64-apple-darwin17.0 (64-bit)
+Running under: macOS Big Sur/Monterey 10.16
 
 Matrix products: default
-BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
-LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
+BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
+LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
 
 locale:
 [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
 
-time zone: Europe/Paris
-tzcode source: internal
-
 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
- [1] ggbeeswarm_0.7.2      car_3.1-2             carData_3.0-5        
- [4] stringr_1.5.0         tidyr_1.3.0           dplyr_1.1.2          
- [7] psych_2.3.6           kableExtra_1.3.4.9000 ggpubr_0.6.0         
-[10] ggthemes_4.2.4        ggplot2_3.4.2         performance_0.10.4   
-[13] lme4_1.1-34           Matrix_1.6-0         
+ [1] ggbeeswarm_0.7.1  car_3.1-1         carData_3.0-5     stringr_1.5.0    
+ [5] tidyr_1.2.1       dplyr_1.0.10      psych_2.2.9       kableExtra_1.3.4 
+ [9] ggpubr_0.5.0      ggthemes_4.2.4    ggplot2_3.4.0     performance_0.9.0
+[13] lme4_1.1-31       Matrix_1.5-3     
 
 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_0.19.3    rstatix_0.7.2     lattice_0.21-8    vctrs_0.6.3      
- [9] tools_4.3.1       generics_0.1.3    parallel_4.3.1    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_4.3.1    mnormt_2.1.1     
-[21] munsell_0.5.0     vipor_0.4.5       htmltools_0.5.5   sass_0.4.7       
-[25] yaml_2.3.7        pillar_1.9.0      nloptr_2.0.3      jquerylib_0.1.4  
-[29] MASS_7.3-60       cachem_1.0.8      boot_1.3-28.1     abind_1.4-5      
-[33] nlme_3.1-162      tidyselect_1.2.0  rvest_1.0.3       digest_0.6.33    
-[37] stringi_1.7.12    purrr_1.0.1       labeling_0.4.2    splines_4.3.1    
-[41] cowplot_1.1.1     fastmap_1.1.1     grid_4.3.1        colorspace_2.1-0 
-[45] cli_3.6.1         magrittr_2.0.3    utf8_1.2.3        broom_1.0.5      
-[49] withr_2.5.0       scales_1.2.1      backports_1.4.1   rmarkdown_2.23   
-[53] httr_1.4.6        gridExtra_2.3     ggsignif_0.6.4    evaluate_0.21    
-[57] knitr_1.43        viridisLite_0.4.2 mgcv_1.8-42       rlang_1.1.1      
-[61] Rcpp_1.0.11       glue_1.6.2        xml2_1.3.5        svglite_2.1.1    
-[65] rstudioapi_0.15.0 minqa_1.2.5       jsonlite_1.8.7    R6_2.5.1         
-[69] systemfonts_1.0.4
+ [1] httr_1.4.4        sass_0.4.4        jsonlite_1.8.4    viridisLite_0.4.1
+ [5] splines_4.2.0     bslib_0.4.2       assertthat_0.2.1  highr_0.10       
+ [9] vipor_0.4.5       yaml_2.3.6        pillar_1.8.1      backports_1.4.1  
+[13] lattice_0.20-45   glue_1.6.2        digest_0.6.31     ggsignif_0.6.4   
+[17] rvest_1.0.3       minqa_1.2.5       colorspace_2.0-3  cowplot_1.1.1    
+[21] htmltools_0.5.4   pkgconfig_2.0.3   broom_1.0.2       purrr_1.0.0      
+[25] scales_1.2.1      webshot_0.5.4     svglite_2.1.0     tibble_3.1.8     
+[29] mgcv_1.8-40       generics_0.1.3    farver_2.1.1      cachem_1.0.6     
+[33] withr_2.5.0       cli_3.5.0         mnormt_2.1.1      magrittr_2.0.3   
+[37] evaluate_0.19     fansi_1.0.3       nlme_3.1-157      MASS_7.3-56      
+[41] rstatix_0.7.1     xml2_1.3.3        beeswarm_0.4.0    tools_4.2.0      
+[45] lifecycle_1.0.3   munsell_0.5.0     compiler_4.2.0    jquerylib_0.1.4  
+[49] systemfonts_1.0.4 rlang_1.0.6       grid_4.2.0        nloptr_2.0.3     
+[53] rstudioapi_0.14   labeling_0.4.2    rmarkdown_2.19    boot_1.3-28      
+[57] gtable_0.3.1      abind_1.4-5       DBI_1.1.2         R6_2.5.1         
+[61] gridExtra_2.3     knitr_1.41        fastmap_1.1.0     utf8_1.2.2       
+[65] insight_0.17.1    stringi_1.7.8     parallel_4.2.0    Rcpp_1.0.9       
+[69] vctrs_0.5.1       tidyselect_1.2.0  xfun_0.36        

OUTPUT/corpus_description.csv

@@ -1,9 +1,9 @@
-"experiments"	"chi_per_corpus"	"rec_r_per_child"	"rec_per_corpus"	"dur_per_corpus"	"age_mean_per_corpus"	"age_r_per_corpus"
-"1"	"bergelson"	"44"	"10-12"	"522"	"14"	"11.2"	"6-17"
-"2"	"cougar"	"26"	"3-45"	"239"	"11.1"	"26.6"	"0-59"
-"3"	"fausey-trio"	"28"	"3-3"	"84"	"13.7"	"8.9"	"6-12"
-"4"	"lucid"	"35"	"4-7"	"235"	"15.4"	"20"	"10-31"
-"5"	"lyon"	"16"	"3-6"	"54"	"14.1"	"19.6"	"2-41"
-"6"	"quechua"	"20"	"2-3"	"48"	"12.5"	"37.6"	"9-78"
-"7"	"warlaumont"	"13"	"2-4"	"38"	"12.5"	"6.3"	"2-18"
-"8"	"winnipeg"	"9"	"2-5"	"34"	"9.1"	"14.5"	"2-33"
+"corpus"	"location"	"chi_per_corpus"	"rec_r_per_child"	"rec_per_corpus"	"dur_per_corpus"	"age_mean_per_corpus"	"age_r_per_corpus"
+"1"	"bergelson"	"Northeast US"	"44"	"10-12"	"522"	"14"	"11.2"	"6-17"
+"2"	"cougar"	"Northwest US"	"26"	"3-45"	"239"	"11.1"	"26.6"	"0-59"
+"3"	"fausey-trio"	"Western US"	"28"	"3-3"	"84"	"13.7"	"8.9"	"6-12"
+"4"	"lucid"	"Northwest England"	"35"	"4-7"	"235"	"15.4"	"20"	"10-31"
+"5"	"lyon"	"Central France"	"16"	"3-6"	"54"	"14.1"	"19.6"	"2-41"
+"6"	"quechua"	"Highlands Bolivia"	"20"	"2-3"	"48"	"12.5"	"37.6"	"9-78"
+"7"	"warlaumont"	"Western US"	"13"	"2-4"	"38"	"12.5"	"6.3"	"2-18"
+"8"	"winnipeg"	"Western Canada"	"9"	"2-5"	"34"	"9.1"	"14.5"	"2-33"