Random forest acoustic space budgies 2019

Data description

## [1] "Round 2"

## [1] 0.00657707

## [1] "Round 3"

## [1] 0.00596853

Variable importance

The relative contribution of each acoustic parameter to the random forest predictive model (only the 15 parameters with the highest contribution are shown)

Acoustic space plots with spectros

These plots show the acoustic space covered by each individual in 2 ways: - Using dots to show the position of each of its calls in the acoustic space - Using kernels to display the density of calls in acoustic space regions

Both plot types are shown consecutively for each individual for comparison.

Acoustic space overlap by treatment

Graphs show the overlap between the acoustic space of week 3 vs week 1 (violin plot and boxplot show the same data):

Session information

## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.2 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=es_CR.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=es_CR.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=es_CR.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=es_CR.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] compiler  parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] lmerTest_3.1-0      sjstats_0.17.5      MuMIn_1.43.6       
##  [4] cowplot_0.9.4       raster_2.8-19       spatstat_1.59-0    
##  [7] rpart_4.1-15        spatstat.data_1.4-0 adehabitatHR_0.4.16
## [10] adehabitatLT_0.3.24 CircStats_0.2-6     boot_1.3-22        
## [13] MASS_7.3-51.4       adehabitatMA_0.3.13 deldir_0.1-16      
## [16] kableExtra_1.1.0    corrplot_0.84       randomForest_4.6-14
## [19] caret_6.0-84        pbapply_1.4-0       smacof_1.10-8      
## [22] plotrix_3.7-5       Hmisc_4.2-0         Formula_1.2-3      
## [25] survival_2.44-1.1   lme4_1.1-21         Matrix_1.2-17      
## [28] ecodist_2.0.1       nlme_3.1-139        AICcmodavg_2.2-2   
## [31] vegan_2.5-5         lattice_0.20-38     permute_0.9-5      
## [34] fossil_0.3.7        shapefiles_0.7      foreign_0.8-71     
## [37] sp_1.3-1            ade4_1.7-13         ggplot2_3.1.1      
## [40] RColorBrewer_1.1-2  readxl_1.3.1        warbleR_1.1.16     
## [43] NatureSounds_1.0.1  seewave_2.1.3       tuneR_1.3.3        
## [46] maps_3.3.0         
## 
## loaded via a namespace (and not attached):
##   [1] tidyselect_0.2.5      fftw_1.0-5            htmlwidgets_1.3      
##   [4] grid_3.6.0            munsell_0.5.0         codetools_0.2-16     
##   [7] withr_2.1.2           colorspace_1.4-1      knitr_1.23           
##  [10] rstudioapi_0.10       stats4_3.6.0          dtw_1.20-1           
##  [13] tensor_1.5            labeling_0.3          emmeans_1.3.5        
##  [16] polyclip_1.10-0       coda_0.19-2           generics_0.0.2       
##  [19] ipred_0.9-9           xfun_0.7              R6_2.4.0             
##  [22] VGAM_1.1-1            bitops_1.0-6          spatstat.utils_1.13-0
##  [25] assertthat_0.2.1      scales_1.0.0          nnet_7.3-12          
##  [28] gtable_0.3.0          goftest_1.1-1         weights_1.0          
##  [31] timeDate_3043.102     rlang_0.3.4           splines_3.6.0        
##  [34] lazyeval_0.2.2        ModelMetrics_1.2.2    acepack_1.4.1        
##  [37] wordcloud_2.6         broom_0.5.2           checkmate_1.9.3      
##  [40] yaml_2.2.0            reshape2_1.4.3        abind_1.4-5          
##  [43] modelr_0.1.4          unmarked_0.12-3       backports_1.1.4      
##  [46] tools_3.6.0           lava_1.6.5            proxy_0.4-23         
##  [49] polynom_1.4-0         Rcpp_1.0.1            plyr_1.8.4           
##  [52] base64enc_0.1-3       purrr_0.3.2           RCurl_1.95-4.12      
##  [55] haven_2.1.0           cluster_2.0.8         magrittr_1.5         
##  [58] data.table_1.12.2     openxlsx_4.1.0        mvtnorm_1.0-10       
##  [61] mitml_0.3-7           sjmisc_2.8.1          hms_0.4.2            
##  [64] evaluate_0.14         xtable_1.8-4          rio_0.5.16           
##  [67] jpeg_0.1-8            soundgen_1.4.0        gridExtra_2.3        
##  [70] ellipse_0.4.1         tibble_2.1.1          mice_3.4.0           
##  [73] crayon_1.3.4          minqa_1.2.4           htmltools_0.3.6      
##  [76] mgcv_1.8-28           tidyr_0.8.3           lubridate_1.7.4      
##  [79] sjlabelled_1.1.0      car_3.0-2             readr_1.3.1          
##  [82] heplots_1.3-5         gdata_2.18.0          insight_0.3.0        
##  [85] pan_1.6               gower_0.2.0           forcats_0.4.0        
##  [88] pkgconfig_2.0.2       numDeriv_2016.8-1     signal_0.7-6         
##  [91] recipes_0.1.5         xml2_1.2.0            foreach_1.4.4        
##  [94] webshot_0.5.1         estimability_1.3      prodlim_2018.04.18   
##  [97] rvest_0.3.3           stringr_1.4.0         digest_0.6.19        
## [100] pracma_2.2.5          rmarkdown_1.13        cellranger_1.1.0     
## [103] htmlTable_1.13.1      Deriv_3.8.5           curl_3.3             
## [106] gtools_3.8.1          jomo_2.6-7            rjson_0.2.20         
## [109] nloptr_1.2.1          carData_3.0-2         Sim.DiffProc_4.3     
## [112] viridisLite_0.3.0     pillar_1.4.0          httr_1.4.0           
## [115] glue_1.3.1            bayestestR_0.2.0      zip_2.0.2            
## [118] iterators_1.0.10      candisc_0.8-0         class_7.3-15         
## [121] stringi_1.4.3         performance_0.2.0     nnls_1.4             
## [124] latticeExtra_0.6-28   dplyr_0.8.0.1