Updated bug in AIC calculation, and loaded missing package.

kgostic · Apr 1, 2019 · 03e663a · 03e663a
1 parent 46692a5
commit 03e663a
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Showing 8 changed files with 529 additions and 14 deletions.
diff --git a/.Rhistory b/.Rhistory
diff --git a/Full_analysis_script_revised_submission.R b/Full_analysis_script_revised_submission.R
@@ -18,6 +18,7 @@ setwd('~/Dropbox/R/Hamsters/') # Set working directory
 library(parallel)
 library(ggplot2)
 library(binom)
+library(RColorBrewer)
 library(gridExtra)
 library(reshape2)
 
@@ -641,7 +642,7 @@ ggsave(filename = figS1, plot = outplot, width = 5, height = 7, dpi = 'print', d
 AICcalc = function(n.pars, nll){
   2*n.pars+2*nll
 }
-AIC.basic.ham = AICcalc(n.pars = 2, nll = opt.pc.abraded.skin$value)
+AIC.basic.ham = AICcalc(n.pars = 2, nll = opt.pc.abraded.skin$objective)
 AIC.mixture.ham = AICcalc(n.pars = 3, nll = opt.aa.BB.abraded.skin$value)
 del.AIC.hamster = c(AIC.basic.ham, AIC.mixture.ham); del.AIC.hamster = del.AIC.hamster-min(del.AIC.hamster)
 del.AIC.hamster

diff --git a/code_outputs/sessionInfo.txt b/code_outputs/sessionInfo.txt
@@ -10,20 +10,22 @@ locale:
 [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
 
 attached base packages:
-[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     
+[1] parallel  stats     graphics  grDevices utils     datasets 
+[7] methods   base     
 
 other attached packages:
- [1] gridExtra_2.3      RColorBrewer_1.1-2 TailRank_3.2.1     oompaBase_3.2.6    binom_1.1-1        forcats_0.3.0      stringr_1.3.1     
- [8] dplyr_0.7.8        purrr_0.2.5        readr_1.3.1        tidyr_0.8.2        tibble_2.0.1       tidyverse_1.2.1    viridis_0.5.1     
-[15] viridisLite_0.3.0  bindrcpp_0.2.2     ggpubr_0.2         magrittr_1.5       reshape2_1.4.3     lubridate_1.7.4    reshape_0.8.8     
-[22] ggplot2_3.1.0     
+[1] RColorBrewer_1.1-2 reshape2_1.4.3     gridExtra_2.3     
+[4] binom_1.1-1        ggplot2_3.1.0     
 
 loaded via a namespace (and not attached):
- [1] tidyselect_0.2.5    haven_2.0.0         lattice_0.20-38     oompaData_3.1.1     colorspace_1.4-0    generics_0.0.2     
- [7] yaml_2.2.0          utf8_1.1.4          rlang_0.3.1         pillar_1.3.1        glue_1.3.0          withr_2.1.2        
-[13] BiocGenerics_0.26.0 modelr_0.1.2        readxl_1.2.0        audio_0.1-5.1       bindr_0.1.1         plyr_1.8.4         
-[19] munsell_0.5.0       gtable_0.2.0        cellranger_1.1.0    rvest_0.3.2         Biobase_2.40.0      labeling_0.3       
-[25] fansi_0.4.0         broom_0.5.1         Rcpp_1.0.0          scales_1.0.0        backports_1.1.3     jsonlite_1.6       
-[31] hms_0.4.2           digest_0.6.18       stringi_1.2.4       grid_3.5.0          cli_1.0.1           tools_3.5.0        
-[37] beepr_1.3           lazyeval_0.2.1      cluster_2.0.7-1     crayon_1.3.4        pkgconfig_2.0.2     xml2_1.2.0         
-[43] assertthat_0.2.0    httr_1.4.0          rstudioapi_0.9.0    R6_2.3.0            nlme_3.1-137        compiler_3.5.0     
+ [1] Rcpp_1.0.0       rstudioapi_0.9.0 bindr_0.1.1     
+ [4] magrittr_1.5     tidyselect_0.2.5 munsell_0.5.0   
+ [7] colorspace_1.4-0 R6_2.3.0         rlang_0.3.1     
+[10] stringr_1.3.1    plyr_1.8.4       dplyr_0.7.8     
+[13] tools_3.5.0      grid_3.5.0       gtable_0.2.0    
+[16] withr_2.1.2      digest_0.6.18    yaml_2.2.0      
+[19] lazyeval_0.2.1   assertthat_0.2.0 tibble_2.0.1    
+[22] crayon_1.3.4     bindrcpp_0.2.2   purrr_0.2.5     
+[25] glue_1.3.0       labeling_0.3     stringi_1.2.4   
+[28] compiler_3.5.0   pillar_1.3.1     scales_1.0.0    
+[31] pkgconfig_2.0.2 
diff --git a/manuscript_figures/Fig2_par_ests.pdf b/manuscript_figures/Fig2_par_ests.pdf
diff --git a/manuscript_figures/Fig3_model_fits.pdf b/manuscript_figures/Fig3_model_fits.pdf
diff --git a/manuscript_figures/Fig4_prob_inf_given_dose_and_route.pdf b/manuscript_figures/Fig4_prob_inf_given_dose_and_route.pdf
diff --git a/scratch_figures/Profiles_basic_model.pdf b/scratch_figures/Profiles_basic_model.pdf
diff --git a/scratch_figures/pI_profiles.pdf b/scratch_figures/pI_profiles.pdf