Date: 2023-09-27 17:53:44
Author: T.Gibson
Run Name: Sim_1


The sensitivity of each parameter within the NIS-intro-detect-sim script is tested and reported.

Three scenarios for site surveillance to detect non indigenous species (NIS) introduction are presented and the time to detection is reported.


Input Parameters

##           Parameter Name Input Value
## 1                   user    T.Gibson
## 2               run_name       Sim_1
## 3                   seed        2022
## 4                num_sim        1000
## 5              num_years          30
## 6              num_sites         100
## 7         establish_risk exponential
## 8             intro_risk exponential
## 9         establish_prob         0.8
## 10            intro_prob         0.8
## 11       mean_visit_rate           1
## 12        detect_dynamic    constant
## 13              det_prob         0.8
## 14          det_prob_min           0
## 15          det_prob_max           1
## 16                seed_n           1
## 17        detect_summary        last
## 18             start_pop           1
## 19         start_possion           F
## 20                 pop_R           2
## 21          growth_model exponential
## 22               pop_cap         500
## 23                  APrb          10
## 24       Abund_Threshold        1000
## 25            Prob_Below         0.1
## 26            Prob_Above         0.8
## 27  sensitivity_analysis        TRUE
## 28   elasticity_analysis        TRUE
## 29 elasticity_proportion        0.25
## 30              defaults     default
## 31              defaults         100
## 32              defaults          30
## 33              defaults exponential
## 34              defaults         0.8
## 35              defaults         0.8
## 36              defaults exponential
## 37              defaults           1
## 38              defaults         0.8
## 39              defaults         0.9
## 40              defaults           1
## 41              defaults         0.1
## 42              defaults    constant
## 43              defaults           1
## 44              defaults           1
## 45              defaults           1
## 46              defaults           F
## 47              defaults           2
## 48              defaults exponential
## 49              defaults         500
## 50              defaults          10
## 51              defaults        1000
## 52              defaults         0.1
## 53              defaults         0.8


Default Sensitivity Parameters

The default parameters used for each run were as follows:

##      name num_sites num_years establish_risk establish_prob intro_prob  intro_risk
## 1 default       100        30    exponential            0.8        0.8 exponential
##   mean_visit_rate p_detection max_p_detect min_p_detect detect_dynamic seed_n start_pop
## 1               1         0.8          0.9          0.1       constant      1         1
##   start_possion pop_R growth_model pop_cap APrb Abund_Threshold Prob_Below Prob_Above
## 1             F     2  exponential     500   10            1000        0.1        0.8


Input Sensitivity Parameters

The ranges and intervals used to produce different values for each of the parameters used in the sensitivity test.

##                  min max interval
## seed_n             0 100       10
## num_sites         50 200       25
## num_years         10  50        5
## mean_visit_rate 0.25   4     0.25
## p_detection      0.1   1      0.1
## establish_prob   0.1   1      0.1


Sensivity Analysis

## Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
## ℹ Please use the `fun` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
## [[1]]
## [[1]]$seed_n

## 
## [[1]]$num_sites

## 
## [[1]]$num_years

## 
## [[1]]$mean_visit_rate
## Warning: Removed 2 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 2 rows containing non-finite values (`stat_summary()`).

## 
## [[1]]$p_detection
## Warning: Removed 46 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 46 rows containing non-finite values (`stat_summary()`).

## 
## [[1]]$establish_prob

## 
## 
## [[2]]
## [[2]]$seed_n
## Warning: Removed 143 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 143 rows containing non-finite values (`stat_summary()`).

## 
## [[2]]$num_sites
## Warning: Removed 11 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 11 rows containing non-finite values (`stat_summary()`).

## 
## [[2]]$num_years
## Warning: Removed 55 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 55 rows containing non-finite values (`stat_summary()`).

## 
## [[2]]$mean_visit_rate
## Warning: Removed 53 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 53 rows containing non-finite values (`stat_summary()`).

## 
## [[2]]$p_detection
## Warning: Removed 141 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 141 rows containing non-finite values (`stat_summary()`).

## 
## [[2]]$establish_prob
## Warning: Removed 11 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 11 rows containing non-finite values (`stat_summary()`).

## 
## 
## [[3]]
## [[3]]$seed_n
## Warning: Removed 6898 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 6898 rows containing non-finite values (`stat_summary()`).

## 
## [[3]]$num_sites
## Warning: Removed 1250 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 1250 rows containing non-finite values (`stat_summary()`).

## 
## [[3]]$num_years
## Warning: Removed 1733 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 1733 rows containing non-finite values (`stat_summary()`).

## 
## [[3]]$mean_visit_rate
## Warning: Removed 2114 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 2114 rows containing non-finite values (`stat_summary()`).

## 
## [[3]]$p_detection
## Warning: Removed 2459 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 2459 rows containing non-finite values (`stat_summary()`).

## 
## [[3]]$establish_prob
## Warning: Removed 932 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 932 rows containing non-finite values (`stat_summary()`).

Version

The version (sha) of https://github.com/CefasRepRes/NIS-intro-detect-sim repository used was: b1896dcafd5261fe804ef0018c4c7680fcfbab6c

## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19043)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
## [3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
## [5] LC_TIME=English_United Kingdom.utf8    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] dplyr_1.1.2       data.table_1.14.8 ReIns_1.0.12      EnvStats_2.7.0   
##  [5] patchwork_1.1.2   ggplot2_3.4.2     gtools_3.9.4      reshape2_1.4.4   
##  [9] truncnorm_1.0-9   here_1.0.1        yaml_2.3.7       
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.2.0  xfun_0.39         bslib_0.5.0       splines_4.2.2    
##  [5] lattice_0.20-45   colorspace_2.1-0  vctrs_0.6.2       generics_0.1.3   
##  [9] htmltools_0.5.5   utf8_1.2.3        survival_3.4-0    rlang_1.1.1      
## [13] pillar_1.9.0      jquerylib_0.1.4   glue_1.6.2        withr_2.5.0      
## [17] foreach_1.5.2     lifecycle_1.0.3   plyr_1.8.8        stringr_1.5.0    
## [21] munsell_0.5.0     gtable_0.3.3      codetools_0.2-18  evaluate_0.21    
## [25] labeling_0.4.2    knitr_1.43        fastmap_1.1.1     doParallel_1.0.17
## [29] parallel_4.2.2    fansi_1.0.4       highr_0.10        Rcpp_1.0.10      
## [33] scales_1.2.1      cachem_1.0.8      jsonlite_1.8.5    farver_2.1.1     
## [37] digest_0.6.31     stringi_1.7.12    grid_4.2.2        rprojroot_2.0.3  
## [41] cli_3.6.1         tools_4.2.2       magrittr_2.0.3    sass_0.4.6       
## [45] tibble_3.2.1      crayon_1.5.2      pkgconfig_2.0.3   Matrix_1.5-1     
## [49] rmarkdown_2.22    rstudioapi_0.14   iterators_1.0.14  R6_2.5.1         
## [53] compiler_4.2.2