Date: 2023-10-16 17:53:43
Author: T.Gibson
Run Name: Sim_1
The elasticity of each parameter within the NIS-intro-detect-sim script is tested and reported. Elasticity analysis is a method of comparing the sensitivity of each parameter where there is no scale in differences between parameters.
Three scenarios for site surveillance to detect non indigenous species (NIS) introduction are presented and the time to detection is reported.
A. Random surveillance, where sites are visited at an equal rate independent of the risk of NIS introduction and establishment at each site.
B. Risk-based surveillance, where sites with a higher probability of NIS introduction and establishment are visited at a higher visit rate due to their elevated risk.
C. Heavy risk-based surveillance, where sites with higher probability of NIS introduction and establishment form the main focus of surveillance programmes and are visited at a substantially higher visit rate due to their elevated risk.
The default parameters used for each run were as follows:
## Parameter Name Input Value
## 1 name default
## 2 num_sites 100
## 3 num_years 30
## 4 establish_risk exponential
## 5 establish_prob 0.8
## 6 intro_prob 0.8
## 7 intro_risk exponential
## 8 mean_visit_rate 1
## 9 p_detection 0.8
## 10 max_p_detect 1
## 11 max_p_detect_elas 1
## 12 min_p_detect 0.1
## 13 detect_dynamic constant
## 14 seed_n 1
## 15 seed_n_elasticity 1
## 16 start_pop 1
## 17 start_possion F
## 18 pop_R 2
## 19 growth_model exponential
## 20 pop_cap 500
## 21 APrb 10
## 22 Abund_Threshold 1000
## 23 Prob_Below 0.1
## 24 Prob_Above 0.8
The following input parameters (num_sites, num_years, mean_visit_rate, p_detection) are increased and decreased by 0.25 to determine whether the parameter is elastic. An elasticity value > 1 indicates elasticity. An elasticity value between 0 and 1 is inelastic.
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The version (sha) of https://github.com/CefasRepRes/NIS-intro-detect-sim repository used was: 258f4915f50668b7331476970d16316401077ccf
## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19043)
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## Matrix products: default
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods
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## other attached packages:
## [1] dplyr_1.1.2 data.table_1.14.8 ReIns_1.0.12
## [4] EnvStats_2.7.0 patchwork_1.1.2 ggplot2_3.4.2
## [7] gtools_3.9.4 reshape2_1.4.4 truncnorm_1.0-9
## [10] here_1.0.1 yaml_2.3.7
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## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.0 xfun_0.39 bslib_0.5.0
## [4] splines_4.2.2 lattice_0.20-45 colorspace_2.1-0
## [7] vctrs_0.6.2 generics_0.1.3 htmltools_0.5.5
## [10] 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
## [16] withr_2.5.0 foreach_1.5.2 lifecycle_1.0.3
## [19] plyr_1.8.8 stringr_1.5.0 munsell_0.5.0
## [22] gtable_0.3.3 codetools_0.2-18 evaluate_0.21
## [25] labeling_0.4.2 knitr_1.43 fastmap_1.1.1
## [28] doParallel_1.0.17 parallel_4.2.2 fansi_1.0.4
## [31] highr_0.10 Rcpp_1.0.10 scales_1.2.1
## [34] cachem_1.0.8 jsonlite_1.8.5 farver_2.1.1
## [37] digest_0.6.31 stringi_1.7.12 cowplot_1.1.1
## [40] grid_4.2.2 rprojroot_2.0.3 cli_3.6.1
## [43] tools_4.2.2 magrittr_2.0.3 sass_0.4.6
## [46] tibble_3.2.1 crayon_1.5.2 pkgconfig_2.0.3
## [49] Matrix_1.5-1 rmarkdown_2.22 rstudioapi_0.14
## [52] iterators_1.0.14 R6_2.5.1 compiler_4.2.2