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.
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.
## 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
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
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
## 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()`).
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