update examples, vignettes, wiki, etc. to deal with change made to sample modules

[achubaty]

e.g., several examples in \dontrun{} blocks need to be updated to account for the changes made to sample module parameterization (see 9de8d4c44530b441dc3dddfedbe37a130547f186 for changes made)

[achubaty]

@eliotmcintire since stackName was added as a param for randomLandscapes, but not for caribou and fire, should I add it to those modules and remove the use of the global stackname?

[eliotmcintire]

Yes. We don't have a good mechanism for global variables yet. I know we have .globals, but it is not integrated into defineModule yet. So, we should remove any use of it for now.

[achubaty]

updated several pieces in the examples and vignettes in 316-defineEvent

[harryprince]

this example seems does not work.

# compare caching ... run once to create cache
system.time(outSim <- spades(Copy(mySim), cache = TRUE, notOlderThan = Sys.time()))

ERROR:

Error in .robustDigest(x, algo = algo, ...) : could not find symbol "objects" in environment of the generic function

sessionInfo:

R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] bindrcpp_0.2.2      RColorBrewer_1.1-2  raster_2.7-15      
 [4] sp_1.3-1            igraph_1.2.2        SpaDES.addins_0.1.1
 [7] SpaDES.tools_0.3.0  SpaDES.core_0.1.1   quickPlot_0.1.6    
[10] reproducible_0.2.6  SpaDES_2.0.2        rlang_0.3.1.9000   

loaded via a namespace (and not attached):
  [1] googledrive_0.1.3        colorspace_1.3-2        
  [3] fpCompare_0.2.2          class_7.3-14            
  [5] gdalUtils_2.0.1.14       rgdal_1.3-6             
  [7] fastdigest_0.6-3         rstudioapi_0.9.0        
  [9] remotes_2.0.2            bit64_0.9-7             
 [11] lubridate_1.7.4          codetools_0.2-15        
 [13] R.methodsS3_1.7.1        knitr_1.20              
 [15] jsonlite_1.6             gridBase_0.4-7          
 [17] R.oo_1.22.0              rgeos_0.4-2             
 [19] shiny_1.2.0              DiagrammeR_1.0.0        
 [21] readr_1.3.1.9000         compiler_3.4.3          
 [23] httr_1.4.0               backports_1.1.3         
 [25] assertthat_0.2.0         lazyeval_0.2.1.9000     
 [27] fasterize_1.0.0          later_0.7.5             
 [29] visNetwork_2.0.5         htmltools_0.3.6         
 [31] tools_3.4.3              gtable_0.2.0            
 [33] glue_1.3.0               dplyr_0.7.8             
 [35] fastmatch_1.1-0          Rcpp_1.0.0              
 [37] rgexf_0.15.3             iterators_1.0.9         
 [39] ffbase_0.12.7            DEoptim_2.2-4           
 [41] stringr_1.3.1            testthat_2.0.1          
 [43] mime_0.6                 miniUI_0.1.1.1          
 [45] devtools_1.13.6          XML_3.98-1.12           
 [47] MASS_7.3-47              scales_1.0.0            
 [49] hms_0.4.2.9001           promises_1.0.1          
 [51] flock_0.7                parallel_3.4.3          
 [53] yaml_2.2.0               curl_3.3                
 [55] memoise_1.1.0            gridExtra_2.3           
 [57] ggplot2_3.1.0.9000       downloader_0.4          
 [59] stringi_1.2.4            RSQLite_2.1.1           
 [61] Rook_1.1-1               versions_0.3            
 [63] archivist_2.3.2          foreach_1.4.4           
 [65] e1071_1.7-0.1            checkmate_1.8.5         
 [67] RandomFieldsUtils_0.3.25 boot_1.3-20             
 [69] pkgconfig_2.0.2          bitops_1.0-6            
 [71] lattice_0.20-35          purrr_0.2.5             
 [73] bindr_0.1.1              sf_0.7-2                
 [75] htmlwidgets_1.3          bit_1.1-14              
 [77] tidyselect_0.2.5         magrittr_1.5            
 [79] R6_2.3.0                 DBI_1.0.0.9001          
 [81] pillar_1.3.1             withr_2.1.2.9000        
 [83] units_0.6-2              RCurl_1.95-4.11         
 [85] tibble_2.0.1             crayon_1.3.4            
 [87] viridis_0.5.1            RandomFields_3.1.50     
 [89] grid_3.4.3               data.table_1.12.0       
 [91] blob_1.1.1               influenceR_0.1.0        
 [93] git2r_0.24.0             CircStats_0.2-6         
 [95] digest_0.6.18            classInt_0.3-1          
 [97] xtable_1.8-3             ff_2.2-14               
 [99] tidyr_0.8.2              httpuv_1.4.5.1          
[101] brew_1.0-6               R.utils_2.7.0           
[103] velox_0.2.0              munsell_0.5.0           
[105] viridisLite_0.3.0        tcltk_3.4.3  

[eliotmcintire]

@harryprince You have installed the development version of reproducible, but you have an old version of SpaDES.core. Please install the development version of SpaDES.core to go with your version of reproducible:

devtools::install_github("PredictiveEcology/SpaDES.core@development")