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sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
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## Matrix products: default
## BLAS:   /opt/microsoft/ropen/4.0.2/lib64/R/lib/libRblas.so
## LAPACK: /opt/microsoft/ropen/4.0.2/lib64/R/lib/libRlapack.so
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## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
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## other attached packages:
## [1] RevoUtils_11.0.2     RevoUtilsMath_11.0.0
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## loaded via a namespace (and not attached):
##  [1] bookdown_0.20     digest_0.6.27     magrittr_2.0.1    evaluate_0.14    
##  [5] highr_0.8         rlang_0.4.10      stringi_1.5.3     rstudioapi_0.13  
##  [9] rmarkdown_2.6     tools_4.0.2       stringr_1.4.0     xfun_0.21        
## [13] yaml_2.2.1        rsconnect_0.8.16  compiler_4.0.2    htmltools_0.5.1.1
## [17] knitr_1.31
  • Taxa of interest are based on [Description and allergenic potential of 11 most important pollen taxa in the CUSSC region ranked by percent abundance relative to the sum of all pollen taxa over 31 NAB stations that meet inclusion criteria, 2003–2017] (https://link.springer.com/article/10.1007/s10453-019-09601-2/tables/2)
  • Spring- and fall-flowering elms are treated separately as suggested by Allison and Yingxiao.
  • I decide to separate grasses into early and late-flowering groups as well because many cities have two pollen peaks.
taxa_list <- c("Quercus", "Cupressaceae", "Ambrosia", "Morus", "Pinaceae", "Ulmus early", "Ulmus late", "Fraxinus", "Betula", "Poaceae early", "Poaceae late", "Acer", "Populus")
taxa_short_list <- str_split(taxa_list, pattern = " ", simplify = T) [, 1]
  • Ten major cities in CONUS with pollen count data and street tree inventory.
  • Detroit only have location info of oak trees, grasses, and ragweeds.
site_list <- c("NY", "SJ", "AT", "ST", "HT", "TP", "DT", "DV", "KC", "SL")
sitename_list <- c("New York", "San Jose", "Austin", "Seattle", "Houston", "Tampa", "Detroit", "Denver", "Kansas City", "St. Louis")
  • Focus on the life cycles from 2018 to 2021, spanning 2017 and 2022.
year_list <- 2018:2021