In bmcnellis/RSFIA: FIA Tree Mortality Analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

stop('Dont knit this.')

This vignette documents the creation of the FIA_plot_weather data object. The DaymetWeatherGrab function will require restarting once in a while because of intermittent file download errors, and will throw an error if the saved file has been completely downloaded already - just increment the starting year when this happens.

data("FIA_mortality_with_explanatory")
lats <- FIA_mortality_with_explanatory$LAT
lons <- FIA_mortality_with_explanatory$LON
out <- "C:/Users/Brandon/Documents/docs/R_workspace/RSFIA/inst/extdata/daymet"

daymet_vars <- RSFIA::ShowDaymetMeta()$fixed_name[2:8]
weather_data <- RSFIA::DaymetWeatherGrab(lats, lons,
                                  start_year = '2000', end_year = '2016',
                                  out_dir = out, vars = daymet_vars)

This part modifies the data. Solar data was not very informative in preliminary trials and also significantly collinear, as was the rain variables sum_rain and mean_rain. Since mean_rain is effectively MAP, sum_rain is dropped here.

weather_data <- RSFIA::CombineWeatherFiles(dir = out)
weather_data <- data.frame(
  weather_data[, c(1, 2)],
  RSFIA::CollapseIdenticalVars(weather_data[, -c(1, 2)]),
  stringsAsFactors = F)
colnames(weather_data)[1:2] <- c('lat', 'lon')
weather_data <- weather_data[, -grep('sum_rain', colnames(weather_data))]
colnames(weather_data) <- gsub('mean_rain$', 'MAP', colnames(weather_data))
colnames(weather_data) <- gsub('mean_max_min', 'MAT', colnames(weather_data))
weather_data <- weather_data[, -grep('solar', colnames(weather_data))]

Once data is modified, this code will save it as an .Rmd:

FIA_plot_daymet <- weather_data
devtools::use_data(FIA_plot_daymet, overwrite = T)

bmcnellis/RSFIA documentation built on June 1, 2019, 7:40 a.m.