Comparing approaches to forecasting species richness using the Breeding Bird Survey

In [1]:

    

library(forecast)
library(Hmisc)
library(dplyr)
library(broom)
library(ggplot2)
library(tidyr)
library(mgcv)
library(lme4)
library(caret)
library(gridExtra)
devtools::load_all()

library(sp)
library(raster)
library(maptools)
library(rgeos)
library(rgdal)
library(maps)
library(viridis)


    

    




Loading required package: zoo

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 # ATTENTION: maps v3.0 has an updated 'world' map.        #
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In [2]:

    

start_yr <- 1982
end_yr <- 2013
min_num_yrs <- 25
richness_w_env <- get_richness_ts_env_data(start_yr, end_yr, min_num_yrs)


    

In [3]:

    

head(richness_w_env)
cat("There are", length(unique(richness_w_env$site_id)), "time-series with at least", min_num_yrs, "years of data between", start_yr, "and", end_yr)


    

    






site_id
year
richness
lat
long
bio1
bio2
bio4
bio5
bio6
⋯
bio10
bio11
bio16
bio17
bio18
bio19
ndvi_sum
ndvi_win
ndvi_ann
elevs

	
1
2001             
1982             
49               
34.868688        
-87.6041417      
15.612916747729  
12.1458334848285 
765.160901860803 
32.1599998474121 
-2.91000008583069
⋯                
24.0583337148031 
7.17500003178914 
441.839996337891 
283.299995422363 
286.500003814697 
398.770004272461 
0.687666666666667
0.365833333333333
0.5605           
210.126277474451 
	
2
2001             
1983             
49               
34.868688        
-87.6041417      
15.0962499578794 
12.0424999545018 
878.92348940742  
34.4300003051758 
-2.52999997138977
⋯                
25.5266666412354 
6.63499983151754 
711.889999389648 
142.71000289917  
142.71000289917  
337.970008850098 
0.643666666666667
0.396            
0.548833333333333
210.126277474451 
	
3
2001             
1984             
65               
34.868688        
-87.6041417      
15.8524999022484 
12.6483332763116 
781.218674275284 
31.3199996948242 
-4.03999996185303
⋯                
23.9866669972738 
6.45166659355164 
428.110008239746 
119.760004520416 
119.760004520416 
275.449993133545 
0.724166666666667
0.369166666666667
0.565            
210.126277474451 
	
4
2001             
1985             
54               
34.868688        
-87.6041417      
15.5324999888738 
11.969999919335  
890.206880304819 
31.5100002288818 
-5.30000019073486
⋯                
23.988333384196  
5.71166666348775 
301.029998779297 
231.919998168945 
301.029998779297 
257.060001373291 
0.720666666666667
0.4165           
0.595            
210.126277474451 
	
5
2001             
1986             
54               
34.868688        
-87.6041417      
16.4687499205271 
12.5474994579951 
807.521006713121 
34.0999984741211 
-2.99000000953674
⋯                
25.5733331044515 
8.13000011444092 
567.989990234375 
195.049999237061 
245.440002441406 
195.049999237061 
0.647            
0.4115           
0.573208333333333
210.126277474451 
	
6
2001             
1987             
58               
34.868688        
-87.6041417      
16.221249739329  
13.2524997492631 
820.299698883502 
34.5299987792969 
-1.33000004291534
⋯                
25.42999903361   
7.77500009536743 
337.099998474121 
205.350002288818 
238.249996185303 
337.099998474121 
0.696666666666667
0.4085           
0.578875         
210.126277474451 









    




There are 669 time-series with at least 25 years of data between 1982 and 2013

In [4]:

    

states <- map_data("state")
map_year = 2009 #pick a year to map

richness_w_env_oneyear <- dplyr::filter(richness_w_env, year == map_year) %>%
  na.omit()
map_richness <- ggplot() +
  geom_polygon(data=states, aes(x=long, y=lat, group=group), color="black", fill="white") +
  geom_point(data=richness_w_env_oneyear, aes(x=long, y=lat, color=richness)) +
  scale_color_viridis() +
  coord_map()
ggsave("figures/map_richness.png", map_richness)

env_oneyear_long <- tidyr::gather(richness_w_env_oneyear, env_var, value, bio1:elevs)
maps_env_vars <- env_oneyear_long %>%
  group_by(env_var) %>%
  do(plots=ggplot() +
    geom_polygon(data=states, aes(x=long, y=lat, group=group), color="black", fill="white") +
    geom_point(data=., aes(x=long, y=lat, color=value)) +
    scale_color_viridis() +
    coord_map() +
    ggtitle(first(.$env_var))
    )
multi_panel_fig <- do.call("arrangeGrob", c(maps_env_vars$plots, ncol=4))
ggsave("figures/map_env_vars.png", multi_panel_fig, width = 20, height = 20)


    

    




Saving 6.67 x 6.67 in image

In [5]:

    

lag <- 10
richness_by_site <- group_by(richness_w_env, site_id)
tsmodel_forecasts <- get_ts_forecasts(richness_by_site, timecol = 'year',
                                      responsecol = 'richness',
                                      exogcols = c("ndvi_sum", "ndvi_win"), lag = lag, pred_int_levels=seq(1, 99, by=1))
head(tsmodel_forecasts$pt_est)
head(tsmodel_forecasts$intervals)


    

    




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In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time seriesWarning message:
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In ets(get_train_data(., responsecol)): Missing values encountered. Using longest contiguous portion of time series





    






site_id
model
timeperiod
obs
pt_fcast

	
1
2001 
naive
2004 
58   
63   
	
2
2001 
naive
2005 
56   
63   
	
3
2001 
naive
2006 
62   
63   
	
4
2001 
naive
2007 
60   
63   
	
5
2001 
naive
2008 
59   
63   
	
6
2001 
naive
2009 
55   
63   









    






site_id
model
timeperiod
obs
pt_fcast
levels
lo
hi

	
1
2001            
arima           
2004            
58              
56.7            
1               
56.6446064129057
56.7553935870942
	
2
2001            
arima           
2004            
58              
56.7            
10              
56.1446204415372
57.2553795584628
	
3
2001            
arima           
2004            
58              
56.7            
11              
56.0887433815289
57.3112566184711
	
4
2001            
arima           
2004            
58              
56.7            
12              
56.0327684419873
57.3672315580126
	
5
2001            
arima           
2004            
58              
56.7            
13              
55.9766862675148
57.4233137324851
	
6
2001            
arima           
2004            
58              
56.7            
14              
55.9204873796776
57.4795126203224

In [6]:

    

richness_w_env_2003 <- filter(richness_w_env, year == 2003)
richness_w_env_pre_2004 <- filter(richness_w_env, year <= 2003)
richness_w_env_2004_2013 <- filter(richness_w_env, year >= 2004)
spatial_bioclim_model_2003 <- lm(richness ~ bio10 + I(bio10^2) + bio11 +
                      I(bio11^2) + bio12 + I(bio12^2), data = richness_w_env_2003)
spatial_env_model_2003 <- lm(richness ~ ndvi_sum + I(ndvi_sum^2) + ndvi_win + I(ndvi_win^2) + bio10 + I(bio10^2) + bio11 +
                      I(bio11^2) + bio12 + I(bio12^2) + elevs + I(elevs^2), data = richness_w_env_pre_2004)
fcast_spatial_bioclim <- forecast(spatial_bioclim_model_2003, newdata = richness_w_env_2004_2013)
fcast_spatial_env <- forecast(spatial_env_model_2003, newdata = richness_w_env_2004_2013, level = seq(1, 99, by=1))
fcast_spatial_bioclim_data <- cbind(richness_w_env_2004_2013, fcast_spatial_bioclim)
fcast_spatial_env_data <- cbind(richness_w_env_2004_2013, fcast_spatial_env)

fcast_spatial_bioclim_data$model <- 'spat_bioclim'
fcast_spatial_bioclim <- dplyr::select(fcast_spatial_bioclim_data,
                                   site_id, model, timeperiod = year, obs = richness,
                                   everything(), -lat, -long, -starts_with("bio"),
                                   -starts_with("ndvi"), -elevs)
fcast_spatial_bioclim <- restruct_ts_forecasts(fcast_spatial_bioclim)

fcast_spatial_env_data$model <- 'spat_env'
fcast_spatial_env <- dplyr::select(fcast_spatial_env_data,
                                   site_id, model, timeperiod = year, obs = richness,
                                   everything(), -lat, -long, -starts_with("bio"),
                                   -starts_with("ndvi"), -elevs)
fcast_spatial_env <- restruct_ts_forecasts(fcast_spatial_env)

head(fcast_spatial_env$pt_est)
head(fcast_spatial_env$intervals)


    

    






site_id
model
timeperiod
obs
pt_fcast

	
1
2001            
spat_env        
2004            
58              
50.8520969820016
	
2
2001            
spat_env        
2005            
56              
48.3649997230175
	
3
2001            
spat_env        
2006            
62              
48.5288018420137
	
4
2001            
spat_env        
2007            
60              
48.2016290030079
	
5
2001            
spat_env        
2008            
59              
51.4674350603092
	
6
2001           
spat_env       
2009           
55             
50.972427428738









    






site_id
model
timeperiod
obs
pt_fcast
levels
lo
hi

	
1
2001            
spat_env        
2004            
58              
50.8520969820016
1               
50.7412973204623
50.9628966435409
	
2
2001            
spat_env        
2004            
58              
50.8520969820016
10              
49.7412123413414
51.9629816226618
	
3
2001            
spat_env        
2004            
58              
50.8520969820016
11              
49.6294455160046
52.0747484479987
	
4
2001            
spat_env        
2004            
58              
50.8520969820016
12              
49.5174828873584
52.1867110766448
	
5
2001            
spat_env        
2004            
58              
50.8520969820016
13              
49.4053057403349
52.2988882236684
	
6
2001            
spat_env        
2004            
58              
50.8520969820016
14              
49.2928951137257
52.4112988502776

In [7]:

    

high_corr_vars <- colnames(richness_w_env_pre_2004)[findCorrelation(cor(richness_w_env_pre_2004, use = "complete.obs"))]
cat("The following highly correlated variables are remove from GAM & LME modeling: ", high_corr_vars)


    

    




The following highly correlated variables are remove from GAM & LME modeling:  bio11 bio1 bio7 bio16

In [8]:

    

spatial_env_gam_model <- gam(richness ~ s(ndvi_sum, bs = "ts") + s(ndvi_win, bs = "ts") + s(elevs, bs = "ts") +
                            s(bio2, bs = "ts") + s(bio3, bs = "ts") + s(bio4, bs = "ts") + s(bio5, bs = "ts") + s(bio6, bs = "ts") +
                            s(bio8, bs = "ts") + s(bio9, bs = "ts") + s(bio10, bs = "ts") + s(bio12, bs = "ts") + s(bio13, bs = "ts") +
                            s(bio14, bs = "ts") + s(bio15, bs = "ts") + s(bio17, bs = "ts") + s(bio18, bs = "ts") + s(bio19, bs = "ts"),
                            family = gaussian, data = richness_w_env_pre_2004
                            )
pt_fcast <- predict(spatial_env_gam_model, newdata = richness_w_env_2004_2013)
fcast_spatial_env_gam <- dplyr::select(fcast_spatial_env$pt_est, site_id, model, timeperiod, obs) %>%
  mutate(model="spat_env_gam") %>%
  cbind(pt_fcast)


    

In [9]:

    

spatial_env_gam_spatial_model <- gam(richness ~ ndvi_sum + ndvi_win + elevs +
                            bio2 + bio3 + bio4 + bio5 + bio6 + 
                            bio8 + bio9 + bio10 + bio12 + bio13 +
                            bio14 + bio15 + bio17 + bio18 + bio19 +
                            s(long, lat, bs = "ds"),
                            family = gaussian, data = richness_w_env_pre_2004
                            )
pt_fcast <- predict(spatial_env_gam_spatial_model, newdata = richness_w_env_2004_2013)
fcast_spatial_env_gam_spatial <- dplyr::select(fcast_spatial_env$pt_est, site_id, model, timeperiod, obs) %>%
  mutate(model="spat_env_gam_spat") %>%
  cbind(pt_fcast)
plot(spatial_env_gam_spatial_model)