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Rmd a00d028 Antonio J Perez-Luque 2021-05-18 analysis of trends

Calcular la tendencia temporal de la serie a nivel de parcela

library("tidyverse")
library("here")
library("sf")
library("flextable")
library("Kendall")
library("ggpubr")
library("ggstatsplot")
library("DHARMa")
coplas2019 <- read_csv(here::here("data/coplas2019sn.csv")) %>% 
    filter(sp_abrev != "ppinea") 


df <- coplas2019 %>% 
  filter(!is.na(especie)) %>% 
  dplyr::select(code, especie, `1993`:`2019`) %>% 
  pivot_longer(names_to = "year", values_to = "infestacion", `1993`:`2019`) 
  • Calculamos la tendencia temporal de la serie usando el test no paramétrico Mann-Kendall (\(tau\))
  • Clasificamos la tendencias en sig y no significativas
parcelas <- unique(df$code)

df_trend <- c() 

for (i in 1:length(parcelas)) { 
  
  aux <- df %>% 
    filter(year > 2004) %>% 
    filter(code == parcelas[i]) %>% dplyr::select(infestacion) 

  #MK 
  mk <- Kendall::MannKendall(aux$infestacion)
  
 #auxNA <- aux$infestacion[!is.na(aux$infestacion)]
 #sen <- trend::sens.slope(auxNA)
  
  out <- data.frame(code = parcelas[i], 
                    mk_tau = mk$tau,
                    mk_pvalue = mk$sl)
                    #sen = sen$estimates,
                    #sen_pvalue = sen$p.value)
  
  df_trend <- rbind(df_trend, out)
}
  
mkdf <- coplas2019 %>% 
  dplyr::select(
    code, elevF, elev_mean, especie) %>% 
  inner_join(df_trend) %>% 
  filter(!is.na(especie))


mkdf <- mkdf %>%  
  mutate(significant = case_when(
    mk_pvalue < 0.05 ~ "sig", 
    TRUE ~ "nosig"
  )) %>% 
  mutate(sig = case_when(
    mk_pvalue < 0.05 ~ 1, 
    TRUE ~ 0))


mkdf$especie <- fct_relevel(mkdf$especie,  
         "P. halepensis", "P. pinaster",
         "P. nigra", "P. sylvestris")
  • Comparación de las tendencias por especie
plot_comparaTaus <- ggstatsplot::ggbetweenstats(
  data = mkdf,
  x = especie,
  y = mk_tau,
  ylab = "Tau (Mann-Kendall)") +
  ggplot2::scale_y_continuous(limits=c(-1,1)) +
  ggplot2::scale_color_manual(values = colores_pinos)

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          1 
  • Las tendencias observadas en el nivel de infestación para cada una de las parcelas analizadas se han agrupado por especies y no se observan diferencias en cuanto a la tendencia (\(tau\) de Mann-Kendall), es decir, no se observan tendencias temporales significativamente diferentes entre especies en nuestra serie de datos.

  • Seguidamente analizamos las tendencias significativas.

pct_sig <- mkdf %>% group_by(especie, significant) %>% 
  summarise(n=n()) %>% 
  mutate(pct_tot = round(n/sum(n)*100,2)) 

pct_sig %>% flextable() %>% autofit()
  • Entre un 15-19 % de las parcelas presentan tendencias significativas, la mayoría positivas, lo que indica un aumento de la incidencia media. Al analizar por especie vemos que P. halepensis (~19%) y P. sylvestris (~19.3%) son las que tienen mayor porcentaje de tendencias significativas.
mksig_plot <- ggplot(mkdf, aes(x=especie, y= mk_tau, shape=significant, fill=especie, colour=especie)) + 
  geom_point(position = position_jitter(), 
             size=1.5) +
  scale_shape_manual(values = c(1, 19)) + 
  theme_bw() + 
  ylab("Mann-Kendall tau") + xlab("") + 
  theme(panel.grid = element_blank()) + 
  scale_color_manual(values = colores_pinos) + 
  geom_label(data=(pct_sig %>% filter(significant == "sig")), 
             aes(x=especie, y=0.9, label=
                   paste0(pct_tot, " %")), 
             fill="white", color = "black") 
ggsave(filename = here::here("output/comparaMKsig_especies.pdf"), 
       width = 6, height = 5)
print(mksig_plot)

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dev.off()
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  • Además, destaca que esas tendencias (las significativas) son las que presentan mayor magnitud (\(\mu_{\tau}\) 0.55 - 0.59)
mkdf %>% 
  filter(significant == "sig") %>% 
  filter(mk_tau > 0) %>% 
  ggstatsplot::grouped_gghistostats(x=mk_tau, 
                                    grouping.var = especie)

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53bcfcc Antonio J Perez-Luque 2021-05-19
11251b2 Antonio J Perez-Luque 2021-05-18

Modelizar la tendencia en función de la Elevación

  • Construimos un GLM para la tendencia (\(\tau\)) frente a la elevación
# modelo glm 
model.tau <- glm(mk_tau ~ elev_mean, data = mkdf, family = "gaussian")

model.tau %>% as_flextable()
# visualiza 
tau_elev <- visreg::visreg(model.tau, gg=TRUE, 
               xlab = "Elevation (m)", 
               ylab = "Mann-Kendall tau") + 
  theme_bw() + 
  geom_point(data=(mkdf %>% filter(sig == 1)), 
              aes(x=elev_mean, y=mk_tau), color = "black", size=1.2)
ggsave(filename = here::here("output/tau_elev.pdf"), 
       width = 9, height = 9, units = "cm")
print(tau_elev)

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dev.off()
null device 
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Validación del modelo

# plots de validación 
par(mfcol=c(2,2))
plot(model.tau)

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s <- simulateResiduals(fittedModel = model.tau)
plot(s)

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Modelo de tendencias significativas vs elevación

  • Voy a analizar solo las tau positivas
  • No parece existir una relación etnre los taus posisitvo y significativos y la elevación,
tauspos <- mkdf %>% filter(mk_tau >= 0)
tp <- glm(sig ~ elev_mean, data = tauspos, family="binomial")
tp %>% as_flextable()
visreg::visreg(tp,
               xlab = "Elevation (m)", 
               ylab = "Prob. tau pos. sig.", 
               scale = "response", 
               ylim=c(0,1))

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11251b2 Antonio J Perez-Luque 2021-05-18

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] DHARMa_0.3.3.0    ggstatsplot_0.7.2 ggpubr_0.4.0      Kendall_2.2      
 [5] flextable_0.6.3   sf_0.9-7          here_1.0.1        forcats_0.5.1    
 [9] stringr_1.4.0     dplyr_1.0.4       purrr_0.3.4       readr_1.4.0      
[13] tidyr_1.1.2       tibble_3.0.6      ggplot2_3.3.3     tidyverse_1.3.0  
[17] workflowr_1.6.2  

loaded via a namespace (and not attached):
  [1] readxl_1.3.1              uuid_0.1-4               
  [3] pairwiseComparisons_3.1.3 backports_1.2.1          
  [5] systemfonts_1.0.0         plyr_1.8.6               
  [7] splines_4.0.2             gmp_0.6-2                
  [9] TH.data_1.0-10            kSamples_1.2-9           
 [11] ipmisc_5.0.2              rstantools_2.1.1         
 [13] digest_0.6.27             SuppDists_1.1-9.5        
 [15] foreach_1.5.1             htmltools_0.5.1.1        
 [17] magrittr_2.0.1            memoise_2.0.0            
 [19] doParallel_1.0.16         paletteer_1.3.0          
 [21] openxlsx_4.2.3            modelr_0.1.8             
 [23] officer_0.3.16            sandwich_3.0-0           
 [25] colorspace_2.0-0          rvest_0.3.6              
 [27] ggrepel_0.9.1             haven_2.3.1              
 [29] xfun_0.20                 crayon_1.4.1             
 [31] jsonlite_1.7.2            lme4_1.1-26              
 [33] zeallot_0.1.0             iterators_1.0.13         
 [35] survival_3.2-7            zoo_1.8-8                
 [37] glue_1.4.2                gtable_0.3.0             
 [39] emmeans_1.5.4             MatrixModels_0.4-1       
 [41] statsExpressions_1.0.1    car_3.0-10               
 [43] Rmpfr_0.8-2               abind_1.4-5              
 [45] scales_1.1.1              mvtnorm_1.1-1            
 [47] DBI_1.1.1                 rstatix_0.6.0            
 [49] PMCMRplus_1.9.0           Rcpp_1.0.6               
 [51] performance_0.7.2         xtable_1.8-4             
 [53] units_0.6-7               foreign_0.8-81           
 [55] httr_1.4.2                ellipsis_0.3.1           
 [57] farver_2.0.3              pkgconfig_2.0.3          
 [59] reshape_0.8.8             qgam_1.3.2               
 [61] multcompView_0.1-8        sass_0.3.1               
 [63] dbplyr_2.1.0              labeling_0.4.2           
 [65] effectsize_0.4.4-1        tidyselect_1.1.0         
 [67] rlang_0.4.10              later_1.1.0.1            
 [69] ggcorrplot_0.1.3          munsell_0.5.0            
 [71] cellranger_1.1.0          tools_4.0.2              
 [73] cachem_1.0.4              cli_2.3.0                
 [75] generics_0.1.0            broom_0.7.4              
 [77] evaluate_0.14             fastmap_1.1.0            
 [79] BWStest_0.2.2             yaml_2.2.1               
 [81] rematch2_2.1.2            knitr_1.31               
 [83] fs_1.5.0                  zip_2.1.1                
 [85] nlme_3.1-152              WRS2_1.1-1               
 [87] pbapply_1.4-3             mime_0.10                
 [89] whisker_0.4               xml2_1.3.2               
 [91] correlation_0.6.1         gap_1.2.2                
 [93] compiler_4.0.2            rstudioapi_0.13          
 [95] curl_4.3                  e1071_1.7-4              
 [97] ggsignif_0.6.0            reprex_1.0.0             
 [99] statmod_1.4.35            bslib_0.2.4              
[101] stringi_1.5.3             highr_0.8                
[103] parameters_0.13.0         gdtools_0.2.3            
[105] lattice_0.20-41           Matrix_1.3-2             
[107] visreg_2.7.0              nloptr_1.2.2.2           
[109] classInt_0.4-3            vctrs_0.3.6              
[111] pillar_1.4.7              lifecycle_1.0.0          
[113] mc2d_0.1-18               jquerylib_0.1.3          
[115] estimability_1.3          data.table_1.13.6        
[117] insight_0.14.0            patchwork_1.1.1          
[119] httpuv_1.5.5              R6_2.5.0                 
[121] promises_1.2.0.1          KernSmooth_2.23-18       
[123] rio_0.5.16                BayesFactor_0.9.12-4.2   
[125] codetools_0.2-18          boot_1.3-26              
[127] MASS_7.3-53               gtools_3.8.2             
[129] assertthat_0.2.1          rprojroot_2.0.2          
[131] withr_2.4.1               multcomp_1.4-16          
[133] mgcv_1.8-33               bayestestR_0.9.0         
[135] parallel_4.0.2            hms_1.0.0                
[137] grid_4.0.2                minqa_1.2.4              
[139] coda_0.19-4               class_7.3-18             
[141] rmarkdown_2.6.6           carData_3.0-4            
[143] git2r_0.28.0              shiny_1.6.0              
[145] lubridate_1.7.10          base64enc_0.1-3