Paper3

.gitignore

@@ -0,0 +1,13 @@
+.Rproj.user
+.Rhistory
+.RData
+.rda
+.RDA
+.Ruserdata
+/archive/
+.csv
+/data/
+/result/
+/nonlinear_sim1000_ss1000_anchor3/
+/nonlinear_sim1000_ss1000_anchor4/
+/nonlinear_sim1000_ss1000_anchor6/

03_table3_multiple-alpha_code.R

@@ -77,7 +77,6 @@ predicted_test<- predict(lm_bks_train, newdata = test_new)
 # s <- coef(lm_bks_train) %>% as.matrix()
 # mm <- model.matrix(lm_bks_train, data = train_new)
 # g(mm, s, nderiv = 1)
-View(bks)
 summary(bks)
 
 

05_figure2_individual_plot.Rmd

@@ -17,9 +17,6 @@ comment = "#>",
 error = FALSE)
 
 ## clean the R environment
-graphics.off()
-rm(list = ls())
-freshr::freshr()
 
 ## load packages
 library(here, quietly = TRUE)
@@ -152,7 +149,7 @@ test_eld_n10 <- pred_matching(
                  train_data = train_data,
                  test_data = test_data,
                  match_methods = "euclidean",
-                 match_num = 10,
+                 match_num = 30,
                  gamlss_formula = "ht ~ cs(time, df = 3)",
                  gamsigma_formula = "~ cs(time, df = 1)",
                  match_plot = TRUE,
@@ -164,7 +161,7 @@ test_mhl_n10 <- pred_matching(
                    train_data = train_data,
                    test_data = test_data,
                    match_methods = "mahalanobis",
-                   match_num = 10,
+                   match_num = 30,
                    gamlss_formula = "ht ~ cs(time, df = 3)",
                    gamsigma_formula = "~ cs(time, df = 1)",
                  match_plot = TRUE,
@@ -203,7 +200,7 @@ test_sgl10_n10 <- pred_matching(
                      train_data = train_data,
                      test_data = test_data,
                      match_methods = "single",
-                     match_num = 10,
+                     match_num = 30,
                      match_time = 12,
                      match_alpha = NULL,
                      gamlss_formula = "ht ~ cs(time, df = 3)",
@@ -215,7 +212,7 @@ test_sgl10_n10 <- pred_matching(
 
 sgl10_n10_m <- test_sgl10_n10$matching_trajectory + 
   ylim(c(80, 210)) +
-  labs(title = parse(text = latex2exp::TeX("$S_{\\kappa = 10}$")),
+  labs(title = parse(text = latex2exp::TeX("$S_{\\kappa = 30}$")),
        y = "Height (cm)",
        x = "Time (year)") +
   theme(axis.text.x = element_text(size = 15),
@@ -229,7 +226,7 @@ sgl10_n10_m <- test_sgl10_n10$matching_trajectory +
 
 eld_n10_m <- test_eld_n10$matching_trajectory + 
   ylim(c(80, 210)) +
-  labs(title = parse(text = latex2exp::TeX("$E_{\\kappa = 10}$")),
+  labs(title = parse(text = latex2exp::TeX("$E_{\\kappa = 30}$")),
        y = "Height (cm)",
        x = "Time (year)") +
   theme(axis.text.x = element_text(size = 15),
@@ -244,7 +241,7 @@ eld_n10_m <- test_eld_n10$matching_trajectory +
 
 mhl_n10_m <- test_mhl_n10$matching_trajectory + 
   ylim(c(80, 210)) +
-  labs(title = parse(text = latex2exp::TeX("$M_{\\kappa = 10}$")),
+  labs(title = parse(text = latex2exp::TeX("$M_{\\kappa = 30}$")),
        y = "Height (cm)",
        x = "Time (year)") +
   theme(axis.text.x = element_text(size = 15),
@@ -285,7 +282,7 @@ mhl_p80_m <- test_mhl_p80$matching_trajectory +
 
 sgl10_n10_t <- test_sgl10_n10$predictive_centiles + 
   ylim(c(80, 210)) +
-  labs(title = parse(text = latex2exp::TeX("$S_{\\kappa = 10}$")),
+  labs(title = parse(text = latex2exp::TeX("$S_{\\kappa = 30}$")),
        y = "Height (cm)",
        x = "Time (year)") +
   theme(axis.text.x = element_text(size = 15),
@@ -299,7 +296,7 @@ sgl10_n10_t <- test_sgl10_n10$predictive_centiles +
 
 eld_n10_t <- test_eld_n10$predictive_centiles + 
     ylim(c(80, 210)) +
-  labs(title = parse(text = latex2exp::TeX("$E_{\\kappa = 10}$")),
+  labs(title = parse(text = latex2exp::TeX("$E_{\\kappa = 30}$")),
        y = "Height (cm)",
        x = "Time (year)") +
   theme(axis.text.x = element_text(size = 15),
@@ -313,7 +310,7 @@ eld_n10_t <- test_eld_n10$predictive_centiles +
 
 mhl_n10_t <- test_mhl_n10$predictive_centiles +
       ylim(c(80, 210)) +
-  labs(title = parse(text = latex2exp::TeX("$M_{\\kappa = 10}$")),
+  labs(title = parse(text = latex2exp::TeX("$M_{\\kappa = 30}$")),
        y = "Height (cm)",
        x = "Time (year)") +
   theme(axis.text.x = element_text(size = 15),
@@ -355,24 +352,24 @@ mhl_p80_t <- test_mhl_p80$predictive_centiles +
 
 
 
-```{r, fig.height= 12, fig.width=10}
+```{r, fig.height= 10, fig.width=8}
 library(ggpubr)
 
 figure1 <- ggarrange(sgl10_n10_m, sgl10_n10_t,
                     # + theme(axis.text.x=element_blank()),
-                    eld_n10_m, eld_n10_t,
+                    # eld_n10_m, eld_n10_t,
                     # + theme(axis.text.x=element_blank()),
-                    mhl_n10_m, mhl_n10_t,
+                    # mhl_n10_m, mhl_n10_t,
                     # + theme(axis.text.x=element_blank()), 
                     mhl_p80_m, mhl_p80_t,
                     mhl_p90_m, mhl_p90_t,
                     # + theme(axis.text.x=element_blank()),
-                    ncol = 2, nrow = 5) + 
+                    ncol = 2, nrow = 3) + 
   theme(plot.margin = margin(2, 0.5, 0.5, 0.5, "cm"))
 
 
 figure1
-ggsave(filename = paste0("figure/S05_trajectory_final_plots_id_", id, "_", Sys.Date(), "_2alpha.png"))
+ggsave(filename = paste0("figure2/S05_trajectory_final_plots_id_", id, "_", Sys.Date(), "_2alpha.png"))
 ```