Exclude selected varieties in the analysis

.gitignore

@@ -1,6 +1,9 @@
 # Data files
 *.csv
 
+# Output figures
+*.png
+
 # History files
 .Rhistory
 .Rapp.history

calculate_repeatability.r

@@ -1,5 +1,11 @@
 # calculate_repeatability.r
+#
+# value ~ 1|EXP.ID + VARIETY + TREATMENT + GROWTH_STAGE
+# value ~ 1|EXP.ID + VARIETY + TREATMENT                Seth's model
+# value ~ 1|EXP.ID + VARIETY                            Current model
+
 
+library(dplyr)
 library(lme4)
 library(heritability)
 
@@ -8,8 +14,12 @@ library(heritability)
 # Input long format data
 path.rgb.long <- ("./df_rgb_long.csv")
 path.hsi.long <- ("./df_hsi_long.csv")
-path.rpt      <- ("./rpt.csv")
+path.rpt      <- ("./rpt_no_public.csv")
 
+# Define varieties that is excluded for repeatability measurement
+exclude.variety <-c("P1", "P2", "P3", "P4") 
+
+# List of "factor (categorical)" variables
 factor.col <- c('EXP.ID', 
                 'POT_BARCODE',
                 'TREATMENT', 
@@ -18,12 +28,17 @@ factor.col <- c('EXP.ID',
                 'View',
                 'frame_nr')
 
-
 # Load RGB and HSI data in long format
 message("Loading data...")
 df.rgb <- read.csv(path.rgb.long)
 df.hsi <- read.csv(path.hsi.long)
 
+# Exclude varieties, as needed
+if (length(exclude.variety)>0){
+    df.rgb <- df.rgb %>% filter(!VARIETY %in% exclude.variety)
+    df.hsi <- df.hsi %>% filter(!VARIETY %in% exclude.variety)
+}
+
 # Combine RGB and HSI data
 df <- rbind(df.rgb, df.hsi)
 
@@ -56,7 +71,7 @@ for(i in 1:nrow(df.rpt)){
                   row$View, 
                   row$frame_nr, 
                   row$variable, 
-                  " (", i, "/", nrow(df.rpt), ")" sep=" "))
+                  " (", i, "/", nrow(df.rpt), ")", sep=" "))
     df.temp <- df[which(df$TREATMENT==row$TREATMENT & 
                         df$GROWTH_STAGE==row$GROWTH_STAGE & 
                         df$View==row$View & 
@@ -89,14 +104,4 @@ write.csv(df.rpt, path.rpt, row.names=F)
 
 
 
-
-# factor(EXP.ID, frame_nr, VARIETY, TREATMENT)
-# value ~ 1|EXP.ID + VARIETY + TREATMENT + GROWTH_STAGE
-# value ~ 1|EXP.ID + VARIETY + TREATMENT                Seth
-# value ~ 1|EXP.ID + VARIETY                            Current
-
-
-
-
-
 # EOF