In bridachristian/DataQualityCheckEuracAlpEnv:

Report start at r report_start

report_start <- params$report_start
final_dataframe <- params$final_dataframe

ff = as.data.frame(final_dataframe,stringsAsFactors = F)

for(i in 3:13){
  ff[,i] = as.numeric(ff[,i])
}


final_2 = as.data.frame(final_dataframe[,1:13],stringsAsFactors = F)


final_2$Status[ff$Status == "Already analyzed"] = "B" 
final_2$Status[ff$Status == "Analyzed with errors"] = "R" 
final_2$Status[ff$Status == "Analyzed and write output" & !all(ff[3,11] == 0)] = "Y" 
final_2$Status[ff$Status == "Analyzed and write output" & all(ff[3,11] == 0)] = "G" 
final_2$Status[ff$Status == "Not analyzed"] = NA

final_2$flag_empty[ff$flag_empty == 1] = "R" 
final_2$flag_empty[ff$flag_empty == 0] = "G"

final_2$flag_logger_number[ff$flag_logger_number == 1] = "R"
final_2$flag_logger_number[ff$flag_logger_number == 0] = "G"

final_2$flag_error_df[ff$flag_error_df == 1] = "R"
final_2$flag_error_df[ff$flag_error_df == -1] = "R" 
final_2$flag_error_df[ff$flag_error_df == 0] = "G"

final_2$flag_date[ff$flag_date == 1] = "R" 
final_2$flag_date[ff$flag_date == 0] = "G"

final_2$flag_duplicates_rows[ff$flag_duplicates_rows == 1] = "Y" 
final_2$flag_duplicates_rows[ff$flag_duplicates_rows == 0] = "G"

final_2$flag_overlap[ff$flag_overlap == 1] = "R" 
final_2$flag_overlap[ff$flag_overlap == 0] = "G"

final_2$flag_missing_records[ff$flag_missing_records == 1] = "R" 
final_2$flag_missing_records[ff$flag_missing_records == 0] = "G"
final_2$flag_missing_records[ff$flag_missing_records == 50] = "GR"

final_2$flag_missing_dates[ff$flag_missing_dates == 1] = "Y" 
final_2$flag_missing_dates[ff$flag_missing_dates == 0] = "G"

final_2$flag_range_variable_to_set[ff$flag_range_variable_to_set == 1] = "Y" 
final_2$flag_range_variable_to_set[ff$flag_range_variable_to_set == 0] = "G"

final_2$flag_range_variable_new[ff$flag_range_variable_new == 1] = "Y" 
final_2$flag_range_variable_new[ff$flag_range_variable_new == 0] = "G"

final_2$flag_out_of_range[ff$flag_out_of_range == 1] = "Y" 
final_2$flag_out_of_range[ff$flag_out_of_range == 0] = "G"


colnames(final_2) = c("Station",
                      "Status",
                      "File is empty",
                      "Logger number",
                      "Structure issues",
                      "Date issues",
                      "Duplicated rows",
                      "Overlap",
                      "Missing records",
                      "Missing dates",
                      "Range to update: old variables ",
                      "Range to update: new variable",
                      "Out of range")

# missing_color = data.frame( rep("R", times= nrow(final_2)), rep("Y", times= nrow(final_2)),rep("G", times= nrow(final_2)),rep(NA, times= nrow(final_2)))
# colnames(missing_color) = c("Red", "Yellow", "Green", "NaN")

# final_2 = cbind(final_2[,1:2],message,final_2[,3:11] )

ff2 = ff[,c(1:13)]
colnames(ff2)  = colnames(final_2)
melt_final = melt(final_2,id.vars = "Station")
melt_ff2 = melt(ff2[,-2],id.vars = "Station")


message = data.frame(final_dataframe[,1], rep("Status", times = nrow(final_dataframe)), final_dataframe [,2])
colnames(message) = colnames(melt_final)

mycolors = c("lightblue","red", "yellow","green","grey","white")
names(mycolors) = c("B", "R", "Y", "G","GR", "NA")
# colScale <- scale_fill_manual(name = "mycolors",values =  mycolors, drop = FALSE)
colScale <- scale_fill_manual(name = "",values = mycolors,
                              limits = c("B","R", "Y", "G", "GR", "NA"),
                              labels = c("Already processed!","Fatal Error!", "Warning!", "OK!","Check disabled!", "Not Evaluated!"),
                              drop = FALSE)


level_station = levels(factor(melt_final$Station))


ggplot(melt_final, aes(x = variable, y = Station))+
  theme(axis.text.x = element_text(angle = 90, hjust = 0, vjust =0),
        panel.background = element_rect(fill = "white", colour = "grey"),
        panel.border = element_rect(fill = "NA", colour = "white"))+
  geom_tile(aes(fill = value),colour = "black")+
  # geom_text(data = melt_ff2,aes(label = value ))+
  colScale+
  scale_y_discrete(limits = rev(level_station))+
  scale_x_discrete(position = "top")



#   geom_text(data = message, aes(label = value), hjust=0, size = 2)

r_link = ff$Report_link
r_link_text =  r_link

d_file <- ff$File_name
d_folder <- ff$Data_folder
d_folder_text =  d_folder


w1 = which(is.na(r_link_text))
w2 = which(!is.na(r_link_text))

w3 = which(is.na(d_folder))
w4 = which(!is.na(d_folder))

r_link_text[w1] = "---"
r_link_text[w2] ="Report available"

# d_folder_text[w3] = "No data file"
# d_folder_text[w4] ="Data available"

ff$Report_link[w1]<- paste0(r_link_text[w1])
ff$Report_link[w2]<- paste0("[", r_link_text[w2], "](", r_link[w2], ")")

ff$Data_folder [w3] <- paste0("---")
ff$Data_folder[w4]<- paste0("[", "Data available", "](",d_folder_text[w4], ")")

ff$File_name[is.na(ff$File_name)] = paste0("---")

new_ff = ff[,c(1,14,15,16)]
colnames(new_ff) = c("Station", "Report", "Data folder", "File name")


knitr::kable(new_ff,row.names = FALSE)

# datatable(new_ff)

Report end at r Sys.time()

bridachristian/DataQualityCheckEuracAlpEnv documentation built on Oct. 27, 2019, 5:55 p.m.