In leppott/ContDataSumViz: Create Visualizations of Continuous Monitoring Data

knitr::opts_chunk$set(echo = FALSE, results = 'asis', warning = FALSE)
# myFiles <- list.files("data")

# import_display <- function(myFile, myCaption="caption TBD") { 
#   # Extension
#   fn_ext <- tools::file_ext(myFile)
#   fn_path <- file.path("data", myFile)
#   
#   # Import and Display
#   if(fn_ext == "jpg" || fn_ext == "png") {
#     # GRAPHIC
#     # display
#     knitr::include_graphics(fn_path)
#   } else {
#     # TABLE
#     if(fn_ext == "tab"|| fn_ext == "txt") {
#       df_data <- read.delim(file.path("data", fn_path))
#     } else if(fn_ext == "csv") {
#       df_data <- read.csv(file.path("data", fn_path))
#     } else if(fn_ext == "xlsx" || fn_ext == "xls") {
#       df_data <- readxl::read_excel(file.path("data", fn_path))
#     }## IF ~ fn_ext (table) ~ END
#     # display
#     DT::datatable(df_data
#               , rownames = FALSE
#               , filter = "top"
#               , caption = myCaption
#               , option = list(scrollX = TRUE
#                               , lengthMenu = c(5, 10, 25, 50, 100)
#                               , autowidth = TRUE))
#   }## IF ~ fn_ext ~ END
#   
# }## FUNCTION ~ read_myFiles ~ END

# Function, list.files(pattern = "^_Captions)

# Files
#myFiles <- list.files("data")
#myFiles_len <- length(myFiles)

# Loop through directories
# Name output by directory name

dn_captions <- file.path("data")
#fn_captions <- "_Captions_SiteX.xlsx" # user supplied
fn_captions <- list.files(dn_captions, pattern = "^_Captions", full.names = TRUE)
df_captions <- data.frame(readxl::read_excel(fn_captions))

# Header 1 (SiteID)
fn_header1 <- "_Header_1_SiteID.txt"
#str_header_siteid <- read.delim(file.path("data", fn_header1))
cat(paste0("**Hero Brook (Site S)**"))
cat("\n\n\n")
cat("Site S is located on Melodious Brook in the Coastal Plain – eastern shore region of
Krypton in the eastern US. It is in the upper Clark River watershed in Kent County. This site was sampled in 2004 and 2008 to 2009. Its watershed is primarily forested (65%), with 34% agriculture.")

cat("\n\n\n")

# myFiles <- list.files("data")
# myFile_num <- grep(myPattern, myFiles)
# myFile_name <- myFiles[myFile_num]
# myFile_ext <- tools::file_ext(myFile_name)
# Import

pat_all <- "^[0-9]+"
file_all <- list.files("data", pattern = pat_all)

for(i in seq_along(file_all[1:3])) {
  pat_i <- paste0("^", i, "_")
  file_i <- grep(pat_i, file_all, value = TRUE)
  #import_display(file_i)
  cap_i <- df_captions[i, "Caption"]
  cat(paste0("\n\n\n**", cap_i, "**\n\n\n"))
  knitr::include_graphics(file.path("data", file_i))
}## FOR ~ i ~ END



# 
# 
# i <- 1
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# myCaption <- df_captions[i, "Caption"]
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# knitr::include_graphics(file.path("data", file_i))
# 
# i <- 2
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# myCaption <- df_captions[i, "Caption"]
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# knitr::include_graphics(file.path("data", file_i))
# 
# i <- 3
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# myCaption <- df_captions[i, "Caption"]
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# knitr::include_graphics(file.path("data", file_i))
# 
# 
# i <- 4
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# df_data <- read.csv(file.path("data", file_i))
# myCaption <- df_captions[i, "Caption"]
# # display
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# DT::datatable(df_data
#           , rownames = FALSE
#           , filter = "top"
#     #      , caption = myCaption
#           , option = list(scrollX = TRUE
#                           , lengthMenu = c(5, 10, 25, 50, 100)
#                           , autowidth = TRUE))
# 
# i <- 5
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# df_data <- read.csv(file.path("data", file_i))
# myCaption <- df_captions[i, "Caption"]
# # display
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# DT::datatable(df_data
#           , rownames = FALSE
#           , filter = "top"
#     #      , caption = myCaption
#           , option = list(scrollX = TRUE
#                           , lengthMenu = c(5, 10, 25, 50, 100)
#                           , autowidth = TRUE))
# 
# i <- 6
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# myCaption <- df_captions[i, "Caption"]
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# knitr::include_graphics(file.path("data", file_i))
# 
# 
# i <- 7
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# myCaption <- df_captions[i, "Caption"]
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# knitr::include_graphics(file.path("data", file_i))
# 
# i <- 8
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# myCaption <- df_captions[i, "Caption"]
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# knitr::include_graphics(file.path("data", file_i))
# 
# i <- 9
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# df_data <- read.csv(file.path("data", file_i))
# myCaption <- df_captions[i, "Caption"]
# # display
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# DT::datatable(df_data
#           , rownames = FALSE
#           , filter = "top"
#     #      , caption = myCaption
#           , option = list(scrollX = TRUE
#                           , lengthMenu = c(5, 10, 25, 50, 100)
#                           , autowidth = TRUE))
# 
# i <- 10
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# myCaption <- df_captions[i, "Caption"]
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# knitr::include_graphics(file.path("data", file_i))
# 
# i <- 11
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# df_data <- read.csv(file.path("data", file_i))
# myCaption <- df_captions[i, "Caption"]
# # display
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# DT::datatable(df_data
#           , rownames = FALSE
#           , filter = "top"
#     #      , caption = myCaption
#           , option = list(scrollX = TRUE
#                           , lengthMenu = c(5, 10, 25, 50, 100)
#                           , autowidth = TRUE))
# 
# i <- 12
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# df_data <- read.csv(file.path("data", file_i))
# myCaption <- df_captions[i, "Caption"]
# # display
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# DT::datatable(df_data
#           , rownames = FALSE
#           , filter = "top"
#     #      , caption = myCaption
#           , option = list(scrollX = TRUE
#                           , lengthMenu = c(5, 10, 25, 50, 100)
#                           , autowidth = TRUE))
# 
# i <- 13
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# df_data <- read.csv(file.path("data", file_i))
# myCaption <- df_captions[i, "Caption"]
# # display
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# DT::datatable(df_data
#           , rownames = FALSE
#           , filter = "top"
#     #      , caption = myCaption
#           , option = list(scrollX = TRUE
#                           , lengthMenu = c(5, 10, 25, 50, 100)
#                           , autowidth = TRUE))
# 
# i <- 14
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# df_data <- read.csv(file.path("data", file_i))
# myCaption <- df_captions[i, "Caption"]
# # display
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# DT::datatable(df_data
#           , rownames = FALSE
#           , filter = "top"
#     #      , caption = myCaption
#           , option = list(scrollX = TRUE
#                           , lengthMenu = c(5, 10, 25, 50, 100)
#                           , autowidth = TRUE))
# 
# i <- 15
# myPattern <- paste0("^", i, "_")
# file_i <- grep(myPattern, myFiles, value = TRUE)
# df_data <- read.csv(file.path("data", file_i))
# myCaption <- df_captions[i, "Caption"]
# # display
# cat(paste0("\n\n\n**", myCaption, "**\n\n\n"))
# DT::datatable(df_data
#           , rownames = FALSE
#           , filter = "top"
#     #      , caption = myCaption
#           , option = list(scrollX = TRUE
#                           , lengthMenu = c(5, 10, 25, 50, 100)
#                           , autowidth = TRUE))

cat(paste0("**Report Generated:** ", format(Sys.time(), '%Y-%m-%d %H:%M:%S')))

leppott/ContDataSumViz documentation built on Jan. 30, 2024, 10 p.m.