rHyperSpec_pdf_report.Rnw

\documentclass[letterpaper]{article}
\author{}
\usepackage{longtable} %allow long form tables
\usepackage{rotating} %allow for tables to be rotated [not used currently]
\usepackage[margin=0.5in]{geometry}
\title{rHyperSpec Results} 
\begin{document}
\maketitle

<<setup, results='hide', echo=FALSE>>=
  library(xtable)
  addtorow          <- list()
  addtorow$pos      <- list()
  addtorow$pos[[1]] <- c(0)
  addtorow$command  <- c(paste("\\hline \n",
                               "\\endhead \n",
                               "\\hline \n",
                               "{\\footnotesize Continued on next page} \n",
                               "\\endfoot \n",
                               "\\endlastfoot \n",sep=""))     
@

<<metadata_table, results='hide', echo=FALSE>>=
  mddata <- read.csv("output/outputFiles/tables/metadata.csv")
  mdtable <- xtable(mddata, caption = "\\textbf{Metadata for hyperspectral data analysis}", 
    align = "llp{12cm}", floating = F, latex.environments = "left")
@


<<print_metadata, results = 'asis', echo=FALSE>>=
    print(mdtable, 
      tabular.environment = "longtable", 
      floating = FALSE,
      include.rownames = FALSE,  # because addtorow will substitute the default row names 
      add.to.row = addtorow,     # this is where you actually make the substitution
      hline.after=c(-1), 
      caption.placement = "top")
@

\newpage

\begin{figure}[h!]
  \centering
  \caption{Raw Calibration Panel Irradiance}
  \includegraphics[width=\columnwidth]{outputFiles/plots/calibration_raw_irradiance_plot.png}
  \label{fig:cal_irrad}
\end{figure}

\begin{figure}[h!]
  \centering
  \caption{Raw Calibration Panel Radiance}
  \includegraphics[width=\columnwidth]{outputFiles/plots/calibration_raw_radiance_plot.png}
  \label{fig:cal_rad}
\end{figure}

\begin{figure}[h!]
  \centering
  \caption{Calibration Panel Reflectance}
  \includegraphics[width=\columnwidth]{outputFiles/plots/calibration_reflectance_plot.png}
  \label{fig:cal_refl}
\end{figure}

\newpage

\begin{figure}[h!]
  \centering
  \caption{Raw Event Irradiance}
  \includegraphics[width=\columnwidth]{outputFiles/plots/event_raw_irradiance_plot.png}
  \label{fig:event_irrad}
\end{figure}

\begin{figure}[h!]
  \centering
  \caption{Raw Event Radiance}
  \includegraphics[width=\columnwidth]{outputFiles/plots/event_raw_radiance_plot.png}
  \label{fig:event_rad}
\end{figure}

\begin{figure}[h!]
  \centering
  \caption{Event Average Normalized Reflectance}
  \includegraphics[width=\columnwidth]{outputFiles/plots/event_reflectance_plot.png}
  \label{fig:event_refl}
\end{figure}

\newpage
\begin{figure}[h!]
  \centering
  \caption{Reflectance Map (by location and wavelength)}
  \includegraphics[width=\columnwidth]{outputFiles/plots/reflectance_map.png}
  \label{fig:refl_map}
\end{figure}
\begin{figure}[h!]
  \centering
  \caption{Plot of selected three indices (see legend)}
  \includegraphics[width=\columnwidth]{outputFiles/plots/triple_index_plot.png}
  \label{fig:triple_index_plot}
\end{figure}

\newpage
<<index_list_table, results='hide', echo=FALSE>>=
  indexdata <- read.csv("Indices.csv")
  indextable <- xtable(indexdata[,c(1,2,7,9)], caption = "\\textbf{Indices Calculated by rHyperSpec.} These indices come from a list kindly provided by Fred Huemmrich. The list may be updated periodically.", 
    digits = 2, align = "lp{3cm}p{2cm}p{3cm}p{7cm}")
@

<<print_index_list, results = 'asis', echo=FALSE>>=
print(indextable, tabular.environment = "longtable", floating = FALSE,
      include.rownames = FALSE,  add.to.row = addtorow,    
      hline.after=c(-1), caption.placement = "top")
@


\newpage
<<indices_calculated_summary_table, results='hide', echo=FALSE>>=
  cisdata <- read.csv("outputFiles/tables/indices-calculated-summary.csv")
  cistable <- xtable(cisdata, caption = "\\textbf{Summary of Calculated Indices}", digits = 2)
@

<<print_index_summary, results = 'asis', echo=FALSE>>=
print(cistable, tabular.environment = "longtable", floating = FALSE,
      include.rownames = FALSE,  add.to.row = addtorow,    
      hline.after=c(-1), caption.placement = "top")
@

\newpage

<<indices_calculated_all_table_1, results='hide', echo=FALSE>>=
  ciadata <- read.csv("outputFiles/tables/indices-calculated-all.csv")
  ciatable1 <- xtable(ciadata[,1:12], 
  caption = "\\textbf{Calculated Indices for Each Location, Group 1}", digits = 3)
@

<<print_index_all_1, results = 'asis', echo=FALSE>>=
print(ciatable1, tabular.environment = "longtable", floating = FALSE,
      include.rownames = FALSE,  add.to.row = addtorow,    
      hline.after=c(-1), caption.placement = "top", latex.environments = "left")
@

<<indices_calculated_all_table_2, results='hide', echo=FALSE>>=
  ciatable2 <- xtable(ciadata[,c(1,13:23)], 
  caption = "\\textbf{Calculated Indices for Each Location, Group 2}", digits = 3)
@

<<print_index_all_2, results = 'asis', echo=FALSE>>=
print(ciatable2, tabular.environment = "longtable", floating = FALSE,
      include.rownames = FALSE,  add.to.row = addtorow,    
      hline.after=c(-1), caption.placement = "top", latex.environments = "left")
@

<<indices_calculated_all_table_3, results='hide', echo=FALSE>>=
  ciatable3 <- xtable(ciadata[,c(1,24:35)], 
  caption = "\\textbf{Calculated Indices for Each Location, Group 3}", digits = 3)
@

<<print_index_all_3, results = 'asis', echo=FALSE>>=
print(ciatable3, tabular.environment = "longtable", floating = FALSE,
      include.rownames = FALSE,  add.to.row = addtorow,    
      hline.after=c(-1), caption.placement = "top", latex.environments = "left")
@

<<indices_calculated_all_table_4, results='hide', echo=FALSE>>=
  ciatable4 <- xtable(ciadata[,c(1,36:47)], 
  caption = "\\textbf{Calculated Indices for Each Location, Group 4}", digits = 3)
@

<<print_index_all_4, results = 'asis', echo=FALSE>>=
print(ciatable4, tabular.environment = "longtable", floating = FALSE,
      include.rownames = FALSE,  add.to.row = addtorow,    
      hline.after=c(-1), caption.placement = "top", latex.environments = "left")
@

<<indices_calculated_all_table_5, results='hide', echo=FALSE>>=
  ciatable5 <- xtable(ciadata[,c(1,48:59)], 
  caption = "\\textbf{Calculated Indices for Each Location, Group 5}", digits = 3)
@

<<print_index_all_5, results = 'asis', echo=FALSE>>=
print(ciatable5, tabular.environment = "longtable", floating = FALSE,
      include.rownames = FALSE,  add.to.row = addtorow,    
      hline.after=c(-1), caption.placement = "top", latex.environments = "left")
@

<<indices_calculated_all_table_6, results='hide', echo=FALSE>>=
  ciatable6 <- xtable(ciadata[,c(1,60:ncol(ciadata))], 
  caption = "\\textbf{Calculated Indices for Each Location, Group 6}", digits = 3)
@
\flushleft
<<print_index_all_6, results = 'asis', echo=FALSE>>=
print(ciatable6, tabular.environment = "longtable", floating = FALSE,
      include.rownames = FALSE,  add.to.row = addtorow,    
      hline.after=c(-1), caption.placement = "top", latex.environments = "left")
@

\end{document}