On Sat, 11 Jul 2015, Liviu Andronic wrote:
Another way to do this is to keep figure floats, labels and cross-refs exclusively in LyX. So the chunk would simply output a graph, and you place the chunk within a LyX float (with associated caption and label). Then use normal LyX workflow.
Might as well keep this in the same thread for posterity's sake. The first figure addes in a float allowed the document to be compiled with pdflatex. When I added a new paragraph with a second figure float compilation fails but the explicit error is not shown. I created a small test file from the document that contains all the knitr chunks and the two figure floats. Attached is the .lyx file (version 2.1.3), the /tmp/.../.log file, and the .RData file from the working directory. This should be enough to replicate the document. I cannot find the error in the log file; more experienced eyes than mine probably can. It is puzzling that the one figure worked, but adding an additional figure broke something. Because this document will have many figures I need to understand how to avoid compilation errors as writing continues. Thanks, Rich
#LyX 2.1 created this file. For more info see http://www.lyx.org/ \lyxformat 474 \begin_document \begin_header \textclass scrreprt \begin_preamble \date{} \usepackage{textcomp,url,multicol} %\setkomafont{sectioning}{\rmfamily} \end_preamble \options abstract=on \use_default_options false \begin_modules natbibapa knitr \end_modules \maintain_unincluded_children false \language english \language_package default \inputencoding auto \fontencoding global \font_roman palatino \font_sans default \font_typewriter default \font_math auto \font_default_family default \use_non_tex_fonts false \font_sc false \font_osf false \font_sf_scale 100 \font_tt_scale 100 \graphics default \default_output_format default \output_sync 0 \bibtex_command bibtex \index_command default \paperfontsize default \spacing single \use_hyperref false \papersize letterpaper \use_geometry false \use_package amsmath 1 \use_package amssymb 1 \use_package cancel 1 \use_package esint 0 \use_package mathdots 1 \use_package mathtools 1 \use_package mhchem 1 \use_package stackrel 1 \use_package stmaryrd 1 \use_package undertilde 1 \cite_engine natbib \cite_engine_type authoryear \biblio_style humannat \use_bibtopic false \use_indices false \paperorientation portrait \suppress_date false \justification true \use_refstyle 0 \index Index \shortcut idx \color #008000 \end_index \secnumdepth 2 \tocdepth 2 \paragraph_separation indent \paragraph_indentation default \quotes_language english \papercolumns 1 \papersides 2 \paperpagestyle default \tracking_changes false \output_changes false \html_math_output 0 \html_css_as_file 0 \html_be_strict false \end_header \begin_body \begin_layout Standard \begin_inset Flex Chunk status open \begin_layout Plain Layout load('.RData') \begin_inset Argument 1 status open \begin_layout Plain Layout echo=FALSE \end_layout \end_inset \end_layout \end_inset \end_layout \begin_layout Standard Some text in here; separating knitr chunks. \end_layout \begin_layout Standard \begin_inset Flex Chunk status open \begin_layout Plain Layout carlin <- read.csv("./carlin.csv", header = TRUE, sep = ",", stringsAsFactors = F) \end_layout \end_inset \end_layout \begin_layout Standard Next paragraph of text. \end_layout \begin_layout Standard \begin_inset Flex Chunk status collapsed \begin_layout Plain Layout carlin$sampdate <- as.Date(carlin$sampdate) \end_layout \begin_layout Plain Layout str(carlin) \end_layout \end_inset \end_layout \begin_layout Standard Another paragraph or two of text. \end_layout \begin_layout Standard \begin_inset Flex Chunk status open \begin_layout Plain Layout summary(carlin) \end_layout \end_inset \end_layout \begin_layout Standard Plots of these distributions are the next step ... \end_layout \begin_layout Standard \begin_inset Flex Chunk status collapsed \begin_layout Plain Layout carlin.1 <- subset(carlin, select = siteid:CO3) \end_layout \begin_layout Plain Layout carlin.2 <- subset(carlin, select = c(siteid, sampdate, Alk:Ca)) \end_layout \begin_layout Plain Layout carlin.3 <- subset(carlin, select = c(siteid, sampdate, Mg:Cr)) \end_layout \begin_layout Plain Layout carlin.4 <- subset(carlin, select = c(siteid, sampdate, Co:Hg)) \end_layout \end_inset \end_layout \begin_layout Standard To plot each chemical constituent's concentration as a function of collection date the data format needs to be reshaped from wide to long: \end_layout \begin_layout Standard \begin_inset Flex Chunk status collapsed \begin_layout Plain Layout library(reshape2) \end_layout \begin_layout Plain Layout carlin.1.melt <- melt(carlin.1, na.rm = F, id.vars = c('siteid', 'sampdate')) \end_layout \begin_layout Plain Layout carlin.2.melt <- melt(carlin.2, na.rm = F, id.vars = c('siteid', 'sampdate')) \end_layout \begin_layout Plain Layout carlin.3.melt <- melt(carlin.3, na.rm = F, id.vars = c('siteid', 'sampdate')) \end_layout \begin_layout Plain Layout carlin.4.melt <- melt(carlin.4, na.rm = F, id.vars = c('siteid', 'sampdate')) \end_layout \end_inset \end_layout \begin_layout Standard The scatter (X-Y) plots use only measured data; missing data are not included. These plots show the measured values over time for each measured constituent. For example, Figure \begin_inset CommandInset ref LatexCommand ref reference "fig: scatter-plot group 1" \end_inset shows that most chemical constitent concentrations are low and have low variability. \begin_inset Float figure wide false sideways false status collapsed \begin_layout Plain Layout \align center \begin_inset Flex Chunk status collapsed \begin_layout Plain Layout library(lattice) \end_layout \begin_layout Plain Layout xyplot(value ~ sampdate | variable, data=carlin.1.melt, rm.na = T, ylab = 'Measured Value', xlab = 'Date') \end_layout \end_inset \end_layout \begin_layout Plain Layout \begin_inset Caption Standard \begin_layout Plain Layout \begin_inset CommandInset label LatexCommand label name "fig: scatter-plot group 1" \end_inset Variability of measured values in group 1 constituents over the period of record at the Carlin station. \end_layout \end_inset \end_layout \begin_layout Plain Layout \end_layout \end_inset Because river discharge (in cubic feet per second) spiked at about 8,000 cfs in the mis-1980s the Y-axis for all panels in the figure have the save range. This compresses low values yet any single constituent can be plotted by itself and the details of its variability over time easily seen. \end_layout \begin_layout Standard The second group of constituents (Figure \begin_inset CommandInset ref LatexCommand ref reference "fig: scatter-plot group 2" \end_inset ) \begin_inset Float figure wide false sideways false status collapsed \begin_layout Plain Layout \align center \begin_inset Flex Chunk status collapsed \begin_layout Plain Layout xyplot(value ~ sampdate | variable, data=carlin.2.melt, rm.na = T, ylab = 'Measured Value', xlab = 'Date' \end_layout \end_inset \end_layout \begin_layout Plain Layout \begin_inset Caption Standard \begin_layout Plain Layout \begin_inset CommandInset label LatexCommand label name "fig: scatter-plot group 2" \end_inset Variability of measured values in group 2 constituents over the period of record at the Carlin station. \end_layout \end_inset \end_layout \end_inset reveals that nutrients (the nitrogen compounds, phosphate, and organic carbon) are all consistenly low with low variability while total dissolved solids (TDS) concentrations are very highly variable both within years (as shown by the different concentrations at the same date) and across the period of observations. Alkalinity and hardness are also quite variable at both time scales. \end_layout \end_body \end_document
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