\contentsline {section}{\numberline {1}Preface}{8}
\contentsline {section}{\numberline {2}Acknowledgements}{9}
\contentsline {section}{\numberline {3}Disclaimer}{10}
\contentsline {section}{\numberline {4}Introduction}{11}
\contentsline {subsection}{\numberline {4.1}Contents}{11}
\contentsline {subsection}{\numberline {4.2}Background}{11}
\contentsline {subsection}{\numberline {4.3}Implementation}{13}
\contentsline {subsection}{\numberline {4.4}Installation}{14}
\contentsline {subsubsection}{\numberline {4.4.1}IBM-compatibles, Apple MacIntosh, Linux}{14}
\contentsline {subsubsection}{\numberline {4.4.2}Other computers}{14}
\contentsline {subsection}{\numberline {4.5}Colour}{15}
\contentsline {section}{\numberline {5}Data preparation}{16}
\contentsline {subsection}{\numberline {5.1}Contents}{16}
\contentsline {subsection}{\numberline {5.2}Simple use}{16}
\contentsline {subsection}{\numberline {5.3}Format of main input file}{16}
\contentsline {subsection}{\numberline {5.4}Options within main input file}{18}
\contentsline {subsection}{\numberline {5.5}Input from a TILIA-type file}{19}
\contentsline {subsection}{\numberline {5.6}Associated files}{20}
\contentsline {subsection}{\numberline {5.7}Output files}{21}
\contentsline {subsection}{\numberline {5.8}Item 4: First character}{22}
\contentsline {subsection}{\numberline {5.9}Item 4: Second character}{23}
\contentsline {subsection}{\numberline {5.10}Prefixes of taxon names for taxa with special input requirements}{23}
\contentsline {subsection}{\numberline {5.11}Prefixes that affect labelling and presentation of axes}{24}
\contentsline {section}{\numberline {6}Format of associated input files}{25}
\contentsline {subsection}{\numberline {6.1}{\tt TS}}{25}
\contentsline {subsection}{\numberline {6.2}{\tt C14}}{25}
\contentsline {subsection}{\numberline {6.3}{\tt CAL}}{26}
\contentsline {subsection}{\numberline {6.4}{\tt CAL} input}{26}
\contentsline {subsection}{\numberline {6.5}{\tt ZONE}}{26}
\contentsline {section}{\numberline {7}Running the programs}{28}
\contentsline {subsection}{\numberline {7.1}Contents}{28}
\contentsline {subsection}{\numberline {7.2}Running {\bf psimpoll}}{28}
\contentsline {subsection}{\numberline {7.3}Running {\bf pscomb}}{29}
\contentsline {section}{\numberline {8}{\bf psimpoll} menus}{30}
\contentsline {subsection}{\numberline {8.1}Main menu}{31}
\contentsline {subsection}{\numberline {8.2}Menu A: scale plot width}{31}
\contentsline {subsubsection}{\numberline {8.2.1}Menu Aa: main output file}{31}
\contentsline {subsubsection}{\numberline {8.2.2}Menu Ab: age-depth output file}{32}
\contentsline {subsubsection}{\numberline {8.2.3}Menu Ac: length}{32}
\contentsline {subsubsection}{\numberline {8.2.4}Menu Ad: height}{32}
\contentsline {subsubsection}{\numberline {8.2.5}Menu Ae: paper size}{32}
\contentsline {subsection}{\numberline {8.3}Menu B: diagram scaling}{33}
\contentsline {subsubsection}{\numberline {8.3.1}Menu Ba: independent scaling}{33}
\contentsline {subsubsection}{\numberline {8.3.2}Menu Bb: scale excluded samples}{33}
\contentsline {subsubsection}{\numberline {8.3.3}Menu Bc: labelling on age-depth scale}{33}
\contentsline {subsubsection}{\numberline {8.3.4}Menu Bd: double column for sums}{34}
\contentsline {subsubsection}{\numberline {8.3.5}Menu Be: skip every nth sample}{34}
\contentsline {subsubsection}{\numberline {8.3.6}Menu Bf: interpolate to constant sample intervals}{34}
\contentsline {subsubsection}{\numberline {8.3.7}Menu Bg: threshold for missing data}{35}
\contentsline {subsection}{\numberline {8.4}Menu C: changing colours}{35}
\contentsline {subsection}{\numberline {8.5}First form: for main output file}{35}
\contentsline {subsubsection}{\numberline {8.5.1}Menu Ca: background colour }{36}
\contentsline {subsubsection}{\numberline {8.5.2}Menu Cb: background colour }{36}
\contentsline {subsubsection}{\numberline {8.5.3}Menu Cc: foreground colour}{36}
\contentsline {subsubsection}{\numberline {8.5.4}Menu Cd: colour of plots}{36}
\contentsline {subsubsection}{\numberline {8.5.5}Menu Ce: colour of title}{36}
\contentsline {subsubsection}{\numberline {8.5.6}Menu Cf: colour of age-depth axis}{36}
\contentsline {subsubsection}{\numberline {8.5.7}Menu Cg: colour of the 14C column}{36}
\contentsline {subsubsection}{\numberline {8.5.8}Menu Ch: colour of the sediment column foreground}{36}
\contentsline {subsubsection}{\numberline {8.5.9}Menu Ci: colour of the zone column foreground}{37}
\contentsline {subsubsection}{\numberline {8.5.10}Menu Cj: colour of x-axes}{37}
\contentsline {subsubsection}{\numberline {8.5.11}Menu Ck: use colours for sediment units}{37}
\contentsline {subsubsection}{\numberline {8.5.12}Menu Cl: use colours for zones}{37}
\contentsline {subsection}{\numberline {8.6}Second form: for age-depth output file}{37}
\contentsline {subsubsection}{\numberline {8.6.1}Menu Ca: background colour }{37}
\contentsline {subsubsection}{\numberline {8.6.2}Menu Cb: background colour }{38}
\contentsline {subsubsection}{\numberline {8.6.3}Menu Cc: colour of main curve}{38}
\contentsline {subsubsection}{\numberline {8.6.4}Menu Cd: colour of confidence interval curve}{38}
\contentsline {subsubsection}{\numberline {8.6.5}Menu Ce: colour of points}{38}
\contentsline {subsubsection}{\numberline {8.6.6}Menu Cf: colour of depth axis}{38}
\contentsline {subsubsection}{\numberline {8.6.7}Menu Cg: colour of x-axis axis}{38}
\contentsline {subsection}{\numberline {8.7}Menu D: diagram style}{39}
\contentsline {subsubsection}{\numberline {8.7.1}Menu Da: Tufte style}{39}
\contentsline {subsubsection}{\numberline {8.7.2}Menu Db: type}{39}
\contentsline {subsubsection}{\numberline {8.7.3}Menu Dc: \unhbox \voidb@x \hbox {$\times $} 10 exaggeration}{39}
\contentsline {subsubsection}{\numberline {8.7.4}Menu Dd: shading}{40}
\contentsline {subsubsection}{\numberline {8.7.5}Menu De: name angle}{40}
\contentsline {subsubsection}{\numberline {8.7.6}Menu Df: join-up across samples}{40}
\contentsline {subsubsection}{\numberline {8.7.7}Menu Dg: histogram width}{40}
\contentsline {subsubsection}{\numberline {8.7.8}Menu Dh: bullet}{40}
\contentsline {subsubsection}{\numberline {8.7.9}Menu Di: bullet threshold}{41}
\contentsline {subsubsection}{\numberline {8.7.10}Menu Dj: Include radiocarbon age locations}{41}
\contentsline {subsubsection}{\numberline {8.7.11}Menu Dk: Factor to adjust width of lines}{41}
\contentsline {subsubsection}{\numberline {8.7.12}Menu Dl: Resolution of curve in age-depth plots}{41}
\contentsline {subsection}{\numberline {8.8}Menu E: files}{42}
\contentsline {subsection}{\numberline {8.9}Menu F: font family}{42}
\contentsline {subsection}{\numberline {8.10}Menu G: font size}{43}
\contentsline {subsection}{\numberline {8.11}Menu H: extreme values for depth or age in plots}{43}
\contentsline {subsection}{\numberline {8.12}Menu I: labelling}{44}
\contentsline {subsubsection}{\numberline {8.12.1}Menu Ik: submenu for choice of labels to be modified}{48}
\contentsline {subsection}{\numberline {8.13}Menu J: print dataset}{50}
\contentsline {subsection}{\numberline {8.14}Menu K: interactive plotting}{50}
\contentsline {subsection}{\numberline {8.15}Menu L: age-depth conversion}{53}
\contentsline {subsubsection}{\numberline {8.15.1}Calibrated ages}{53}
\contentsline {subsubsection}{\numberline {8.15.2}Menu La: convert depths to ages}{55}
\contentsline {subsubsection}{\numberline {8.15.3}Menu Lb: top age}{55}
\contentsline {subsubsection}{\numberline {8.15.4}Menu Lc: basal age}{55}
\contentsline {subsubsection}{\numberline {8.15.5}Menu Ld: age model}{56}
\contentsline {subsubsection}{\numberline {8.15.6}Menu Le: number of terms for polynomial age models}{57}
\contentsline {subsubsection}{\numberline {8.15.7}Menu Lf: laboratory error-multiplier}{57}
\contentsline {subsubsection}{\numberline {8.15.8}Menu Lg: timescale with depth scale}{58}
\contentsline {subsubsection}{\numberline {8.15.9}Menu Lh: AD/BC scale}{58}
\contentsline {subsubsection}{\numberline {8.15.10}Menu Li: Calibration}{58}
\contentsline {subsubsection}{\numberline {8.15.11}Menu Lj: Mode or weighted average with calibrated dates}{59}
\contentsline {subsection}{\numberline {8.16}Menu M: data analyses}{59}
\contentsline {subsubsection}{\numberline {8.16.1}Menu Ma: rate of change}{60}
\contentsline {subsubsection}{\numberline {8.16.2}Menu Mb: rarefaction}{61}
\contentsline {subsubsection}{\numberline {8.16.3}Menu Mc: zonation}{62}
\contentsline {subsubsection}{\numberline {8.16.4}Menu Md: principal components}{67}
\contentsline {subsubsection}{\numberline {8.16.5}Menu Me: Correspondence analysis}{69}
\contentsline {paragraph}{Menu Mea: Detrended correspondence analysis}{70}
\contentsline {paragraph}{Menu Meb: Downweighting of rare types}{70}
\contentsline {paragraph}{Menu Mec: Rescaling of axes}{70}
\contentsline {paragraph}{Menu Med: Number of times to rescale axes}{70}
\contentsline {paragraph}{Menu Mee: Rescaling threshold}{70}
\contentsline {paragraph}{Menu Mef: Number of segments}{70}
\contentsline {subsubsection}{\numberline {8.16.6}Menu Mf: Fourier}{71}
\contentsline {subsubsection}{\numberline {8.16.7}Menu Mg: statistical description}{72}
\contentsline {subsubsection}{\numberline {8.16.8}Menu Mh: independent splitting}{74}
\contentsline {subsubsection}{\numberline {8.16.9}Menu Mi: threshold values}{75}
\contentsline {subsubsection}{\numberline {8.16.10}Menu Mj: recalculation}{75}
\contentsline {subsection}{\numberline {8.17}Menu N: confidence intervals}{76}
\contentsline {subsubsection}{\numberline {8.17.1}Menu N1: fine-scale variation}{77}
\contentsline {subsubsection}{\numberline {8.17.2}Menu N2: method}{77}
\contentsline {subsubsection}{\numberline {8.17.3}Menu N3: random number generation}{78}
\contentsline {subsubsection}{\numberline {8.17.4}Menu N4: random number seed}{78}
\contentsline {subsubsection}{\numberline {8.17.5}Menu N5: number of simulations}{78}
\contentsline {subsubsection}{\numberline {8.17.6}Menu N6: Include negative accumulation rates in models}{79}
\contentsline {subsubsection}{\numberline {8.17.7}Menu N7: Attempts to model dates without -ve acc. rates}{79}
\contentsline {subsection}{\numberline {8.18}Menu O: save configuration file}{80}
\contentsline {subsection}{\numberline {8.19}Menu P: read script file}{80}
\contentsline {subsection}{\numberline {8.20}Menu U: utilities}{80}
\contentsline {subsection}{\numberline {8.21}Menu X: run program}{81}
\contentsline {section}{\numberline {9}{\bf pscomb} menus}{82}
\contentsline {subsection}{\numberline {9.1}Main menu}{82}
\contentsline {subsection}{\numberline {9.2}Menu E: files}{82}
\contentsline {subsection}{\numberline {9.3}Menu I: labelling}{83}
\contentsline {subsection}{\numberline {9.4}Menu K: interactive plotting}{83}
\contentsline {subsection}{\numberline {9.5}Menu U: utilities}{85}
\contentsline {section}{\numberline {10}Technical matters}{86}
\contentsline {subsection}{\numberline {10.1}Contents}{86}
\contentsline {subsection}{\numberline {10.2}Programming language}{86}
\contentsline {subsection}{\numberline {10.3}Computers}{86}
\contentsline {subsection}{\numberline {10.4}PostScript}{87}
\contentsline {subsection}{\numberline {10.5}Fonts and character encoding}{88}
\contentsline {subsection}{\numberline {10.6}Compatibility}{89}
\contentsline {subsection}{\numberline {10.7}Page layout}{89}
\contentsline {subsection}{\numberline {10.8}Known problems and limitations}{91}
\contentsline {section}{\numberline {11}Error messages}{92}
\contentsline {subsection}{\numberline {11.1}Contents}{92}
\contentsline {subsection}{\numberline {11.2}General information on errors}{92}
\contentsline {subsection}{\numberline {11.3}List of messages}{93}
\contentsline {subsection}{\numberline {11.4}Error messages}{97}
\contentsline {subsubsection}{\numberline {11.4.1}Explanation of messages}{97}
\contentsline {section}{\numberline {12}Sample input files}{104}
\contentsline {subsection}{\numberline {12.1}Contents}{104}
\contentsline {subsection}{\numberline {12.2}Data presented as proportions}{105}
\contentsline {subsection}{\numberline {12.3}Data presented as concentrations for conversion to accumulation rates}{105}
\contentsline {subsection}{\numberline {12.4}{\tt TS} file}{106}
\contentsline {subsection}{\numberline {12.5}{\tt C14} file}{106}
\contentsline {subsection}{\numberline {12.6}{\tt CAL} file}{107}
\contentsline {subsection}{\numberline {12.7}{\tt CAL} input file}{107}
\contentsline {subsection}{\numberline {12.8}{\tt ZONE} file}{108}
\contentsline {subsection}{\numberline {12.9}{\tt .SCR} file}{108}
\contentsline {subsection}{\numberline {12.10}{\tt .CFG} file}{108}
\contentsline {subsection}{\numberline {12.11}{\tt psimpoll.COL} file}{111}
\contentsline {section}{\numberline {13}Variables saved in {\tt .CFG} files}{114}
\contentsline {section}{\numberline {14}Examples of {\bf psimpoll} output}{123}
\contentsline {section}{References}{126}