Manual for psimpoll and pscomb

QUB | Archaeology and Palaeoecology | The 14Chrono Centre

Manual for psimpoll and pscomb

Sample input files

Data presented as concentrations for conversion to accumulation rates
Data presented as proportions
TS file
C14 file
CAL file
CAL input file
ZONE file
.SCR file
.CFG file
psimpoll.COL file

The sample psimpoll input files below illustrate most of the features described above. Items are numbered on the left to correspond to the item numberings used in Data preparation, and should be compared with them. Item numbering should, of course, be omitted from actual files.

Data presented as proportions

1 Dallican Water, Lunnasting, Shetland
2 8
3 4
4 %d
5 720 716 712 708
6 _Betula, 0.2004 0.0674 0.1635 0.3001
6 -_Juniperus communis, 0.0118 0.0019 0.0115 0.0058
6 Cyperaceae, 0.1886 0.0520 0.1885 0.0996
6 _Potentilla_ t., 0.0000 0.0058 0.0096 0.0029
6  <
  4
  Sum Trees & Shrubs, 0.4401 0.2505 0.2788 0.4286
  Sum Ericales, 0.0255 0.0039 0.0654 0.1400
  Sum Herbs, 0.5226 0.7380 0.5058 0.2771
  Sum Filicales, 0.0118 0.0077 0.1500 0.1544
6 !Palynol. richness
  250
  20.1672 17.0265 23.3079
  19.4393 15.7504 23.1283
  20.3516 17.5684 23.1348
  14.7937 12.1803 17.4070
6 =Rate of change, 0.366249 0.420106 0.236846 -1
6 *Main sum, 509 519 520 693

Data presented as concentrations for conversion to accumulation rates


1 Dallican Water, Lunnasting, Shetland
2 3
3 4
4 bd
5 720 716 712 708
6 _Betula, 6595 2702 10670 48175
6 #Sum Trees & Shrubs, 14095 9882 18202 68788
6 &Charcoal, 0 0.399084 0.055816 0.064629
7 -49333
8 -1
9 -0.5
10 -1
11 763 639 393 213
12 -0.5
13 -1
14 -1

`TS` file

`C14` file

`CAL` file

1 4
2 433
  439
  dallCL01
2 478
  486
  dallCL02
2 698
  710
  dallCL03

`CAL` input file

Normally written by BCal (so line-numbering omitted). But can be created in by hand. Content consists solely of a series of pairs of values. The first of each pair is an age in calendar years (negative earlier than 0BP), and the second is a probability. The pairs and the values by separated by spaces, TABs or newlines. A very simple (but useful) can be:

-1200 1.0

which means that the age is 1200 with 100% probability. More usually, the file will look like this (topmost lines only):

-6868 1.982710762154017E-5
-6867 1.982710762154017E-5
-6866 0.0
-6865 0.0
-6864 0.0
-6863 0.0
-6862 0.0
-6861 0.0
-6860 0.0
-6859 1.982710762154017E-5
-6858 1.982710762154017E-5
-6857 0.0
-6856 1.982710762154017E-5
-6855 0.0
-6854 1.982710762154017E-5
-6853 3.965421524308034E-5
-6852 1.982710762154017E-5

`ZONE` file

1 4
2 D-4
  D-3
  D-2
  D-1
3 436.000
  547.000
  706.000
4 red
  yellow
  green
  blue

`.SCR` file

0
1b
2e
3f
4g.2
5g.2eb

`.CFG` file

A .CFG file includes the current values for all variables that can be modified by the menus. An example is shown below, continuing on the next page. Numbers and text beginning down the left margin of the page are the file contents. Labels at the right are the names of the psimpoll variables that hold these numbers. Some string variables may be empty, and where that happens in this particular file there is no entry in the left margin. Lines beginning `...' should be read as continuing from the line above. A separate list of the variables gives more information about the type of quantity each contains.

0.002000                                  gl.page.minpl
24000.000000                              gl.page.wide
0.750000                                  gl.page.prop
O                                         coll.style
0                                         coll.ix10
a:\dallAD                                 agedep.fname
a:\dallp.PS                               outmain.fname
H                                         gl.font.code
0.000000                                  gl.font.ufac
45                                        coll.rot
                                          head.base
                                          head.subtitle
                                          head.zone
                                          head.sed
0 -1                                      coll.join  intfg
-1 0.000000 50.000000 0.000000 50.000000 3 5 1.000000  
                                  ... age.flag age.up age.upsd age.base
                                  ... age.basesd age.model age.npterm age.c14k
a:\dallZONE                               zone.fname
a:\dallC14                                inage.fname
a:\dallTS                                 ints.fname
0 0.300000 1                              ci.flag ci.cvsed ci.n
1                                         gl.mran
TIMER                                     gl.seed
100                                       ci.nran
0 0                                       rarer.flag rarer.n
-1 0.050000 5 5 D-        zoner.flag  num.thresh  zoner.n zoner.meth  zoner.pre
0 1                                       roc.flag  roc.diss
{14}C ages (yr BP)                        head.age[C14BP]
Depth                                     head.ps1[DEPTH]
cm                                        head.ps2[DEPTH]
0                                         num.stat
a:\dallSTAT                               stat.fname
0                                         pca.flag
3                                         pca.matrix
6                                         pca.naxes
0                                         four.flag
0                                         lev.adsc
0                                         pca.tran
0                                         zoner.tran
-1                                        coll.indspl
0                                         zoner.ransam
-1                                        gl.recalc
0.500000                                  coll.shade
-1 400.000000 700.000000                  lev.udata lev.umax lev.umin
0                                         coll.all
0                                         ipdat
0                                         roc.smooth
0.000000 0                                coll.hist coll.indscale
grains cm{-3}                             sunit[0]
grains g{-1}                              sunit[1]
grains cm{-2} year{-1}                    sunit[2]
cm{2} cm{-3}                              sunit[3]
cm{2} cm{-2} year{-1}                     sunit[4]
cm{2} g{-1}                               sunit[5]
cm{2} grain{-1}                           sunit[6]
cent.{-1}                                 sunit[7]
ratio                                     sunit[8]
power                                     sunit[9]
0                                         four.tran
0                                         coll.script
0                                         coll.bull
0.500000                                  coll.lval
0                                         age.timx
Age ({14}C yr BP)                         head.time[C14BP]
0                                         gl.sum2col
0 10                                      roc.model.ci roc.model.n
0 10                                      pca.model.ci pca.model.n
0 10                                      zoner.model.ci zoner.model.n
0.000000 0.000000                         lev.majmark lev.minmark
0                                         coll.skip
0                                         age.adbc
0                                         gl.tufte
-1                                        coll.c14scale
a:\dallDAT                                dat.fname
0                                         ipform
5.000000                                  coll.penwid
0                                         coll.interp
1.000000                                  lev.interp
0.000000                                  lev.intstart
0.000000                                  lev.intstop
a:\dallAD.ps                              adplot.fname
0.002                                     gl.adpage.minpl
Age ({14}C yr BP)                         head.adxaxis[C14BP}
Depth (cm)                                head.adyaxis
1                                         gl.palette.back
0                                         gl.palette.fore
0                                         coll.colpl 
0                                         coll.coltit
0                                         coll.coldep
0                                         coll.col14c
0                                         coll.colts
0                                         coll.colzone
0                                         coll.colxax
-1                                        gl.colts
-1                                        gl.colzone
-0.99                                     gl.neglev
0                                         agerange.colpl 
0                                         agerange.colsdpl
0                                         agerange.col14c
0                                         agerange.coldep
0                                         agerange.colxax
0                                         lev.inttype
21000.000000                              gl.papwid
29700.000000                              gl.papht
0                                         ca.flag
0                                         ca.tran
0                                         ca.iweigh
0                                         ca.irescfg
4                                         ca.iresc
0                                         ca.dca
26                                        ca.mk
0.000000                                  ca.resth
0 10                                      ca.model.ci ca.model.n
dallCAL                                   incal.fname
0                                         age.cal
Age (Cal. yr BP)                          head.adxaxis[CALBP]
Cal. ages (yr BP)                         head.age[CALBP]
{14}C ages (yr AD/BC)                     head.age[C14AD]
Cal. ages (yr AD/BC)                      head.age[CALAD]
Age ({14}C yr AD/BC)                      head.adxaxis[C14AD]
Age (Cal. yr AD/BC)                       head.adxaxis[CALAD]
Age                                       head.ps1[C14BP]
yr BP                                     head.ps2[C14BP]
Age                                       head.ps1[CALBP]
yr BP                                     head.ps2[CALBP]
Age                                       head.ps1[C14AD]
yr AD/BC                                  head.ps2[C14AD]
Age                                       head.ps1[CALAD]
yr AD/BC                                  head.ps2[CALAD]
0                                         ci.negar
-1                                        gl.calval
1000000                                   ci.looplim
Age (Cal. yr BP)                          head.time[CALBP]
Age ({14}C yr AD/BC)                      head.time[C14AD]
Age (Cal. yr AD/BC)                       head.time[CALAD]
                                          head.dendro
 Total dispersion                         sunit[10]
1000                                      gl.adres
0                                         age.ngterm
0                                         gl.showmem
0                                         outdata.method
4.27                                      gl.ver
0                                         coll.taxaright
0                                         coll.taxano

`psimpoll.COL` file

This file contains the colour palette used by the program, and consists of colours defined using the CMYK system, and keyed to an identifier and a name. Subsequent use of the colours needs only the name (in most cases) or the identifier (rarely).

# psimpoll 3.00 colour palette
# K.D. Bennett 1998
#
# Colours are made up of the four components of the CMYK scheme
# (Cyan Magenta Yellow blacK) on a scale from 0.0 (none of that component)
# to 1.0 (full expression of that component)
#
# The first line of values must contain a single value giving the number
# of calours described
#
# Then each colour is described on a line by itself, identified by a number,
# which may be of any positive value from 0 to 2147483647
#
# The order of values is:
# identifier cyan magenta yellow black name
#
# All lines beginning '#' are ignored (comment lines)
#
# It is recommended that the default settings are not changed
#
220
0 0.0 0.0 0.0 1.0		black
1 0.0 0.0 0.0 0.0		white
2 1.0 0.0 0.0 0.0		cyan
3 0.0 1.0 0.0 0.0		magenta
4 0.0 0.0 1.0 0.0		yellow
5 0.0 1.0 1.0 0.0		red
6 0.0 1.0 0.4 0.0		ruby
7 0.0 0.4 1.0 0.0		orange
8 1.0 0.0 1.0 0.0		green
9 0.4 0.0 1.0 0.0		lime
10 1.0 0.4 0.0 0.0		blue
11 0.4 1.0 0.0 0.0		purple 
12 1.0 1.0 0.0 0.0		violet
13 1.0 0.0 0.4 0.0		turquoise
14 0.5 0.75 1.0 0.0		brown
15 0.0 0.0 0.0 0.5		grey
# Munsell colours follow, taken from the Munsell to CMYK conversion program
# available from Munsell (R) at http://www.munsell.com
180 0.20 0.21 0.20 0.17		N8/0
171 0.19 0.20 0.20 0.34		N7/0
160 0.19 0.20 0.20 0.48		N6/0
150 0.19 0.20 0.20 0.59		N5/0
140 0.19 0.20 0.20 0.67		N4/0
130 0.19 0.20 0.20 0.73		N3/0
120 0.19 0.20 0.20 0.75		N2.5/0
10068 0.20 0.64 0.74 0.12	10R6/8
10066 0.20 0.53 0.61 0.21	10R6/6

# Many lines cut out for conciseness in this the manual

5253 0.19 0.24 0.35 0.54	5Y5/3
5252 0.19 0.23 0.30 0.56	5Y5/2
5251 0.19 0.21 0.25 0.57	5Y5/1
5244 0.19 0.24 0.33 0.63	5Y4/4
5243 0.19 0.23 0.30 0.64	5Y4/3
5242 0.19 0.22 0.27 0.65	5Y4/2
5241 0.19 0.21 0.24 0.66	5Y4/1
5232 0.19 0.21 0.24 0.71	5Y3/2
5231 0.19 0.20 0.22 0.72	5Y3/1
52252 0.19 0.21 0.23 0.74	5Y2.5/2
52251 0.19 0.20 0.21 0.74	5Y2.5/1

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Manual for psimpoll and pscomb

Sample input files

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