Set Options

Specification of principle for command and programme control structures.

v1.3 – Feb. 2007 . Author: JM. Lauritsen, EpiData Association.

Default behaviour of software is bound to tradition and experience. The intention of EpiData software design is to allow for user control in a simple manner, but based on replication principles and good practices of data definitions (meta data) and the simplicity logic implemented in Stata (www.stata.com), where the philosophy is that the user should only indicate as much as needed, but also that the user is in complete control.

Approach to control in EpiData Analysis

Interface and execution of commands is controlled by implementation of a number of rules and definitions. There is a separation of what the user can control (run time defined) and what is built in (design time defined -hard coded) and only under control of the development team. The general rule is that overall logic and performance is defined as built in to ensure consistency, but for aspects typically dominated by user preference that part would be run-time rules. The typical user will not need to know all of this, but will see the usage when using assisted command building tools, e.g. the graph specification wizards.

Three types of run time specification rules have been implemented:

  1. Rules that work in general – these are called ”set specifications”.
  2. Rules that apply for a given command for a single ”run” of that command – these are called options.
  3. Rules which define default setting of options.

1: Generally affect interface (menu's, character set, font, sizes) or formats (table design, format). Most of these will only be of interest to advanced users.

2: Control a given command. Eg. how many decimals in percentages in current table.

3: An easy way to define default, e.g. if the user always wants 2 decimals in percentages. Technically these are implemented as ”set specifications”.

How to see definitions and options ?

Set : Execute the command ”set”, which will show current value of all currently defined ”set”

Options: Are shown in the command reference (the file shown when pressing F1) with each command. Notice that some options are general and therefore not repeated with each command.

In a later phase EpiData Analysis will have an ”options” part in the file menu, untill then users must issue ”set specifications” as commands or includie in epidataanalysis.ini 

The next sections of this documents shows current definitions.

Set Specification commands.

All must be used as :

 set < specification from table below > = value
 e.g.: set display command history=off

Interface Control:

Option values notes
DISPLAY COMMAND HISTORY on off Depending on setting the user can specify which of the interface elements should be open.
DISPLAY COMMAND PROMPT on off
DISPLAY COMMANDTREE on off
DISPLAY DATABROWSER on off
DISPLAY MAINMENU on off
DISPLAY TOOLBAR on off
DISPLAY VARIABLES on off
DISPLAY WORKTOOLBAR on off
LANGUAGE various language of menu's, help files tc.
EDITOR PRINT INFO on off add date, time when printing from editor
PRINT PREVIEW CM on off work in centimeter (on) or inch(off)

Interface front size and type

Option values notes
VIEWER FONT CHARSET ISO-8859-1 Alfabeth type etc., e.g. for Chinese: SET viewer font charset = “gb2312” set viewer font name=“Arial Unicode MS”
VIEWER FONT NAME Verdana, Times
VIEWER FONT SIZE 10
WINDOW FONT SIZE 12 All supplementary parts
EDITOR FROT SIZE 12
STYLE SHEET filename styles in output or not
STYLE SHEET EXTERNAL on off include styles in output or output
START PAGE file name file to show on startup ( default: start.htm)

Information after commands:

Option values notes
ECHO on off Defines what is going to be shown after execution of a command. E.g. show info=on will result in all supplementary information.
SHOW COMMAND on off
SHOW ERROR on off
SHOW INFO on off
SHOW RESULT on off echo is a short form for: result+command+info
READ DELETEDoff on include (on) or exclude (off) records marked for deletion

Graph definitions

Option values notes
GRAPH CLIPBOARDon off always copy to clipboard
GRAPH COLOUR default color numbers for series, e.g. 11111111
GRAPH FILENAME FOLDER on off full folder nano or no folder
GRAPH FILENAME SHOW on off include the footnote below graph
GRAPH FONT SIZE 10
GRAPH FOOTNOTEtext default is:“EpiData Analysis Grahp”
GRAPH SAVE on off save graph
GRAPH SAVETYPEpng wmf bmp default: png
GRAPH SIZE X400
GRAPH SIZE Y300

Table design

Option values notes
TABLE DESIGNlineThe style sheets containing class name definitions
TABLE DESIGN FREQline
TABLE DESIGN GRAPHgraph
TABLE DESIGN STATfilled
TABLE DESIGN SYSTEMsystem

Percent formats in tables P1()

Option values
TABLE PERCENT FORMAT COLP1{}
TABLE PERCENT FORMAT ROWP1[]
TABLE PERCENT FORMAT TOTAL%
TABLE PERCENT HEADER%
TABLE PERCENT HEADER COL%
TABLE PERCENT HEADER ROW%
TABLE PERCENT HEADER TOTAL%

Format for confidence intervals

Option values
TABLE CI FORMATC()-
TABEL CI HEADER(95%CI)

History and default output

Option values notes
HISTORY COMMAND PGMon offadd to history when running pgm files
HISTORY COMMENTon offinclude comments in history
HISTORY NAMEfilenameUpon quit, save history file name (def: temp)
OUTPUT FOLDERfolder name
OUTPUT NAMEeaoutput.htmForlder for output and history
OUTPUT OPENon offstandard logfile name at initiation turn logfile on at start of programme

User preference for output:

Option values notes
SHOW VAR VALUEdefault/V/VVshiwing of variable and value labels.
SHOW VAR NAMEdefault/VN/VNNsee in “options” for clarifications

Variable creation

Option values notes
RECODE INTERVAL TEXT- text to put btw. x-y in recode values
VAR GENERATE TYPEf/iDefault variable type with “gen” commans f.float, i:integer

Excact tests

Option values notes
RANDOM SEED9Number of simulations and starting point for random seed
RANDOM SIMULTATIONS500

Internal development information

DEBUG FILENAMEfilenameFor internal development. Writes out information at subroutine level depending on value af debug level
DEBUG LEVEL0…5
SHOWSYSTEMINFOON OFF

General Options

Q“Quit” - Hide output for this command/Q
WFrequency Weighted counts on variable.tab v1/w=“wvar”
Default no options)show variable label and value labels, but exclude var name if included in start of label
VShow value labels and value/VV
VVShow values instead of value labels/V
VNShow variable name and label/VN
VNNOnly variable name, exklude label/VNN

Options for frequencies, cross tabulation and statistics tables

Table cell contests and summary tables

Option values notes
MAllow missing variables as a category/M
MN(was CC)Complete Cases=no missing in any variable/NM
S Summary table shown after other tables. (Content of summary table defined by other options)/S
NTDo not show subtables (when stratifying)/NT
NCDo not show crude table when stratifying/NC
OAOutbreak analysis (first var=ill versus v2…vn)/OA
MT”Multi” Crosstables (First variable x all other)/MT
MR Multiple Response (not implemented yet)-(count several variables into one table and show number go responses and number of cases)/MR
R C TOShow Row Column Total percentages/R/C/TO
PCTPercentages in seperate columns/R/C/PCT
CPCumulative Percentages shown in (frequency tables)
D0 D1 D2Number of decimals in percentages/R/D0

Sort Options in cross tables (and frequency tables)

Option values notes
default (no options)ascending order by values of column & Row
SDdescending on value of 1st column and 1st row/SD
SRAT SCAT SRDT SCDT{Row/Column}{Ascending/Descending}Tota/SRAT /SCAT
SLD SLAascending/descending on labels row+column. Specified column/row for sorting (numerical):
SRA= SRD= SCA= SCD=S{Row/Column}{Ascending/Descending}/SRA=2 /Scd=2

Estimation and statistical tests

all tablesTTest: Chi2 for tables. F or T test in means/T
..GAMGoodmann & Kruskall Gamma/GAM
..ExExact Test (Fishers Exact) for nxk tables/ex
2×2 tablesRRRisk Ratio (counts)/rr
..RRYRisk Ratios (Population at risk) (not implemented yet)
..OOdds Ratio + Chi<sup>2<sup> /O
..OAOutbreak Analysis Table/OA
..EPIOutcome by Many exposure vars. (/O + /SD)/EPI
FrequencyCIConfidence Interval (frequency tables)/CI
allSSummary table of counts, statistics etc.
AllE1 E2 E3 E4 E5Decimal points for the estimators and statistics/E
summery ofTMantel-Haenzel/Partial Gamma/t
stratifiedOBSIn summary table all counts are shown (2×2 only)/obs

Options all Graphs

Option Explanation example
hgrid vgridShow grid lines within graph area/hgrid
xhide yhideDo not show axis (x resepectively y axis )/yhide
xinv yinvReverse scaling axis/xinv
xlog ylogChange axis scale to logaritmic/ylog
noxtick noytickRemove ticks on axis/noxtick
xmin xmax ymin ymaxForce minimum and maximum to these values/xmin=1 xmax=10
xtext ytextText to show as axis explanation/xtext=”1,20,yes,1”
xline ylineShow line(-s) at value/xline=10
xlined ylinedShow dotted line(-s) at value/ylined=15
xinc yincAxis increment/xinc=5
xl90Change angle of texts on x axis to 90/XL90
yvalueShow Y value in a small box next to each (x,y)/yvalue
saveSave graph to a file with indicated name/save=”p3.png”
editOpen graph for editing/edit
ti sub fnTitle, subtitle and footnote texts/fn=”My project”
legendshow legend/ti=”title”
/sub=”sub title”

Options in SPC Charts

Option Explanation example
B (was break)Divide spc graph at one or more breakpoints/B=12 /b=24
TApply testing/T
NT (was notest)Do not show table of tests/nt
NEGLCLAllow negative lower control limit/neglcl
EXPExclude point/exp=10
EXVExclude values from this and above/exp=12
EXZExclude points where Y=0/exz
XlUse values from variable for ticks on X axis.xl=v2
TabShow table of counts below graph/tab

Other Special Graph Options

xonlyHistogram: Only include x values with data/xonly
xallBar: Include all x values from min to max
sortHistogram and Bar: sort on x value
NO (was hideout)Boxplot: Hide outliers = No outliers/NO

Other Command specific options

command and option explanation example
Erasepng allErase all png files regardless of name
noconfirmDo so without confirmation for each file.
readcloseclose any open data file
typeH1 H2 H3 H4 H5 CLASSindicates the paragraph html code for the added text.
showclassclass to use for text in a file shown with ”show”/class=“p”
stattables aggregatep1..p99 MEAN IQR IDR DES(for a complete list see command reference) -
LogOpenA(append)append to existing file/Close/replace
CloseClose an open logfile
ReplaceReplace the file indicated (overwrite)
Agg StattablesCloseReplace current data in memory by aggregated file
ListNONo observation numbers shown/NO
file commands which saveREPLACEFor (savedata, savepgm, logopen, graphs – save) allow replacing of file with same name/REPLACE
techdocs/analysis/setoptions.txt · Last modified: 2015/07/03 08:32 by gitte.fuusager
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