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---+ rreport To Do List 1 %Y%%RED% TERRI %ENDCOLOR% =accrualReport=: * Have made several improvements: 1 Modified order of generated plots and tables. 1 'Subjects randomized over time' plot: 1 Can now specify (up to) two =EntryDate= variables. 1 =xlim= has been modified to the 'floor' of the minimum date to the 'ceiling' of the maximum date are used - i.e., if 4/16/06-6/20/06 specified as =dateRange=, then =xlim=c(4/1/06, 6/30/06)=. 1 On the date (x-) axis, 'minor' (i.e., shorter) tick marks are used to denote each month, and 'major' (i.e., longer) tick marks are used to denoted every six months, which are labeled. 1 Output of other tables and plots depends on whether just =Minor= or =Minor= and =Major= are specified. * If just =Minor= specified, then 'Number of subjects randomized by Minor' plot and 'Number of Minors having a given number of subjects randomized' plot are generated. * If =Minor= and =Major= specified, then 'Number of subjects randomized by Major' plot (with number of =Minors= within each =Major= given), 'Number of subjects randomized by site' plot (automatically implements =combineEqual= if greater than 40 levels; and adds the number of subjects per site if =combineEqual=), and 'Number of sites having a given number of subjects randomized' plot are generated. Also generates table of =combineEqual= abbreviations. The definition of 'site' is given in each appropriate table caption. 1 %Y%%RED% TERRI %ENDCOLOR% =rangeCheck=: * Have split into two separate functions: =rangeCheck= and =makeNA=. * =rangeCheck= creates a <nop>LaTeX table that displays the frequency of various lab parameter values outside a defined range. The table has three columns: (1) Lab parameter; (2) Defined range; and (3) 'Out of range' (the percent and frequency of values outside the defined range). * %X% Improvements to make: Have =rangeCheck= create a second table (and/or dot plot) that summarized the sites (country and center) (and IDs) that have records outside the defined range of each lab parameter. * =makeNA= replaces the values of a data frame that are outside the defined range with =NA=. 1 =aeReport2=: 1 %Y%%RED% THOMAS %ENDCOLOR% Allow to have short captions for table of contents. 1 Develop a plot method. 1 %RED% THOMAS %ENDCOLOR% Allow to generate a title and table headings even if the table will be blank (i.e., nrow(data) = 0). 1 %Y%%RED% THOMAS %ENDCOLOR% Make it easy to direct the output to a cumulative appendix that has multiple sections. Modify to have an option to put in the body of the report only those events having a combined frequency of at least =minfreq=. When =minfreq= is used, the existing long table should go to an appendix. Create a sentence that links to the appendix (both in text and as a hyperlink). * See =listTable= item. 1 =listTable=: 1 For functions that create listings of individual patient records, make it easy to direct the output to a cumulative appendix that has multiple sections. Default for =listTable= will go appendix but user can override this for special listings such as severe events of a certain type. Text written to the appendix can keep =append= ing to =gentex/app.tex=. Will need to generate =\section= commands automatically. 1 %RED% THOMAS %ENDCOLOR% Move functionality into latex.data.frame. 1 Dot charts: * %RED% THOMAS %ENDCOLOR% Possible solution: include dot charts in table output via a =dotchart=TRUE= argument. 1 Add a new =mincat= option to appropriate functions. Dot charts having fewer than =mincat= categories depicted in the entire chart should be suppressed. A good value of =mincat= might be 7. 1 See if producing either a dot chart for categorical variables or a table but not both will work. 1 Dot charts should have category frequencies added in the right margin and P-values in the (probably) left margin; idea is to have as much information as possible in graphs, then to see if committee members can dispense with tables; will have to see which details are OK to omit from a graph (e.g. treatment sample sizes as these are usually almost equal). 1 Hmisc: 1 Submit =floor.chron= and =ceiling.chron= to the =chron= maintainer for consideration of inclusion in =chron=. 1 %RED% THOMAS %ENDCOLOR% Create a new function =scaleReport= or adapt =mixedvarReport= and other functions to report discrete-value scale variables (such as those on an integer 1-5 scale) as mean and SD and with a dot chart showing all unique values of the scale. Don't use quantiles, box plots, <nop>ECDFs, or binned histograms for scales. *Better*: define function =discreteNum= that can be used when defining a data frame or in a call to =summary.formula=, e.g. =summary(treat ~ age + discreteNum(painSeverity))=. =discreteNum= implies you the way to compute descriptive stats is to not use quantiles but to use mean, SD, and occasionally mode. 1 %RED% THOMAS %ENDCOLOR% Improve =dotchart2= to switch to smaller font for left margin labels or to word-wrap them, to avoid squeezing dot charts to be too narrow. Specify a minimum width allowed? 1 Be able to define different number of lines for the first page and then subsequent pages in a longtable = TRUE argument call. 1 Fix units to always be placed in the right of the column in a mixedvarReport call -- \hfill in <nop>LaTeX doesn't always work. 1 Be able to break the table into mutliple tables based on categorical "response" variable in a method = "reverse" (i.e., the categorical variable has 6 levels, so break the table up into three tables each with 2 levels of the response). 1 Confidence intervals for differences in two proportions * Wherever such confidence intervals of their half-widths are calculated, including in the new stuff Thomas is implemented with micro plots inside tables, use the Newcombe method. This is the default in the =ci.pd= function in the =Epi= package, which should be a required package for =rreport= 1 Other function specific: 1 %RED% SVETLANA %ENDCOLOR% Change =mixedvarReport= and =labreport= to use new defaults: * %Y% in open reports, suppress ECDFs and just show histograms * %Y% in closed reports, choose ECDF if two treatments, replace this with box-percentile plot if > 2 treatments. * add an option of plotting contin. variables (not histograms) contDataPlot =TRUE. 1 %RED% SVETLANA %ENDCOLOR% Change =mixedvarReport= and =labreport= to use new defaults: * %Y% design and code automatic latex markers management. 1 %RED% SVETLANA %ENDCOLOR% Develop a new function for comparing a data frame with the previous version; extremely concise (more concise than =describe= ); output is for analysts in statistical center and sponsor; need to have an =ID= variable so can compute number of subjects added/removed and count number of unique subjects. Should be added to =Hmisc= for one pair but a superfunction added to =rreport= to do this automatically a series of data frames. 1 Look into replacing global variables (such as graphics output option) with something like =option( )= or =.Options$element=. 1 Need visit-oriented =mixedvarReport=. 1 %RED% TERRI %ENDCOLOR% Improve =put2web= to put in the body of the e-mail which pages to print. Have =rreport= tell =LaTeX= to save the page number of the start of the appendix. * See =aeReport2= and =listTable= appendix related items. 1 %Y% %BLUE%THOMAS%ENDCOLOR% %RED% TERRI %ENDCOLOR% =publishPdf= 'scp -p' problem and permission problems in general: * Need to be able to upload and to have real date/time stamps. * Using Subversion solves premission problems and date/time stamping as well as providing and archive of previous report versions. 1 =rreport= in general: 1 %RED% TERRI/SVETLANA %ENDCOLOR% Change "enrollment" to "screened" everywhere in =Oreport= and =report= .tex files. 1 %RED% TERRI %ENDCOLOR% Create Rd help files for all existing rreport functions. 1 Develop a procedure for validating pivotal calculations against the blinded sponsor's calculations by creating dummy treatment assignments that are given to the sponsor. 1 Make plans for an automatic validation process by having rreport generate Stata code to repeat analyses. 1 Possible to consolidate the unique number of functions in rreport? 1 Make directory structure more user determined -- =fileNames.s=. 1 Construct =Makefiles= for mutliple-step procedures (suggested in Frank's email). * That is, split =report.s= into =datamanip.report.s= and =generateoutput.report.s=. 1 Incorporate =ggplot= package. 1 %Y% FIXED arg =append=TRUE= in mixedvarReport possibly causes outputted images to overwrite each other. 1 Table 34, 38, 39, 43 (REDUCE, open report, section 12.1,Occurance of HGPIN for subjects diagnosed with cancer, table 34): put into scientific notation in LaTeX (improve latex.summary.formula.reverse) - ask Frank what he meant. 1 Make mixedvarReport() plot only categorical variables with number of levels less than three when argument 'categDataPlot' equals TRUE.(Frank - REDUCE) 1 Make ecdf() and mixedvarReport() plot the data in a given range - given =xlim=. (Frank - REDUCE) 1 Before running report.s create an empty appendix file to prevent errors of appending to it several times or overiding it when it is not empty.
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Topic revision: r23 - 24 Oct 2006,
SvetlanaEden
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