Description Usage Arguments Details Author(s) See Also Examples
Produce a table of comparisons for reports and manuscripts
1 2 3 4 5 6 7 8 9 10 11 12 13  catconttable(data, vars, byVar, vars.cat = NULL, fisher = NULL,
fisher.arg = NULL, cmh = NULL, row.score = NULL, col.score = NULL,
normal = NULL, var.equal = NULL, median = NULL, odds = NULL,
odds.scale = NULL, odds.unit = NULL, none = NULL, row.p = TRUE,
alpha = 0.05, B = 1000, seed = NULL)
cattable(data, vars, byVar, fisher = NULL, fisher.arg = NULL, cmh = NULL,
row.score = NULL, col.score = NULL, mcnemar = NULL, correct = NULL,
none = NULL, odds = NULL, row.p = TRUE, alpha = 0.05, minl = 5)
conttable(data, vars, byVar, normal = NULL, var.equal = NULL,
median = NULL, none = NULL, odds = NULL, odds.scale = NULL,
odds.unit = NULL, alpha = 0.05, B = 1000, seed = NULL)

data 
A 
vars 
A character vector naming the variables to be compared 
byVar 
A character(1) giving the grouping variable. This allows more than one level. Numeric variables are coerced to factors. 
vars.cat 
A character vector that can be used to specify which, if
any, numeric variables in 
fisher 
A character vector giving the names of variables that should be compared with Fisher's Exact test. Currently, there is no implementation to determine this automatically. 
fisher.arg 
A list of additional arguments to pass to 
cmh 
A character vector giving the names of variables that should be compared with ManthelHaenszel's Test for Linear Trend. This is not yet written and will be ignored. 
row.score 
Currently ignored 
col.score 
Currently ignored 
normal 
A character vector that assigns variables in 
var.equal 
A character vector that assigns variables in 
median 
A character vector that assigns variables that shoudl be summarized with a median, quartiles, or min and max. 
odds 
A character vector giving the names of variables for which odds ratios should be calculated. For categorical measures, this is the primary test of comparison. For numeric measures, this is calculated in addition to another test. 
odds.scale 
For numeric variables only. A list with named elements
that gives the scale on which the odds ratio should be presented. For
example, if the odds for variable 
odds.unit 
For numeric variables only. A list with named elements
that gives the units on which the odds ratio should be presented. For
example, if the odds of variable 
none 
A character vector naming variables in 
row.p 
Toggles if row or column proportions are calculated. 
alpha 
Significance levels for tests. 
B 
The number of Bootstrap samples for bootstrapped confidence intervals. 
seed 
The seed to use in starting the Bootstrapping. 
mcnemar 
a character vector giving the names of variables that should be compared using McNemar's test. 
correct 
Character vector giving the variables for which a continuity correction should be applied in McNemar's test. 
minl 
Minimum length for levels abbreviations. The function

catconttable
is a wrapper that determines the type of
variable and calls either cattable or conttable as appropriate. For this
to work properly, all factor variables must be defined before the function
call.
In contrast, if cattable is called directly, variables are coerced to factors, which could lead to peculiar results if a numeric value is given.
Benjamin Nutter
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81  #Read in the delivery dataset from the lazyWeave package
data(Delivery)
#Use conttable to summarize maternal age, ga weeks, weight (grams)
#and grava by delivery type. The dataset name is specified under the "data="
#option, the variables of interest are listed under "vars=", and the Klevel by variable
#is specified under "byVar=".
#Default is to report mean and bootstrapped 95% CI for mean. Tests of location are by
#default either Wilcoxon rank sum (K=2) or KruskalWallis (K>2) rank sum. The "seed="
#option allows for reproducibility by setting the seed for getting bootstrapped samples.
d_type.contable < conttable(data=Delivery,
vars=c("maternal.age", "ga.weeks", "wt.gram", "grava"),
byVar="delivery.type")
#Specifying weights by delivery type as a normally distributed variables, reports means,
#standard deviations and a ttest of equality of the means for delivery type. Variables listed
#under "var.equal=" are assumed to have equal variances in all levels of byVar. Otherwise,
#variances are allowed to be unequal.
d_type.conttable < conttable(data=Delivery,
vars=c("maternal.age", "ga.weeks", "wt.gram", "grava", "apgar1"),
byVar="delivery.type",
normal=c("wt.gram", "maternal.age"),
var.equal="ga.weeks")
#List variables under "median=" to report median, 25th and 75th percentiles.
d_type.conttable < conttable(data=Delivery,
vars=c("maternal.age", "ga.weeks", "wt.gram", "grava", "apgar1"),
byVar="delivery.type",
normal=c("wt.gram", "maternal.age"),
var.equal="ga.weeks",
median=c("grava","apgar1"))
#Use cattable to summarize child sex, laceration, and laceration degree by delivery type.
#Row percent, overall counts, and counts by delivery type are reported. Column percents can
#be specified by the row.p=FALSE option.
#By default chisquare tests of independence are performed.
d_type.cattable < cattable(data=Delivery,
vars=c("child.sex", "laceration"),
byVar="delivery.type")
#For variables listed under "fisher=" Fisher's exact test of independence is performed.
#The reported test statistic is the odds ratio.
d_type.cattable < cattable(data=Delivery,
vars=c("child.sex", "laceration"),
fisher=c("child.sex"),
byVar="delivery.type")
#All variables listed in a single table
d_type.catconttable < catconttable(data=Delivery,
vars=c("maternal.age", "ga.weeks", "child.sex", "wt.gram",
"grava", "apgar1", "laceration"),
median=c("grava", "apgar1"),
normal="maternal.age",
fisher="child.sex",
byVar="delivery.type")
## Not run:
#Code for writing ctable objects to a file. See write.ctable() for more information
#Write to PDF
options(lazyReportFormat='latex')
lazy.write(
lazy.file.start(),
write.ctable(d_type.catconttable),
lazy.file.end(),
OutFile="SampleOutput.tex")
#Generate a pdf in the working directory
lazy.build("SampleOutput.tex")
unlink("SampleOutput.tex")
unlink("SampleOutput.pdf")
## End(Not run)

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