ClinReport (version 0.9.1.1)

report.doc: Transform a desc object to a flexTable object ready to export to Word using officer

Description

report.doc Export the table to MS word in "clinical standard" format.

Usage

report.doc(table, ...)
# S3 method for desc
report.doc(table, title, colspan.value = "", doc = NULL,
  init.numbering = F, numbering = T, font.name = "Times", ...)

Arguments

table

a desc object that report statistics (the results of report.quanti or report.quali)

...

Other arguments

title

Character. The title of the table

colspan.value

Character. Add the label of the x1 variable levels (typically "Treatment Groups")

doc

NULL or a rdocx object

init.numbering

Boolean. If TRUE Start numbering of the output at 1, otherwise it increase the output numbering of 1 unit

numbering

Boolean. If TRUE Output numbers are added before the title.

font.name

Character. Passed to font function. Set the font of the output in Word

Details

It creates a flextable object from a desc object and can eventually add it directly into a rdocx object. @return A flextable object or a rdocx object.

See Also

report.quali report.quanti report.lsmeans

Examples

# NOT RUN {

# }
# NOT RUN {
library(officer)
library(flextable)
library(reshape2)
library(emmeans)
library(lme4)
library(nlme)

data(data)

tab1=report.quanti(data=data,y="y_numeric",
	x1="GROUP",x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID")

tab2=report.quali(data=data,y="y_logistic",
	x1="GROUP",x2="TIMEPOINT",at.row="TIMEPOINT",total=T,subjid="SUBJID")


tab3=report.quali(data=data,y="VAR",y.label="Whatever")

tab4=report.quali(data=data,y="VAR",y.label="Whatever",
	subjid="SUBJID")


tab5=report.quali(data=data,y="VAR",y.label="Whatever",x1="GROUP",
	subjid="SUBJID")


mod1=lm(y_numeric~GROUP+TIMEPOINT+GROUP*TIMEPOINT,data=data)
test1=emmeans(mod1,~GROUP|TIMEPOINT)
tab.mod1=report.lsmeans(lsm=test1,x1.name="GROUP",
x2.name="TIMEPOINT",at.row="TIMEPOINT")


mod2=lm(y_numeric~GROUP,data=data)
test2=emmeans(mod2,~GROUP)
tab.mod2=report.lsmeans(lsm=test2,x1.name="GROUP")


mod3=lme(y_numeric~GROUP+TIMEPOINT+GROUP*TIMEPOINT,
random=~1|SUBJID,data=data,na.action=na.omit)
test3=emmeans(mod3,~GROUP|TIMEPOINT)
tab.mod3=report.lsmeans(lsm=test3,x1.name="GROUP",
x2.name="TIMEPOINT",at.row="TIMEPOINT")


mod4=glm(y_logistic~GROUP+TIMEPOINT+GROUP*TIMEPOINT,
family=binomial,data=data,na.action=na.omit)
test4=emmeans(mod4,~GROUP|TIMEPOINT)
tab.mod4=report.lsmeans(lsm=test4,x1.name="GROUP",
x2.name="TIMEPOINT",at.row="TIMEPOINT")


mod5=glm(y_logistic~GROUP+TIMEPOINT+GROUP*TIMEPOINT,
family=binomial,data=data,na.action=na.omit)
test5=emmeans(mod5,~GROUP|TIMEPOINT)
tab.mod5=report.lsmeans(lsm=test5,x1.name="GROUP",
x2.name="TIMEPOINT",at.row="TIMEPOINT",type="response")


mod6=glm(y_poisson~GROUP+TIMEPOINT+GROUP*TIMEPOINT,
family=poisson,data=data,na.action=na.omit)
test6=emmeans(mod6,~GROUP|TIMEPOINT)

tab.mod6=report.lsmeans(lsm=test6,x1.name="GROUP",
x2.name="TIMEPOINT",at.row="TIMEPOINT",type="response")

mod7=lm(y_numeric~+GROUP+TIMEPOINT+VAR,
data=data,na.action=na.omit)
test7=emmeans(mod7,~GROUP:VAR|TIMEPOINT)
tab.mod7=report.lsmeans(lsm=test7,x1.name="GROUP",
x2.name="TIMEPOINT",x3.name="VAR",at.row="TIMEPOINT")



doc=read_docx()

doc=body_add_par(doc,"A beautiful reporting using ClinReport", style = "heading 1")

doc=report.doc(tab1,title="Quantitative statistics (2 explicative variables)",
	colspan.value="Treatment group",doc=doc,init.numbering=T)


doc=report.doc(tab2,title="Qualitative statistics (2 explicative variables)",
	colspan.value="Treatment group",doc=doc)


doc=report.doc(tab3,title="Qualitative statistics (1 variable only)",doc=doc)


doc=report.doc(tab.mod1,title="Linear Model LS-Means results using lm with interactions",
	colspan.value="Treatment group",doc=doc)

doc=report.doc(tab.mod2,title="Linear Model LS-Means results using lm without interaction",
	colspan.value="Treatment group",doc=doc)

doc=report.doc(tab.mod3,title="Linear Mixed Model LS-Means results using lme",
	colspan.value="Treatment group",doc=doc)

doc=report.doc(tab.mod4,title="Generalized Linear Mixed Model LS-Means results using lme",
	colspan.value="Treatment group",doc=doc)


doc=report.doc(tab.mod6,title="Poisson Model LS-Means results",
	colspan.value="Treatment group",doc=doc)


file=paste(tempfile(),".docx",sep="")
print(doc, target =file)
shell.exec(file)

# }
# NOT RUN {
# }