Type: Package
Title: Cohort Data Analyses
Version: 0.1.6
Author: Jari Haukka [aut, cre]
Maintainer: Jari Haukka <jari.haukka@helsinki.fi>
Depends: R (≥ 3.6), Epi, cmprsk, ggplot2
Imports: stats, survival, DiagrammeR, DiagrammeRsvg, rsvg, mgcv
Suggests: knitr, rmarkdown, lattice, mstate, testthat
Description: Functions to make lifetables and to calculate hazard function estimate using Poisson regression model with splines. Includes function to draw simple flowchart of cohort study. Function boxesLx() makes boxes of transition rates between states. It utilizes 'Epi' package 'Lexis' data.
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.2.1
NeedsCompilation: no
Packaged: 2022-11-22 13:00:23 UTC; jkhaukka
Repository: CRAN
Date/Publication: 2022-11-23 12:00:04 UTC

Boxes plot summarizing Lexis object

Description

Creates boxes graph describing Lexis

Usage

boxesLx(
  x,
  layout = "circo",
  prop.penwidth = FALSE,
  scale.Y = 1,
  rankdir = "TB",
  node.attr = "shape=box",
  edge.attr = "minlen=1",
  show.loop = FALSE,
  show.persons = FALSE,
  fontsizeN = 14,
  fontsizeL = 8,
  show.gr = TRUE
)

Arguments

x

Lexis object

layout

Graphviz layout "circo", "dot", "twopi" or, "neato". It determines general layout of graph.

prop.penwidth

use line width relative to incidence. If TRUE linewidths of showing transition rates beween states are relative to log of rate.

scale.Y

scale for incidence. Scale factor rates, default is 1.

rankdir

for graph, default is TB. NOTE! this works best with layout "dot"

node.attr

general node attributers. Attributes like shape, color, fillcolor, etc. for nodes. Consult Graphviz documentation for details https://www.graphviz.org/doc/info/attrs.html.

edge.attr

general edge (line) attributers. Attributes like color, arrowhead, fontcolor etc. for edges. Consult Graphviz documentation for details https://www.graphviz.org/doc/info/attrs.html

show.loop

, should loop (staying in same state be shown), default FALSE

show.persons

, should number of persons be shown (entry->exit), default FALSE

fontsizeN

font size for nodes

fontsizeL

font size for edges

show.gr

should graph be shown. If TRUE, function DiagrammeR::grViz is used to show graph.

Value

Character vector containing Graphviz script. This may used to create graph by DiagrammeR::grViz function.

Author(s)

Jari Haukka jari.haukka@helsinki.fi

See Also

grViz

Examples

library(DiagrammeR)
library(survival)
library(Epi)
library(mstate)
data(ebmt3)
bmt <- Lexis(exit = list(tft = rfstime/365.25),
             exit.status = factor(rfsstat, labels = c("Tx", "RD")),
                          data = ebmt3)
bmtr <- cutLexis(bmt, cut = bmt$prtime/365.25, precursor.states = "Tx",
                                           new.state = "PR")

summary(bmtr)
kk<-boxesLx(bmtr)
## Not run: 
# Graph to file
gv2image(kk, file="k1", type="pdf")

## End(Not run)
boxesLx(bmtr,layout="dot",rankdir = "LR",show.loop = FALSE,show.persons = TRUE)
boxesLx(bmtr,node.attr='shape=hexagon color=navy style=filled fillcolor=lightblue',
edge.attr = ' color=steelblue arrowhead=vee fontcolor="#8801d7" ',
layout="circo",prop.penwidth=TRUE)

Estimates hazard function using Poisson model

Description

Estimates hazard function using Poisson model

Usage

estim.hazard(
  formula,
  data,
  time,
  status,
  breaks,
  knots,
  time.eval = breaks,
  alpha = 0.05,
  use.GAM = FALSE,
  print.GAM.summary = FALSE,
  ...
)

Arguments

formula

formula with Surv in LHS, NOTE! only one variable in RHS

data

data used by formula

time

time variables

status

status indicator Lowest value used as sensoring. If only one unique value detected, all are assumed events

breaks

time is splitted with these values

knots

knots for natural splines used in estimation of hazard function

time.eval

in which time points hazard function is evaluate.

alpha

significance level for confidence intervals

use.GAM

logical determining if generalized additive model (GAM) is used

print.GAM.summary

logical determining if summary of GAM is printed

...

parameters for glm

Value

Returns data frame with time and hazard function values with attribute 'estim.hazard.param' containing estimation parameters (breaks and knots)

Author(s)

Jari Haukka jari.haukka@helsinki.fi

Examples

library(survival)
tmp.hz<-estim.hazard(time=lung$time,status=lung$status)
head(tmp.hz,2)
attributes(tmp.hz)$estim.hazard.param # estimation parameters
tmp.hz2<-estim.hazard(formula=Surv(time,status)~sex,data=lung)
head(tmp.hz2,2)

Function makes image from graphviz code

Description

Function makes image from graphviz code

Usage

gv2image(gv, file = "gv", type = "png", engine = "dot", ...)

Arguments

gv

character string containing graphviz code

file

file name for image, character string

type

type of ('pdf', 'png', 'ps', 'raw','svg','webp') as character string

engine

grViz engine, defaults is 'dot'

...

parameters for rsvg_

Value

Invisible name of file created.

Author(s)

Jari Haukka jari.haukka@helsinki.fi

Function makes flowchart in graphviz

Description

Function makes flowchart in graphviz

Usage

mkflowchart(N, text.M, text.P, type = 1)

Arguments

N

Population sizes

text.M

Text for exclusions, length one less than N

text.P

Text for main boxes, must be same length with N

type

flowchart type (1 or 2)

Value

Character string, graphviz language

Author(s)

Jari Haukka jari.haukka@helsinki.fi

Examples

DiagrammeR::grViz(mkflowchart(N=c(743,32,20),
text.M=c("Excluded","Excluded \n other with reasons"),
text.P=c("Studies","Relevant studies","Included in final review"),type=1))

Function makes rate table with confidence intervals for crude incidences (rates)

Description

Function makes rate table with confidence intervals for crude incidences (rates)

Usage

mkratetable(formula, data, alpha = 0.05, add.RR = FALSE, lowest.N = 0, ...)

Arguments

formula

where Surv object is on lhs and marginal variable(s) on rhs. Marginal variables should usually be factors

data

data.frame to be used

alpha

confidence level, default is 0.05

add.RR

should rate ratio (RR) be added

lowest.N

lowest frequency to be shown

...

additional parameter for function survival::pyears

Value

table with columns named after marginal variables and n, event, incidence, se, exact.lower95ci and exact.upper95ci variables

Note

packages survival is utilized. Frequencies lower than lowest.N replaced by 999999 Person-years scaled by default with 365.25

Author(s)

Jari Haukka jari.haukka@helsinki.fi

See Also

survival pyears

Examples

library(survival)
tmp.lt1<-mkratetable(Surv(time,status)~ sex,data=lung)
tmp.lt2<-mkratetable(Surv(time,status)~ sex+ph.ecog,data=lung,add.RR=TRUE,lowest.N=10)

Plots cumulative incidence rates

Description

Plots cumulative incidence rates

Usage

plotcuminc(ftime, fstatus, cencode, pop.length = 50, group, ...)

Arguments

ftime

failure time variable

fstatus

variable with distinct codes for different causes of failure and also a distinct code for censored observations

cencode

value of fstatus variable which indicates the failure time is censored.

pop.length

number of population sizes shown

group

plots will be made for each group. If missing then treated as all one group

...

additional parameters

Value

if missing group ggplot2 object or if group given named list of ggplot2 objects

Note

package cmprsk and ggplot2 are utilized

Author(s)

Jari Haukka jari.haukka@helsinki.fi

See Also

survival pyears

Examples

set.seed(2)
ss <- rexp(100)
gg <- factor(sample(1:3,100,replace=TRUE),1:3,c('a','b','c'))
cc <- sample(0:2,100,replace=TRUE)
print(plotcuminc(ftime=ss,fstatus=cc,cencode=0))
print(plotcuminc(ftime=ss,fstatus=cc,cencode=0,group=gg))

Function makes plot(s) from ratetable

Description

Function makes plot(s) from ratetable

Usage

plotratetable(rt, RR = FALSE)

Arguments

rt

Rate table produced by function mkratetable

RR

Boolean, if TRUE rate ratios plotted

Value

ggplot object, or list if multiple variables in rate table

Examples

library(ggplot2)
library(survival)
tmp.lt1<-mkratetable(Surv(time,status)~ ph.ecog,data=lung,add.RR = FALSE)
plotratetable(tmp.lt1)
tmp.lt2<-mkratetable(Surv(time,status)~ sex+ph.ecog+cut(age,4),data=lung,add.RR=TRUE,lowest.N=1)
plotratetable(tmp.lt2,TRUE)