Building Augmented Data to Run Multi-State Models with 'msm' Package

A fast and general method for restructuring classical longitudinal data into augmented ones. The reason for this is to facilitate the modeling of longitudinal data under a multi-state framework using the 'msm' package.


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msmtools introduces a fast and general method for restructuring classical longitudinal datasets into augmented ones. The reason for this is to facilitate the modeling of longitudinal data under a multi-state framework using the msm package.

Installation

# Install the released version from CRAN:
install.packages( "msmtools" )
 
# Install the development version from GitHub:
devtools::install_github( "contefranz/msmtools" )

Overview

msmtools comes with 4 functions:

  • augment(): the main function of the package. This is the workhorse which takes care of the data reshaping. It is very efficient and fast so highly dimensional datasets can be processed with ease;

  • polish(): it helps in find and remove those transition which occur at the same time but lead to different states within a given subject;

  • prevplot(): this is a plotting function which mimics the usage of msm() function plot.prevalence.msm(), but with more things. Once you ran a multi-state model, use this function to plot a comparison between observed and expected prevalences;

  • survplot(): the aims of this function are double. You can use survplot() as a plotting tool for comparing the empirical and the fitted survival curves. Or you can use it to build and get the datasets used for the plot. The function is based on msm plot.survfit.msm(), but does more things and it is considerably faster.

For more information about msmtools, please check out the vignette with vignette( "msmtools" ).

Bugs and issues can be reported at www.github.com/contefranz/msmtools/issues.


News

msmtools 1.3


Major changes

  • The new function polish() is introduced. This adds support in the preprocessing part of the analysis. polish() addresses the specific problem of different transitions occurring at the same exact time within a given subject. This is a case for which a multi-state model fails to estimate the probability associated with the two transitions. At the moment, the whole subject specified by data_key is deleted.

Minor changes

  • Global variables are now correctly declared on top of functions using utils::globalVariables(). This prevents the assignment to NULL in the preable of functions which decreases the elegance of the code.

  • The printing of information is now way more simplier and is not based on sink() anymore. This has been done to be less intrusive into the OS when redirecting on console messages. Also, no more OS type check is done so that the control with argument verbose is the most general possible. Warnings are still controlled as usual, so that they get printed, if any, just after the function call.

Other changes

  • The vignette has been updated to include new functionalities and it is now in HTML format which provides a faster and lighter access.

  • Improved the documentation's readability in the 'Value' section for augment() and survplot().

  • In the documentation of augment() now there is an explicit example which returns a data.frame.

  • Windows builds of msmtools are now constantly checked through Appveyor.

  • The author/maintainer e-mail has changed to match his new affiliation and now is [email protected].

Bug fixes

  • After augment() has been run, results are now visible at the very first call. This means that you can finally print on console the augmented dataset right away.

  • pandoc versions prior 1.17 does not fully support spaces in file names and caused a warning when compiling msmtools under Fedora using both clang ang gcc. Now all file names are without spaces. msmtools 1.3 has been built using pandoc 1.19.2 and pandoc-citeproc 0.10.4.1


msmtools 1.2


Major changes

  • msmtools can now run with R 3.0.0 and above for retro compatibility reasons.

  • augment() gains the new argument check_NA which allows the user to decide if the function should run some checks to find missing data in the following arguments: data_key, n_events, pattern, t_start and t_end. Default is FALSE. Missing data checks are always carried out on more_status.

  • augment() gains the new argument convert which if set to TRUE efficiently converts the output to the old school data.frame class.

  • survplot() gains the new argument return.all which saves you some typing time when requesting both the data of the Kaplan-Meier and the fitted survival. Arguments return.km and return.p now are set to NULL by default instead of FALSE.

  • survplot() gains the new argument convert which if set to TRUE efficiently converts any object returned to the old school data.frame class.

Changes in functions

  • augment() now also accepts an object of class data.frame as input. If so, the function internally converts it to a data.table.

  • augment() now accepts t_augmented without quotes too. Default name is still "augmented".

  • augment() gets a whole new implementation which comes into play when pattern has only 2 values ('alive' and 'dead'). Now the procedure runs with computational time only slightly longer than the standard 3 values in pattern. This is due thanks to the fast joins method adopted.

  • augment() now is much faster when defining the target size for the reshaping. This was a bottleneck which caused memory issues and wasted time.

  • General memory optimization in the function augment(). Now the function uses ~ 30% less memory.

Other changes

  • All the functions now have more detailed and better written helps.

  • Some minor changes in the vignette to encapsulate new functionalities.

Bug fixes

  • In augment(), the sequential status is now correctly computed. There was a wrong call which blocked the object defined by n_events.

  • In augment(), when pattern was detected with two unique values, inconsistent results were produced during the status flag assignment. This was due to a wrong rounding of the amount of augmenting factor for each unit.



msmtools 1.1


Changes in functions

  • augment() now is way faster then in v1.0 thanks to a new implementation when defining patterns.

  • augment() now uses the faster uniqueN() to extract the number of unique values in a vector.

Bug fixes

  • augment() now correctly repositions new created variables.

Other changes

  • augment() in-line help now provides correct information on what it returns.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("msmtools")

1.3 by Francesco Grossetti, a year ago


https://github.com/contefranz/msmtools


Report a bug at https://github.com/contefranz/msmtools/issues


Browse source code at https://github.com/cran/msmtools


Authors: Francesco Grossetti [aut, cre]


Documentation:   PDF Manual  


Task views: Survival Analysis


GPL-3 license


Imports data.table, msm, survival

Suggests testthat, knitr, rmarkdown


See at CRAN