Package 'LocalControl'

Title:	Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence
Description:	Implements novel nonparametric approaches to address biases and confounding when comparing treatments or exposures in observational studies of outcomes. While designed and appropriate for use in studies involving medicine and the life sciences, the package can be used in other situations involving outcomes with multiple confounders. The package implements a family of methods for non-parametric bias correction when comparing treatments in observational studies, including survival analysis settings, where competing risks and/or censoring may be present. The approach extends to bias-corrected personalized predictions of treatment outcome differences, and analysis of heterogeneity of treatment effect-sizes across patient subgroups. For further details, please see: Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.
Authors:	Nicolas R. Lauve [aut] , Stuart J. Nelson [aut] , S. Stanley Young [aut] , Robert L. Obenchain [aut] , Melania Pintilie [ctb], Martin Kutz [ctb], Christophe G. Lambert [aut, cre]
Maintainer:	Christophe G. Lambert <[email protected]>
License:	Apache License 2.0 \| file LICENSE
Version:	1.1.4
Built:	2024-12-04 07:22:21 UTC
Source:	CRAN

Help Index

Simulated cardiac medication data for survival analysis
Framingham heart study data extract on smoking and hypertension.
Lindner Center for Research and Education study on Abciximab cost-effectiveness and survival
Local Control
Deprecated LocalControl functions
Local Control Classic
Calculate confidence intervals around the cumulative incidence functions (CIFs) generated by LocalControl when outcomeType = "survival".
Provides a bootstrapped confidence interval estimate for LocalControl LTDs.
Plot cumulative incidence functions (CIFs) from Local Control.
Plots the local treatment difference as a function of radius for LocalControl.
Test for Within-Bin X-covariate Balance in Supervised Propensiy Scoring
LOESS Smoothing of Outcome by Treatment in Supervised Propensiy Scoring
Propensity Score prediction of Treatment Selection from Patient Baseline X-covariates
Change the Number of Bins in Supervised Propensiy Scoring
Examine Treatment Differences on an Outcome Measure in Supervised Propensiy Scoring
Prepare for Accumulation of (Outcome,Treatment) Results in Unsupervised Propensity Scoring
Artificial Distribution of LTDs from Random Clusters
Returns a series of boxplots comparing LTD distributions given different numbers of clusters.
Display Sensitivity Analysis Graphic in Unsupervised Propensiy Scoring
Hierarchical Clustering of Patients on X-covariates for Unsupervised Propensiy Scoring
Instrumental Variable LATE Linear Fitting in Unsupervised Propensiy Scoring
Plot the LTD distribution as a function of the number of clusters.
Nearest Neighbor Distribution of LTDs in Unsupervised Propensiy Scoring

Simulated cardiac medication data for survival analysis

Description

This dataset was created to demonstrate the effects of Local Control on correcting bias within a set of data.

Format

A data frame with 1000 rows and 6 columns:

id: Unique identifier for each row.
time: Time in years to the outcome specified by status.
status: 1 if the patient experienced cardiac arrest. 0 if censored before that.
drug: Medication the patient received for cardiac health (drug 1 or drug 0).
age: Age of the patient, ranges from 18 to 65 years.
bmi: Patient body mass index. Majority of observations fall between 22 and 30.

Author(s)

Lauve NR, Lambert CG

Framingham heart study data extract on smoking and hypertension.

Description

Data collected over a 24 year study suitable for competing risks survival analysis of hypertension and death as a function of smoking.

Format

A data frame with 2316 rows and 11 columns:

female: Sex of the patient. 1=female, 0=male.
totchol: Total cholesterol of patient at study entry.
age: Age of the patient at study entry.
bmi: Patient body mass index.
BPVar: Average units of systolic and diastolic blood pressure above normal: ((SystolicBP-120)/2) + (DiasystolicBP-80)
heartrte: Patient heartrate taken at study entry.
glucose: Patient blood glucose level.
cursmoke: Whether or not the patient was a smoker at the time of study entry.
outcome: Did the patient die, experience hypertension, or leave the study without experiencing either event.
time_outcome: The time at which the patient experienced outcome.
cigpday: Number of cigarettes smoked per day at time of study entry.

References

Dawber TR, Meadors GF, Moore FE Jr. Epidemiological approaches to heart disease: the Framingham Study. Am J Public Health Nations Health. 1951;41(3):279-281.
Teaching Datasets - Public Use Datasets. https://biolincc.nhlbi.nih.gov/teaching/.

Lindner Center for Research and Education study on Abciximab cost-effectiveness and survival

Description

The effects of Abciximab use on both survival and cardiac billing.

Format

A data frame with 996 rows and 10 columns:

lifepres: Life years preserved post treatment: 0 (died) vs. 11.6 (survived).
cardbill: Cardiac related billing in dollars within 12 months.
abcix: Indicates whether the patient received Abciximab treatment: 1=yes 0=no.
stent: Was a stent depolyed? 1=yes, 0=no.
height: Patient height in centimeters.
female: Patient sex: 1=female, 0=male.
diabetic: Was the patient diabetic? 1=yes, 0=no.
acutemi: Had the patient suffered an acute myocardial infarction witih the last seven days? 1=yes, 0=no.
ejecfrac: Left ventricular ejection fraction.
ves1proc: Number of vessels involved in the first PCI procedure.

References

Kereiakes DJ, Obenchain RL, Barber BL, Smith A, McDonald M, Broderick TM, Runyon JP, Shimshak TM, Schneider JF, Hattemer CR, Roth EM, Whang DD, Cocks D, Abbottsmith CW. Abciximab provides cost-effective survival advantage in high-volume interventional practice. Am Heart J. 2000;140(4):603-610.

Local Control

Description

Implements a non-parametric methodology for correcting biases when comparing the outcomes of two treatments in a cross-sectional or case control observational study. This implementation of Local Control uses nearest neighbors to each point within a given radius to compare treatment outcomes. Local Control matches along a continuum of similarity (radii), clustering the near neighbors to a given observation by variables thought to be sources of bias and confounding. This is analogous to combining a host of smaller studies that are each homogeneous within themselves, but represent the spectrum of variability of observations across diverse subpopulations. As the clusters get smaller, some of them can become noninformative, whereby all cluster members contain only one treatment, and there is no basis for comparison. Each observation has a unique set of near-neighbors, and the approach becomes more akin to a non-parametric density estimate using similar observations within a covariate hypersphere of a given radius. The global treatment difference is taken as the average of the treatment differences of the neighborhood around each observation.

While LocalControlClassic uses the number of clusters as a varying parameter to visualize treatment differences as a function of similarity of observations, this function instead uses a varying radius. The maximum radius enclosing all observations corresponds to the biased estimate which compares the outcome of all those with treatment A versus all those with treatment B. An easily interpretable graph can be created to illustrate the change in estimated outcome difference between two treatments, on average, across all clusters, as a function of using smaller and more homogenous clusters. The LocalControlNearestNeighborsConfidence procedure statistically resamples this Local Control process to generate confidence estimates. It is also helpful to plot a box-plot of the local treatment difference at a radius of zero, requiring that every observation has at least one perfect match on the other treatment. When perfect matches exist, one can estimate the treatment difference without making assumptions about the relative importance of the clustering variables. The plot.LocalControlCS function will plot both visualizations in a single graph.

Usage

LocalControl(
  data,
  modelForm = NULL,
  outcomeType = "default",
  treatmentColName,
  outcomeColName,
  cenCode = 0,
  clusterVars,
  timeColName = "",
  treatmentCode,
  labelColName = "",
  radStepType = "exp",
  radDecayRate = 0.8,
  radMinFract = 0.01,
  radiusLevels = numeric(),
  normalize = TRUE,
  verbose = FALSE,
  numThreads = 1
)
LocalControl(
  data,
  modelForm = NULL,
  outcomeType = "default",
  treatmentColName,
  outcomeColName,
  cenCode = 0,
  clusterVars,
  timeColName = "",
  treatmentCode,
  labelColName = "",
  radStepType = "exp",
  radDecayRate = 0.8,
  radMinFract = 0.01,
  radiusLevels = numeric(),
  normalize = TRUE,
  verbose = FALSE,
  numThreads = 1
)

Arguments

`data`	DataFrame containing all variables which will be used for the analysis.
`modelForm`	A formula containing the necessary variables for Local Control analysis. This can be used as an alternative to the primary interface for cross-sectional studies. The formula should be in the following format: "outcome ~ treatment \| clusterVar1 ... clusterVarN".
`outcomeType`	Specifys the outcome type for the analysis.
`treatmentColName`	A string containing the name of a column in data. The column contains the treatment variable specifying the treatment groups.
`outcomeColName`	A string containing the name of a column in data. The column contains the outcome variable to be compared between the treatment groups.
`cenCode`	A value specifying which of the outcome values corresponds to a censored observation.
`clusterVars`	A character vector containing column names in data. Each column contains an X-variable, or covariate which will be used to form patient clusters.
`timeColName`	A string containing the name of a column in data. The column contains the time to outcome for each of the observations in data.
`treatmentCode`	(optional) A string containing one of the factor levels from the treatment column. If provided, the corresponding treatment will be considered "Treatment 1". Otherwise, the first "level" of the column will be considered the primary treatment.
`labelColName`	(optional) A string containing the name of a column from data. The column contains labels for each of the observations in data, defaults to the row indices.
`radStepType`	(optional) Used in the generation of correction radii. The step type used to generate each correction radius after the maximum. Currently accepts "unif" and "exp" (default). "unif" for uniform decay ex: (radDecayRate = 0.1) (1, 0.9, 0.8, 0.7, ..., ~minRadFract, 0) "exp" for exponential decay ex: (radDecayRate = 0.9) (1, 0.9, 0.81, 0.729, ..., ~minRadFract, 0)
`radDecayRate`	(optional) Used in the generation of correction radii. The size of the "step" between each of the generated correction radii. If radStepType == "exp", radDecayRate must be a value between (0,1). This value defaults to 0.8.
`radMinFract`	(optional) Used in the generation of correction radii. A floating point number representing the smallest fraction of the maximum radius to use as a correction radius.
`radiusLevels`	(optional) By default, Local Control builds a set of radii to fit data. The radiusLevels parameter allows users to override the construction by explicitly providing a set of radii.
`normalize`	(optional) Logical value. Tells local control if it should or should not normalize the covariates. Default is TRUE.
`verbose`	(optional) Logical value. Display or suppress the console output during the call to Local Control. Default is FALSE.
`numThreads`	(optional) An integer value specifying the number of threads which will be assigned to the analysis. The maximum number of threads varies depending on the system hardware. Defaults to 1 thread.

Value

A list containing the results from the call to LocalControl.

outcomes: List containing two dataframes for the average T1 and T0 outcomes within each cluster at each radius.
counts: List containing two dataframes which hold the number of T1 and T0 patients within each cluster at each radius.
ltds: Dataframe containing the average LTD within each cluster at each radius.
summary: Dataframe containing summary statistics about the analysis for each radius.
params: List containing the parameters used to call LocalControl.

References

Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1-32. Available from: http://dx.doi.org/10.18637/jss.v096.i04
Fischer K, Gartner B, Kutz M. Fast Smallest-Enclosing-Ball Computation in High Dimensions. In: Algorithms - ESA 2003. Springer, Berlin, Heidelberg; 2003:630-641.
Martin Kutz, Kaspar Fischer, Bernd Gartner. miniball-1.0.3. https://github.com/hbf/miniball.

Examples

 # cross-sectional

 data(lindner)
 linVars <- c("stent", "height", "female", "diabetic", "acutemi",
              "ejecfrac", "ves1proc")
 csresults = LocalControl(data = lindner,
                          clusterVars = linVars,
                          treatmentColName = "abcix",
                          outcomeColName = "cardbill",
                          treatmentCode = 1)
 plot(csresults)


 # survival / competing risks example

 data(cardSim)
 crresults = LocalControl(data = cardSim, outcomeType = "survival",
                          outcomeColName = "status",
                          timeColName = "time",
                          treatmentColName = "drug",
                          treatmentCode = 1,
                          clusterVars = c("age", "bmi"))
 plot(crresults)
# cross-sectional

 data(lindner)
 linVars <- c("stent", "height", "female", "diabetic", "acutemi",
              "ejecfrac", "ves1proc")
 csresults = LocalControl(data = lindner,
                          clusterVars = linVars,
                          treatmentColName = "abcix",
                          outcomeColName = "cardbill",
                          treatmentCode = 1)
 plot(csresults)


 # survival / competing risks example

 data(cardSim)
 crresults = LocalControl(data = cardSim, outcomeType = "survival",
                          outcomeColName = "status",
                          timeColName = "time",
                          treatmentColName = "drug",
                          treatmentCode = 1,
                          clusterVars = c("age", "bmi"))
 plot(crresults)

Deprecated LocalControl functions

Description

These functions are provided for compatibility with previous versions of LocalControl. They may eventually be completely removed.

Details

`localControlNearestNeighbors`	Now called using `LocalControl` with the outcomeType = "cross-sectional".
`localControlCompetingRisks`	Now called using `LocalControl` with the outcomeType = "survival".
`plotLocalControlCIF`	Now called using `plot.LocalControlCR`.
`plotLocalControlLTD`	Now called using `plot.LocalControlCS`.

Local Control Classic

Description

LocalControlClassic was originally contained in the deprecated CRAN package USPS, this function is a combination of three of the original USPS functions, UPShclus, UPSaccum, and UPSnnltd. This replicates the original implementation of the Local Control functionality in Robert Obenchain's USPS package. Some of the features have been removed due to deprecation of R packages distributed through CRAN. For a given number of patient clusters in baseline X-covariate space, LocalControlClassic() characterizes the distribution of Nearest Neighbor "Local Treatement Differences" (LTDs) on a specified Y-outcome variable.

Usage

LocalControlClassic(
  data,
  clusterVars,
  treatmentColName,
  outcomeColName,
  faclev = 3,
  scedas = "homo",
  clusterMethod = "ward",
  clusterDist = "euclidean",
  clusterCounts = c(50, 100, 200)
)
LocalControlClassic(
  data,
  clusterVars,
  treatmentColName,
  outcomeColName,
  faclev = 3,
  scedas = "homo",
  clusterMethod = "ward",
  clusterDist = "euclidean",
  clusterCounts = c(50, 100, 200)
)

Arguments

`data`	The data frame containing all baseline X covariates.
`clusterVars`	List of names of X variable(s).
`treatmentColName`	Name of treatment factor variable.
`outcomeColName`	Name of outcome Y variable.
`faclev`	Maximum number of different numerical values an outcome variable can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.
`scedas`	Scedasticity assumption: "homo" or "hete".
`clusterMethod`	Type of clustering method, defaults to "complete". Currently implemented methods: "ward", "single", "complete" or "average".
`clusterDist`	Distance type to use, defaults to "euclidean". Currently implemented: "euclidiean", "manhattan", "maximum", or "minkowski".
`clusterCounts`	A vector containing different number of clusters in baseline X-covariate space which Local Control will iterate over.

Value

Returns a list containing several elements.

`hiclus`	Name of clustering object created by UPShclus().
`dframe`	Name of data.frame containing X, t & Y variables.
`trtm`	Name of treatment factor variable.
`yvar`	Name of outcome Y variable.
`numclust`	Number of clusters requested.
`actclust`	Number of clusters actually produced.
`scedas`	Scedasticity assumption: "homo" or "hete"
`PStdif`	Character string describing the treatment difference.
`nnhbindf`	Vector containing cluster number for each patient.
`rawmean`	Unadjusted outcome mean by treatment group.
`rawvars`	Unadjusted outcome variance by treatment group.
`rawfreq`	Number of patients by treatment group.
`ratdif`	Unadjusted mean outcome difference between treatments.
`ratsde`	Standard error of unadjusted mean treatment difference.
`binmean`	Unadjusted mean outcome by cluster and treatment.
`binvars`	Unadjusted variance by cluster and treatment.
`binfreq`	Number of patients by bin and treatment.
`awbdif`	Across cluster average difference with cluster size weights.
`awbsde`	Standard error of awbdif.
`wwbdif`	Across cluster average difference, inverse variance weights.
`wwbsde`	Standard error of wwbdif.
`faclev`	Maximum number of different numerical values an outcome variable can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.
`youtype`	"continuous" => only next eight outputs; "factor" => only last three outputs.
`aovdiff`	ANOVA summary for treatment main effect only.
`form2`	Formula for outcome differences due to bins and to treatment nested within bins.
`bindiff`	ANOVA summary for treatment nested within cluster.
`sig2`	Estimate of error mean square in nested model.
`pbindif`	Unadjusted treatment difference by cluster.
`pbinsde`	Standard error of the unadjusted difference by cluster.
`pbinsiz`	Cluster radii measure: square root of total number of patients.
`symsiz`	Symbol size of largest possible Snowball in a UPSnnltd() plot with 1 cluster.
`factab`	Marginal table of counts by Y-factor level and treatment.
`cumchi`	Cumulative Chi-Square statistic for interaction in the three-way, nested table.
`cumdf`	Degrees of-Freedom for the Cumulative Chi-Squared.

References

Obenchain, RL. USPS package: Unsupervised and Supervised Propensity Scoring in R. https://cran.r-project.org/src/contrib/Archive/USPS/ 2005.
Obenchain, RL. The ”Local Control” Approach to Adjustment for Treatment Selection Bias and Confounding (illustrated with JMP Scripts). Observational Studies. Cary, NC: SAS Press. 2009.
Obenchain RL. The local control approach using JMP. In: Faries D, Leon AC, Haro JM, Obenchain RL, eds. Analysis of Observational Health Care Data Using SAS. Cary, NC: SAS Institute; 2010:151-194.
Obenchain RL, Young SS. Advancing statistical thinking in observational health care research. J Stat Theory Pract. 2013;7(2):456-506.
Faries DE, Chen Y, Lipkovich I, Zagar A, Liu X, Obenchain RL. Local control for identifying subgroups of interest in observational research: persistence of treatment for major depressive disorder. Int J Methods Psychiatr Res. 2013;22(3):185-194.
Lopiano KK, Obenchain RL, Young SS. Fair treatment comparisons in observational research. Stat Anal Data Min. 2014;7(5):376-384.
Young SS, Obenchain RL, Lambert CG (2016) A problem of bias and response heterogeneity. In: Alan Moghissi A, Ross G (eds) Standing with giants: A collection of public health essays in memoriam to Dr. Elizabeth M. Whelan. American Council on Science and Health, New York, NY, pp 153-169.

Examples

 data(lindner)

 cvars <- c("stent","height","female","diabetic","acutemi",
            "ejecfrac","ves1proc")
 numClusters <- c(1, 2, 10, 15, 20, 25, 30, 35, 40, 45, 50)
 results <- LocalControlClassic( data = lindner,
                                clusterVars = cvars,
                                treatmentColName = "abcix",
                                outcomeColName = "cardbill",
                                clusterCounts = numClusters)
 UPSLTDdist(results,ylim=c(-15000,15000))

data(lindner)

 cvars <- c("stent","height","female","diabetic","acutemi",
            "ejecfrac","ves1proc")
 numClusters <- c(1, 2, 10, 15, 20, 25, 30, 35, 40, 45, 50)
 results <- LocalControlClassic( data = lindner,
                                clusterVars = cvars,
                                treatmentColName = "abcix",
                                outcomeColName = "cardbill",
                                clusterCounts = numClusters)
 UPSLTDdist(results,ylim=c(-15000,15000))

Calculate confidence intervals around the cumulative incidence functions (CIFs) generated by LocalControl when outcomeType = "survival".

Description

Given the output of LocalControl, this function produces pointwise standard error estimates for the cumulative incidence functions (CIFs) using a modified version of Choudhury's approach (2002). This function currently supports the creation of 90%, 95%, 98%, and 99% confidence intervals with linear, log(-log), and arcsine transformations of the estimates.

Usage

LocalControlCompetingRisksConfidence(
  LCCompRisk,
  confLevel = "95%",
  confTransform = "asin"
)
LocalControlCompetingRisksConfidence(
  LCCompRisk,
  confLevel = "95%",
  confTransform = "asin"
)

Arguments

`LCCompRisk`	Output from a successful call to LocalControl with outcomeType = "survival".
`confLevel`	Level of confidence with which the confidence intervals will be formed. Choices are: "90%", "95%", "98%", "99%".
`confTransform`	Transformation of the confidence intervals, defaults to arcsin ("asin"). "log" and "linear" are also implemented.

References

Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1-32. Available from: http://dx.doi.org/10.18637/jss.v096.i04
Choudhury JB (2002) Non-parametric confidence interval estimation for competing risks analysis: application to contraceptive data. Stat Med 21:1129-1144. doi: 10.1002/sim.1070

Examples

 data(cardSim)
 results = LocalControl(data = cardSim,
                        outcomeType = "survival",
                        outcomeColName = "status",
                        timeColName = "time",
                        treatmentColName = "drug",
                        treatmentCode = 1,
                        clusterVars = c("age", "bmi"))

 conf = LocalControlCompetingRisksConfidence(results)

data(cardSim)
 results = LocalControl(data = cardSim,
                        outcomeType = "survival",
                        outcomeColName = "status",
                        timeColName = "time",
                        treatmentColName = "drug",
                        treatmentCode = 1,
                        clusterVars = c("age", "bmi"))

 conf = LocalControlCompetingRisksConfidence(results)

Provides a bootstrapped confidence interval estimate for LocalControl LTDs.

Description

Given a number of bootstrap iterations and the params used to call LocalControl with outcomeType = "default", this function calls LocalControl nBootstrap times. The 50% and 95% quantiles are drawn from the distribution of results to produce the LTD confidence intervals.

Usage

LocalControlNearestNeighborsConfidence(
  data,
  nBootstrap,
  randSeed,
  treatmentColName,
  treatmentCode = "",
  outcomeColName,
  clusterVars,
  labelColName = "",
  numThreads = 1,
  radiusLevels = numeric(),
  radStepType = "exp",
  radDecayRate = 0.8,
  radMinFract = 0.01,
  normalize = TRUE,
  verbose = FALSE
)
LocalControlNearestNeighborsConfidence(
  data,
  nBootstrap,
  randSeed,
  treatmentColName,
  treatmentCode = "",
  outcomeColName,
  clusterVars,
  labelColName = "",
  numThreads = 1,
  radiusLevels = numeric(),
  radStepType = "exp",
  radDecayRate = 0.8,
  radMinFract = 0.01,
  normalize = TRUE,
  verbose = FALSE
)

Arguments

`data`	DataFrame containing all variables which will be used for the analysis.
`nBootstrap`	The number of times to resample and run LocalControl for the confidence intervals.
`randSeed`	The seed used to set random number generator state prior to resampling. No default value, provide one for reproducible results.
`treatmentColName`	A string containing the name of a column in data. The column contains the treatment variable specifying the treatment groups.
`treatmentCode`	(optional) A string containing one of the factor levels from the treatment column. If provided, the corresponding treatment will be considered "Treatment 1". Otherwise, the first "level" of the column will be considered the primary treatment.
`outcomeColName`	A string containing the name of a column in data. The column contains the outcome variable to be compared between the treatment groups. If outcomeType = "survival", the outcome column holds the failure/censor assignments.
`clusterVars`	A character vector containing column names in data. Each column contains an X-variable, or covariate which will be used to form patient clusters.
`labelColName`	(optional) A string containing the name of a column from data. The column contains labels for each of the observations in data, defaults to the row indices.
`numThreads`	(optional) An integer value specifying the number of threads which will be assigned to the analysis. The maximum number of threads varies depending on the system hardware. Defaults to 1 thread.
`radiusLevels`	(optional) By default, Local Control builds a set of radii to fit data. The radiusLevels parameter allows users to override the construction by explicitly providing a set of radii.
`radStepType`	(optional) Used in the generation of correction radii. The step type used to generate each correction radius after the maximum. Currently accepts "unif" and "exp" (default). "unif" for uniform decay ex: (radDecayRate = 0.1) (1, 0.9, 0.8, 0.7, ..., ~minRadFract, 0) "exp" for exponential decay ex: (radDecayRate = 0.9) (1, 0.9, 0.81, 0.729, ..., ~minRadFract, 0)
`radDecayRate`	(optional) Used in the generation of correction radii. The size of the "step" between each of the generated correction radii. If radStepType == "exp", radDecayRate must be a value between (0,1). This value defaults to 0.8.
`radMinFract`	(optional) Used in the generation of correction radii. A floating point number representing the smallest fraction of the maximum radius to use as a correction radius.
`normalize`	(optional) Logical value. Tells local control if it should or should not normalize the covariates. Default is TRUE.
`verbose`	(optional) Logical value. Display or suppress the console output during the call to Local Control. Default is FALSE.

References

Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1-32. Available from: http://dx.doi.org/10.18637/jss.v096.i04
Kereiakes DJ, Obenchain RL, Barber BL, Smith A, McDonald M, Broderick TM, Runyon JP, Shimshak TM, Schneider JF, Hattemer CR, Roth EM, Whang DD, Cocks D, Abbottsmith CW. Abciximab provides cost-effective survival advantage in high-volume interventional practice. Am Heart J. 2000 Oct;140(4):603-610. PMID: 11011333

Examples

## Not run: 
#input the abciximab study data of Kereiakes et al. (2000).
data(lindner)

linVars <- c("stent", "height", "female", "diabetic", "acutemi",
             "ejecfrac", "ves1proc")
results <- LocalControl(data = lindner,
                        clusterVars = linVars,
                        treatmentColName = "abcix",
                        outcomeColName = "cardbill",
                        treatmentCode = 1)

#Calculate the confidence intervals via resampling.
confResults = LocalControlNearestNeighborsConfidence(
                                        data = lindner,
                                        clusterVars = linVars,
                                        treatmentColName = "abcix",
                                        outcomeColName = "cardbill",
                                        treatmentCode = 1, nBootstrap = 20)

# Plot the local treatment difference with confidence intervals.
plot(results, confResults)

## End(Not run)

## Not run: 
#input the abciximab study data of Kereiakes et al. (2000).
data(lindner)

linVars <- c("stent", "height", "female", "diabetic", "acutemi",
             "ejecfrac", "ves1proc")
results <- LocalControl(data = lindner,
                        clusterVars = linVars,
                        treatmentColName = "abcix",
                        outcomeColName = "cardbill",
                        treatmentCode = 1)

#Calculate the confidence intervals via resampling.
confResults = LocalControlNearestNeighborsConfidence(
                                        data = lindner,
                                        clusterVars = linVars,
                                        treatmentColName = "abcix",
                                        outcomeColName = "cardbill",
                                        treatmentCode = 1, nBootstrap = 20)

# Plot the local treatment difference with confidence intervals.
plot(results, confResults)

## End(Not run)

Plot cumulative incidence functions (CIFs) from Local Control.

Description

Given the results from LocalControl with outcomeType = "survival", plot a corrected and uncorrected cumulative incidence function (CIF) for both groups.

Usage

## S3 method for class 'LocalControlCR'
plot(
  x,
  ...,
  rad2plot,
  xlim,
  ylim = c(0, 1),
  col1 = "blue",
  col0 = "red",
  xlab = "Time",
  ylab = "Cumulative incidence",
  legendLocation = "topleft",
  main = "",
  group1 = "Treatment 1",
  group0 = "Treatment 0"
)
## S3 method for class 'LocalControlCR'
plot(
  x,
  ...,
  rad2plot,
  xlim,
  ylim = c(0, 1),
  col1 = "blue",
  col0 = "red",
  xlab = "Time",
  ylab = "Cumulative incidence",
  legendLocation = "topleft",
  main = "",
  group1 = "Treatment 1",
  group0 = "Treatment 0"
)

Arguments

`x`	Return object from LocalControl with outcomeType = "survival".
`...`	Arguments passed on to `graphics::plot.default` `type` 1-character string giving the type of plot desired. The following values are possible, for details, see `plot`: `"p"` for points, `"l"` for lines, `"b"` for both points and lines, `"c"` for empty points joined by lines, `"o"` for overplotted points and lines, `"s"` and `"S"` for stair steps and `"h"` for histogram-like vertical lines. Finally, `"n"` does not produce any points or lines. `log` a character string which contains `"x"` if the x axis is to be logarithmic, `"y"` if the y axis is to be logarithmic and `"xy"` or `"yx"` if both axes are to be logarithmic. `sub` a subtitle for the plot. `ann` a logical value indicating whether the default annotation (title and x and y axis labels) should appear on the plot. `axes` a logical value indicating whether both axes should be drawn on the plot. Use graphical parameter `"xaxt"` or `"yaxt"` to suppress just one of the axes. `frame.plot` a logical indicating whether a box should be drawn around the plot. `panel.first` an ‘expression’ to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids or scatterplot smooths. Note that this works by lazy evaluation: passing this argument from other `plot` methods may well not work since it may be evaluated too early. `panel.last` an expression to be evaluated after plotting has taken place but before the axes, title and box are added. See the comments about `panel.first`. `asp` the $y/x$ aspect ratio, see `plot.window`. `xgap.axis,ygap.axis` the $x/y$ axis gap factors, passed as `gap.axis` to the two `axis()` calls (when `axes` is true, as per default).
`rad2plot`	The index or name ("rad_#") of the radius to plot. By default, the radius with pct_informative closest to 0.8 will be selected.
`xlim`	The x axis bounds. Defaults to c(0, max(lccrResults$Failtimes)).
`ylim`	The y axis bounds. Defaults to c(0,1).
`col1`	The plot color for group 1.
`col0`	The plot color for group 0.
`xlab`	The x axis label. Defaults to "Time".
`ylab`	The y axis label. Defaults to "Cumulative incidence".
`legendLocation`	The location to place the legend. Default "topleft".
`main`	The main plot title. Default is empty.
`group1`	The name of the primary group (Treatment 1).
`group0`	The name of the secondary group (Treatment 0).

References

Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1-32. Available from: http://dx.doi.org/10.18637/jss.v096.i04

Examples

data("cardSim")
results = LocalControl(data = cardSim,
                       outcomeType = "survival",
                       outcomeColName = "status",
                       timeColName = "time",
                       treatmentColName = "drug",
                       treatmentCode = 1,
                       clusterVars = c("age", "bmi"))
plot(results)

data("cardSim")
results = LocalControl(data = cardSim,
                       outcomeType = "survival",
                       outcomeColName = "status",
                       timeColName = "time",
                       treatmentColName = "drug",
                       treatmentCode = 1,
                       clusterVars = c("age", "bmi"))
plot(results)

Plots the local treatment difference as a function of radius for LocalControl.

Description

Creates a plot where the y axis represents the local treatment difference, while the x axis represents the percentage of the maximum radius. If the confidence summary (nnConfidence) is provided, the 50% and 95% confidence estimates are also plotted.

Usage

## S3 method for class 'LocalControlCS'
plot(
  x,
  ...,
  nnConfidence,
  ylim,
  legendLocation = "bottomleft",
  ylab = "LTD",
  xlab = "Fraction of maximum radius",
  main = ""
)
## S3 method for class 'LocalControlCS'
plot(
  x,
  ...,
  nnConfidence,
  ylim,
  legendLocation = "bottomleft",
  ylab = "LTD",
  xlab = "Fraction of maximum radius",
  main = ""
)

Arguments

`x`	Return object from LocalControl with "default" outcomeType.
`...`	Arguments passed on to `graphics::plot.default` `type` 1-character string giving the type of plot desired. The following values are possible, for details, see `plot`: `"p"` for points, `"l"` for lines, `"b"` for both points and lines, `"c"` for empty points joined by lines, `"o"` for overplotted points and lines, `"s"` and `"S"` for stair steps and `"h"` for histogram-like vertical lines. Finally, `"n"` does not produce any points or lines. `xlim` the x limits (x1, x2) of the plot. Note that `x1 > x2` is allowed and leads to a ‘reversed axis’. The default value, `NULL`, indicates that the range of the finite values to be plotted should be used. `log` a character string which contains `"x"` if the x axis is to be logarithmic, `"y"` if the y axis is to be logarithmic and `"xy"` or `"yx"` if both axes are to be logarithmic. `sub` a subtitle for the plot. `ann` a logical value indicating whether the default annotation (title and x and y axis labels) should appear on the plot. `axes` a logical value indicating whether both axes should be drawn on the plot. Use graphical parameter `"xaxt"` or `"yaxt"` to suppress just one of the axes. `frame.plot` a logical indicating whether a box should be drawn around the plot. `panel.first` an ‘expression’ to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids or scatterplot smooths. Note that this works by lazy evaluation: passing this argument from other `plot` methods may well not work since it may be evaluated too early. `panel.last` an expression to be evaluated after plotting has taken place but before the axes, title and box are added. See the comments about `panel.first`. `asp` the $y/x$ aspect ratio, see `plot.window`. `xgap.axis,ygap.axis` the $x/y$ axis gap factors, passed as `gap.axis` to the two `axis()` calls (when `axes` is true, as per default).
`nnConfidence`	Return object from LocalControlNearestNeighborsConfidence
`ylim`	The y axis bounds. Defaults to c(0,1).
`legendLocation`	The location to place the legend. Default "topleft".
`ylab`	The y axis label. Defaults to "LTD".
`xlab`	The x axis label. Defaults to "Fraction of maximum radius".
`main`	The main plot title. Default is empty.

References

Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1-32. Available from: http://dx.doi.org/10.18637/jss.v096.i04

Examples

data(lindner)
# Specify clustering variables.
linVars <- c("stent", "height", "female", "diabetic",
             "acutemi", "ejecfrac", "ves1proc")

# Call Local Control once.
linRes <- LocalControl(data = lindner,
                       clusterVars = linVars,
                       treatmentColName = "abcix",
                       outcomeColName = "cardbill",
                       treatmentCode = 1)

# Plot the local treatment differences from Local Control without
# confidence intervals.
plot(linRes, ylim =  c(-6000, 3600))

#If the confidence intervals are calculated:
#linConfidence = LocalControlNearestNeighborsConfidence(
#                                      data = lindner,
#                                      clusterVars = linVars,
#                                      treatmentColName = "abcix",
#                                      outcomeColName = "cardbill",
#                                      treatmentCode = 1, nBootstrap = 100)

# Plot the local treatment difference with confidence intervals.
#plot(linRes, linConfidence)

data(lindner)
# Specify clustering variables.
linVars <- c("stent", "height", "female", "diabetic",
             "acutemi", "ejecfrac", "ves1proc")

# Call Local Control once.
linRes <- LocalControl(data = lindner,
                       clusterVars = linVars,
                       treatmentColName = "abcix",
                       outcomeColName = "cardbill",
                       treatmentCode = 1)

# Plot the local treatment differences from Local Control without
# confidence intervals.
plot(linRes, ylim =  c(-6000, 3600))

#If the confidence intervals are calculated:
#linConfidence = LocalControlNearestNeighborsConfidence(
#                                      data = lindner,
#                                      clusterVars = linVars,
#                                      treatmentColName = "abcix",
#                                      outcomeColName = "cardbill",
#                                      treatmentCode = 1, nBootstrap = 100)

# Plot the local treatment difference with confidence intervals.
#plot(linRes, linConfidence)

Test for Within-Bin X-covariate Balance in Supervised Propensiy Scoring

Description

Test for Conditional Independence of X-covariate Distributions from Treatment Selection within Given, Adjacent PS Bins. The second step in Supervised Propensity Scoring analyses is to verify that baseline X-covariates have the same distribution, regardless of treatment, within each fitted PS bin.

Usage

SPSbalan(envir, dframe, trtm, yvar, qbin, xvar, faclev = 3)
SPSbalan(envir, dframe, trtm, yvar, qbin, xvar, faclev = 3)

Arguments

`envir`	The local control environment
`dframe`	Name of augmented data.frame written to the appn="" argument of SPSlogit().
`trtm`	Name of the two-level treatment factor variable.
`yvar`	The outcome variable.
`qbin`	Name of variable containing bin numbers.
`xvar`	Name of one baseline covariate X variable used in the SPSlogit() PS model.
`faclev`	Maximum number of different numerical values an X-covariate can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining a proportion.

Value

An output list object of class SPSbalan. The first four are returned with a continuous x-variable. The next 4 are used if it is a factor variable.

aovdiff: ANOVA output for marginal test.
form2: Formula for differences in X due to bins and to treatment nested within bins.
bindiff: ANOVA output for the nested within bin model.
df3: Output data.frame containing 3 variables: X-covariate, treatment and bin.
factab: Marginal table of counts by X-factor level and treatment.
tab: Three-way table of counts by X-factor level, treatment and bin.
cumchi: Cumulative Chi-Square statistic for interaction in the three-way, nested table.
cumdf: Degrees of-Freedom for the Cumulative Chi-Squared.

Author(s)

Bob Obenchain <[email protected]>

References

Cochran WG. (1968) The effectiveness of adjustment by subclassification in removing bias in observational studies. Biometrics 24: 205-213.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Rosenbaum PR, Rubin RB. (1983) The Central Role of the Propensity Score in Observational Studies for Causal Effects. Biometrika 70: 41-55.
Rosenbaum PR, Rubin DB. (1984) Reducing Bias in Observational Studies Using Subclassification on a Propensity Score. J Amer Stat Assoc 79: 516-524.

LOESS Smoothing of Outcome by Treatment in Supervised Propensiy Scoring

Description

Express Expected Outcome by Treatment as LOESS Smooths of Fitted Propensity Scores.

Usage

SPSloess(
  envir,
  dframe,
  trtm,
  pscr,
  yvar,
  faclev = 3,
  deg = 2,
  span = 0.75,
  fam = "symmetric"
)
SPSloess(
  envir,
  dframe,
  trtm,
  pscr,
  yvar,
  faclev = 3,
  deg = 2,
  span = 0.75,
  fam = "symmetric"
)

Arguments

`envir`	Local control classic environment.
`dframe`	data.frame of the form returned by SPSlogit().
`trtm`	the two-level factor on the left-hand-side in the formula argument to SPSlogit().
`pscr`	fitted propensity scores of the form returned by SPSlogit().
`yvar`	continuous outcome measure or result unknown at the time patient was assigned (possibly non-randomly) to treatment; "NA"s are allowed in yvar.
`faclev`	optional; maximum number of distinct numerical values a variable can assume and yet still be converted into a factor variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining a proportion.
`deg`	optional; degree (1=linear or 2=quadratic) of the local fit.
`span`	optional; span (0 to 2) argument for the loess() function.
`fam`	optional; "gaussian" or "symmetric".

Details

SPSloess

Once one has fitted a somewhat smooth curve through scatters of observed outcomes, Y, versus the fitted propensity scores, X, for the patients in each of the two treatment groups, one can consider the question: "Over the range where both smooth curves are defined (i.e. their common support), what is the (weighted) average signed difference between these two curves?"

If the distribution of patients (either treated or untreated) were UNIFORM over this range, the (unweighted) average signed difference (treated minus untreated) would be an appropriate estimate of the overall difference in outcome due to choice of treatment.

Histogram patient counts within 100 cells of width 0.01 provide a naive "non-parametric density estimate" for the distribution of total patients (treated or untreated) along the propensity score axis. The weighted average difference (and standard error) displayed by SPSsmoot() are based on an R density() smooth of these counts.

In situations where the propensity scoring distribution for all patients in a therapeutic class is known to differ from that of the patients within the current study, that population weighted average would also be of interest. Thus the SPSloess() output object contains two data frames, logrid and lofit, useful in further computations.

logrid: loess grid data.frame containing 11 variables and 100 observations. The PS variable contains propensity score "cell means" of 0.005 to 0.995 in steps of 0.010. Variables F0, S0 and C0 for treatment 0 and variables F1, S1 and C1 for treatment 1 contain fitted smooth spline values, standard error estimates and patient counts, respectively. The DIF variable is simply (F1-F0), the SED variable is sqrt(S1*S1+S0*S0), the HST variable is proportional to (C0+C1), and the DEN variable is the estimated probability density of patients along the PS axis. Observations with "NA" for variables F0, S0, F1 or S1 represent "extremes" where the lowess fits could not be extrapolated because no observed outcomes were available.
losub0, losub1: loess fit data.frame contains 4 variables for each distinct PS value in lofit. These 4 variables are named PS, YAVG, TRT==0 and 1, respectively, and FIT = spline prediction for the specified degrees-of-freedom (default df=1.)
span: loess span setting.
lotdif: outcome treatment difference mean.
lotsde: outcome treatment difference standard deviation.

Author(s)

Bob Obenchain <[email protected]>

References

Cleveland WS, Devlin SJ. (1988) Locally-weighted regression: an approach to regression analysis by local fitting. J Amer Stat Assoc 83: 596-610.
Cleveland WS, Grosse E, Shyu WM. (1992) Local regression models. Chapter 8 of Statistical Models in S eds Chambers JM and Hastie TJ. Wadsworth & Brooks/Cole.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Ripley BD, loess() based on the 'cloess' package of Cleveland, Grosse and Shyu.

Propensity Score prediction of Treatment Selection from Patient Baseline X-covariates

Description

Use a logistic regression model to predict Treatment Selection from Patient Baseline X-covariates in Supervised Propensity Scoring.

Usage

SPSlogit(envir, dframe, form, pfit, prnk, qbin, bins = 5, appn = "")
SPSlogit(envir, dframe, form, pfit, prnk, qbin, bins = 5, appn = "")

Arguments

`envir`	name of the working local control classic environment.
`dframe`	data.frame containing X, t and Y variables.
`form`	Valid formula for glm()with family = binomial(), with the two-level treatment factor variable as the left-hand-side of the formula.
`pfit`	Name of variable to store PS predictions.
`prnk`	Name of variable to store tied-ranks of PS predictions.
`qbin`	Name of variable to store the assigned bin number for each patient.
`bins`	optional; number of adjacent PS bins desired; default to 5.
`appn`	optional; append the pfit, prank and qbin variables to the input dfname when appn=="", else save augmented data.frame to name specified within a non-blank appn string.

Details

The first phase of Supervised Propensity Scoring is to develop a logit (or probit) model predicting treatment choice from patient baseline X characteristics. SPSlogit uses a call to glm()with family = binomial() to fit a logistic regression.

Value

An output list object of class SPSlogit:

dframe: Name of input data.frame containing X, t & Y variables.
dfoutnam: Name of output data.frame augmented by pfit, prank and qbin variables.
trtm: Name of two-level treatment factor variable.
form: glm() formula for logistic regression.
pfit: Name of predicted PS variable.
prank: Name of variable containing PS tied-ranks.
qbin: Name of variable containing assigned PS bin number for each patient.
bins: Number of adjacent PS bins desired.
glmobj: Output object from invocation of glm() with family = binomial().

Author(s)

Bob Obenchain <[email protected]>

References

Cochran WG. (1968) The effectiveness of adjustment by subclassification in removing bias in observational studies. Biometrics 24: 205-213.
Kereiakes DJ, Obenchain RL, Barber BL, et al. (2000) Abciximab provides cost effective survival advantage in high volume interventional practice. Am Heart J 140: 603-610.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Rosenbaum PR, Rubin RB. (1983) The Central Role of the Propensity Score in Observational Studies for Causal Effects. Biometrika 70: 41-55.
Rosenbaum PR, Rubin DB. (1984) Reducing Bias in Observational Studies Using Subclassification on a Propensity Score. J Amer Stat Assoc 79: 516-524.

Change the Number of Bins in Supervised Propensiy Scoring

Description

Change the Number of Bins in Supervised Propensiy Scoring

Usage

SPSnbins(envir, dframe, prnk, qbin, bins = 8)
SPSnbins(envir, dframe, prnk, qbin, bins = 8)

Arguments

`envir`	name of the working local control classic environment.
`dframe`	Name of data.frame of the form output by SPSlogit().
`prnk`	Name of PS tied-rank variable from previous call to SPSlogit().
`qbin`	Name of variable to contain the re-assigned bin number for each patient.
`bins`	Number of PS bins desired.

Details

Part or all of the first phase of Supervised Propensity Scoring will need to be redone if SPSbalan() detects dependence of within-bin X-covariate distributions upon treatment choice. Use SPSnbins() to change (increase) the number of adjacent PS bins. If this does not achieve balance, invoke SPSlogit() again to modify the form of your PS logistic model, typically by adding interaction and/or curvature terms in continuous X-covariates.

Value

An output data.frame with new variables inserted:

dframe2: Modified version of the data.frame specified as the first argument to SPSnbins().

Author(s)

Bob Obenchain <[email protected]>

References

Cochran WG. (1968) The effectiveness of adjustment by subclassification in removing bias in observational studies. Biometrics 24: 205-213.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Rosenbaum PR, Rubin DB. (1984) Reducing Bias in Observational Studies Using Subclassification on a Propensity Score. J Amer Stat Assoc 79: 516-524.

Examine Treatment Differences on an Outcome Measure in Supervised Propensiy Scoring

Description

Examine Within-Bin Treatment Differences on an Outcome Measure and Average these Differences across Bins.

Usage

SPSoutco(envir, dframe, trtm, qbin, yvar, faclev = 3)
SPSoutco(envir, dframe, trtm, qbin, yvar, faclev = 3)

Arguments

`envir`	name of the working local control classic environment.
`dframe`	Name of augmented data.frame written to the appn="" argument of SPSlogit().
`trtm`	Name of treatment factor variable.
`qbin`	Name of variable containing the PS bin number for each patient.
`yvar`	Name of an outcome Y variable.
`faclev`	Maximum number of different numerical values an X-covariate can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.

Details

Once the second phase of Supervised Propensity Scoring confirms, using SPSbalan(), that X-covariate Distributions have been Balanced Within-Bins, the third phase can start: Examining Within-Bin Outcome Difference due to Treatment and Averaging these Differences across Bins. Graphical displays of SPSoutco() results feature R barplot() invocations.

Value

An output list object of class SPSoutco:

dframe: Name of augmented data.frame written to the appn="" argument of SPSlogit().
trtm: Name of the two-level treatment factor variable.
yvar: Name of an outcome Y variable.
bins: Number of variable containing bin numbers.
PStdif: Character string describing the treatment difference.
rawmean: Unadjusted outcome mean by treatment group.
rawvars: Unadjusted outcome variance by treatment group.
rawfreq: Number of patients by treatment group.
ratdif: Unadjusted mean outcome difference between treatments.
ratsde: Standard error of unadjusted mean treatment difference.
binmean: Unadjusted mean outcome by cluster and treatment.
binvars: Unadjusted variance by cluster and treatment.
binfreq: Number of patients by bin and treatment.
awbdif: Across cluster average difference with cluster size weights.
awbsde: Standard error of awbdif.
wwbdif: Across cluster average difference, inverse variance weights.
wwbsde: Standard error of wwbdif.
form: Formula for overall, marginal treatment difference on X-covariate.
faclev: Maximum number of different numerical values an X-covariate can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.
youtype: "contin"uous => only next six outputs; "factor" => only last four outputs.
aovdiff: ANOVA output for marginal test.
form2: Formula for differences in X due to bins and to treatment nested within bins.
bindiff: ANOVA summary for treatment nested within bin.
pbindif: Unadjusted treatment difference by cluster.
pbinsde: Standard error of the unadjusted difference by cluster.
pbinsiz: Cluster radii measure: square root of total number of patients.
factab: Marginal table of counts by Y-factor level and treatment.
tab: Three-way table of counts by Y-factor level, treatment and bin.
cumchi: Cumulative Chi-Square statistic for interaction in the three-way, nested table.
cumdf: Degrees of-Freedom for the Cumulative Chi-Squared.

Author(s)

Bob Obenchain <[email protected]>

References

Cochran WG. (1968) The effectiveness of adjustment by subclassification in removing bias in observational studies. Biometrics 24: 205-213.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Rosenbaum PR, Rubin RB. (1983) The Central Role of the Propensity Score in Observational Studies for Causal Effects. Biometrika 70: 41-55.
Rosenbaum PR, Rubin DB. (1984) Reducing Bias in Observational Studies Using Subclassification on a Propensity Score. J Amer Stat Assoc 79: 516-524.

Prepare for Accumulation of (Outcome,Treatment) Results in Unsupervised Propensity Scoring

Description

Specify key result accumulation parameters: Treatment t-Factor, Outcome Y-variable, faclev setting, scedasticity assumption, and name of the UPSgraph() data accumulation object.

Usage

UPSaccum(envir, dframe, trtm, yvar, faclev = 3, scedas = "homo")
UPSaccum(envir, dframe, trtm, yvar, faclev = 3, scedas = "homo")

Arguments

`envir`	name of the working local control classic environment.
`dframe`	Name of data.frame containing the X, t & Y variables.
`trtm`	Name of treatment factor variable.
`yvar`	Name of outcome Y variable.
`faclev`	Maximum number of different numerical values an outcome variable can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.
`scedas`	Scedasticity assumption: "homo" or "hete"

Details

The second phase in an Unsupervised Propensity Scoring analysis is to prepare to accumulate results over a wide range of values for "Number of Clusters." As the number of such clusters increases, individual clusters will tend to become smaller and smaller and, thus, more and more compact in covariate X-space.

Value

hiclus: Name of a diana, agnes or hclust object created by UPShclus().
dframe: Name of data.frame containing the X, t & Y variables.
trtm: Name of treatment factor variable.
yvar: Name of outcome Y variable.
faclev: Maximum number of different numerical values an outcome variable can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining a proportion.
scedas: Scedasticity assumption: "homo" or "hete"
accobj: Name of the object for accumulation of I-plots to be ultimately displayed using UPSgraph().
nnymax: Maximum NN LTD Standard Error observed; Upper NN plot limit; initialized to zero.
nnxmin: Minimum NN LTD observed; Left NN plot limit; initialized to zero.
nnxmax: Maximum NN LTD observed; Right NN plot limit; initialized to zero.

Author(s)

Bob Obenchain <[email protected]>

References

Obenchain RL. (2004) Unsupervised Propensity Scoring: NN and IV Plots. Proceedings of the American Statistical Association (on CD) 8 pages.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.

Artificial Distribution of LTDs from Random Clusters

Description

For a given number of clusters, UPSaltdd() characterizes the potentially biased distribution of "Local Treatment Differences" (LTDs) in a continuous outcome y-variable between two treatment groups due to Random Clusterings. When the NNobj argument is not NA and specifies an existing UPSnnltd() object, UPSaltdd() also computes a smoothed CDF for the NN/LTD distribution for direct comparison with the Artificial LTD distribution.

Usage

UPSaltdd(
  envir,
  dframe,
  trtm,
  yvar,
  faclev = 3,
  scedas = "homo",
  NNobj = NA,
  clus = 50,
  reps = 10,
  seed = 12345
)
UPSaltdd(
  envir,
  dframe,
  trtm,
  yvar,
  faclev = 3,
  scedas = "homo",
  NNobj = NA,
  clus = 50,
  reps = 10,
  seed = 12345
)

Arguments

`envir`	name of the working local control classic environment.
`dframe`	Name of data.frame containing a treatment-factor and the outcome y-variable.
`trtm`	Name of treatment factor variable with two levels.
`yvar`	Name of continuous outcome variable.
`faclev`	Maximum number of different numerical values an outcome variable can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.
`scedas`	Scedasticity assumption: "homo" or "hete"
`NNobj`	Name of an existing UPSnnltd object or NA.
`clus`	Number of Random Clusters requested per Replication; ignored when NNobj is not NA.
`reps`	Number of overall Replications, each with the same number of requested clusters.
`seed`	Seed for Monte Carlo random number generator.

Details

Multiple calls to UPSaltdd() for different UPSnnltd objects or different numbers of clusters are typically made after first invoking UPSgraph().

Value

dframe: Name of data.frame containing X, t & Y variables.
trtm: Name of treatment factor variable.
yvar: Name of outcome Y variable.
faclev: Maximum number of different numerical values an outcome variable can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.
scedas: Scedasticity assumption: "homo" or "hete"
NNobj: Name of an existing UPSnnltd object or NA.
clus: Number of Random Clusters requested per Replication.
reps: Number of overall Replications, each with the same number of requested clusters.
pats: Number of patients with no NAs in their yvar outcome and trtm factor.
seed: Seed for Monte Carlo random number generator.
altdd: Matrix of LTDs and relative weights from artificial clusters.
alxmin: Minimum artificial LTD value.
alxmax: Maximum artificial LTD value.
alymax: Maximum weight among artificial LTDs.
altdcdf: Vector of artificial LTD x-coordinates for smoothed CDF.
qq: Vector of equally spaced CDF values from 0.0 to 1.0.
nnltdd: Optional matrix of relevant NN/LTDs and relative weights.
nnlxmin: Optional minimum NN/LTD value.
nnlxmax: Optional maximum NN/LTD value.
nnlymax: Optional maximum weight among NN/LTDs.
nnltdcdf: Optional vector of NN/LTD x-coordinates for smoothed CDF.
nq: Optional vector of equally spaced CDF values from 0.0 to 1.0.

Author(s)

Bob Obenchain <[email protected]>

References

Obenchain RL. (2004) Unsupervised Propensity Scoring: NN and IV Plots. Proceedings of the American Statistical Association (on CD) 8 pages.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Rosenbaum PR, Rubin RB. (1983) The Central Role of the Propensity Score in Observational Studies for Causal Effects. Biometrika 70: 41-55.
Rubin DB. (1980) Bias reduction using Mahalanobis metric matching. Biometrics 36: 293-298.

Returns a series of boxplots comparing LTD distributions given different numbers of clusters.

Description

Given the output of LocalControlClassic, this function uses all or some of the UPSnnltd objects contained to create a series of boxplots of the local treatment difference at each of the different numbers of requested clusters.

Usage

UPSboxplot(envir, clusterSubset = c())
UPSboxplot(envir, clusterSubset = c())

Arguments

`envir`	A LocalControlClassic environment containing UPSnnltd objects.
`clusterSubset`	(optional) A vector containing requested cluster counts. If provided, the boxplot is created using only the UPSnnltd objects corresponding to the requested cluster counts.

Value

Returns the call to boxplot with the formula: "ltd ~ numclst".

Adds the "ltdds" object to the Local Control environment.

Examples


data(lindner)
cvars <- c("stent","height","female","diabetic","acutemi",
           "ejecfrac","ves1proc")
numClusters <- c(1, 5, 10, 20, 40, 50)

results <- LocalControlClassic(data = lindner,
                               clusterVars = cvars,
                               treatmentColName = "abcix",
                               outcomeColName = "cardbill",
                               clusterCounts = numClusters)

bxp <- UPSboxplot(results)

data(lindner)
cvars <- c("stent","height","female","diabetic","acutemi",
           "ejecfrac","ves1proc")
numClusters <- c(1, 5, 10, 20, 40, 50)

results <- LocalControlClassic(data = lindner,
                               clusterVars = cvars,
                               treatmentColName = "abcix",
                               outcomeColName = "cardbill",
                               clusterCounts = numClusters)

bxp <- UPSboxplot(results)

Display Sensitivity Analysis Graphic in Unsupervised Propensiy Scoring

Description

Plot summary of results from multiple calls to UPSnnltd() and/or UPSivadj() after an initial setup call to UPSaccum(). The UPSgraph() plot displays any sensitivity of the LTD and LOA Distributions to choice of Number of Clusters in X-space.

Usage

UPSgraph(envir, nncol = "red", nwcol = "green3", ivcol = "blue", ...)
UPSgraph(envir, nncol = "red", nwcol = "green3", ivcol = "blue", ...)

Arguments

`envir`	name of the working local control classic environment.
`nncol`	optional; string specifying color for display of the Mean of the LTD distribution when weighted by cluster size from any calls to UPSnnltd().
`nwcol`	optional; string specifying color for display of the Mean of the LTD distribution when weighted inversely proportional to variance from any calls to UPSnnltd().
`ivcol`	optional; string specifying color for display of the Difference in LOA predictions, at PS = 100% minus that at PS = 0%, from any calls to UPSivadj().
`...`	Additional arguments to pass to the plotting function.

Details

The third phase of Unsupervised Propensity Scoring is a graphical Sensitivity Analysis that depicts how the Overall Means of the LTD and LOA distributions change with the number of clusters.

Author(s)

Bob Obenchain <[email protected]>

References

Kaufman L, Rousseeuw PJ. (1990) Finding Groups in Data. An Introduction to Cluster Analysis. New York: John Wiley and Sons.
Obenchain RL. (2004) Unsupervised Propensity Scoring: NN and IV Plots. Proceedings of the American Statistical Association (on CD) 8 pages.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Rubin DB. (1980) Bias reduction using Mahalanobis metric matching. Biometrics 36: 293-298.

Hierarchical Clustering of Patients on X-covariates for Unsupervised Propensiy Scoring

Description

Derive a full, hierarchical clustering tree (dendrogram) for all patients (regardless of treatment received) using Mahalonobis between-patient distances computed from specified baseline X-covariate characteristics.

Usage

UPShclus(envir, dframe, xvars, method, metric)
UPShclus(envir, dframe, xvars, method, metric)

Arguments

`envir`	name of the working local control classic environment.
`dframe`	Name of data.frame containing baseline X covariates.
`xvars`	List of names of X variable(s).
`method`	Hierarchical Clustering Method: "diana", "agnes" or "hclus".
`metric`	A valid distance metric for clustering.

Details

The first step in an Unsupervised Propensity Scoring alalysis is always to hierarchically cluster patients in baseline X-covariate space. UPShclus uses a Mahalabobis metric and clustering methods from the R "cluster" library for this key initial step.

Value

An output list object of class UPShclus:

dframe: Name of data.frame containing baseline X covariates.
xvars: List of names of X variable(s).
method: Hierarchical Clustering Method: "diana", "agnes" or "hclus".
upshcl: Hierarchical clustering object created by choice between three possible methods.

Author(s)

Bob Obenchain <[email protected]>

References

Kaufman L, Rousseeuw PJ. (1990) Finding Groups in Data. An Introduction to Cluster Analysis. New York: John Wiley and Sons.
Kereiakes DJ, Obenchain RL, Barber BL, et al. (2000) Abciximab provides cost effective survival advantage in high volume interventional practice. Am Heart J 140: 603-610.
Obenchain RL. (2004) Unsupervised Propensity Scoring: NN and IV Plots. Proceedings of the American Statistical Association (on CD) 8 pages.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Rubin DB. (1980) Bias reduction using Mahalanobis metric matching. Biometrics 36: 293-298.

Instrumental Variable LATE Linear Fitting in Unsupervised Propensiy Scoring

Description

For a given number of patient clusters in baseline X-covariate space and a specified Y-outcome variable, linearly smooth the distribution of Local Average Treatment Effects (LATEs) plotted versus Within-Cluster Treatment Selection (PS) Percentages.

Usage

UPSivadj(envir, numclust)
UPSivadj(envir, numclust)

Arguments

`envir`	name of the working local control classic environment.
`numclust`	Number of clusters in baseline X-covariate space.

Details

Multiple calls to UPSivadj(n) for varying numbers of clusters n are made after first invoking UPShclus() to hierarchically cluster patients in X-space and then invoking UPSaccum() to specify a Y outcome variable and a two-level treatment factor t. UPSivadj(n) linearly smoothes the LATE distribution when plotted versus within cluster propensity score percentages.

Value

An output list object of class UPSivadj:

hiclus: Name of clustering object created by UPShclus().
dframe: Name of data.frame containing X, t & Y variables.
trtm: Name of treatment factor variable.
yvar: Name of outcome Y variable.
numclust: Number of clusters requested.
actclust: Number of clusters actually produced.
scedas: Scedasticity assumption: "homo" or "hete"
PStdif: Character string describing the treatment difference.
ivhbindf: Vector containing cluster number for each patient.
rawmean: Unadjusted outcome mean by treatment group.
rawvars: Unadjusted outcome variance by treatment group.
rawfreq: Number of patients by treatment group.
ratdif: Unadjusted mean outcome difference between treatments.
ratsde: Standard error of unadjusted mean treatment difference.
binmean: Unadjusted mean outcome by cluster and treatment.
binfreq: Number of patients by bin and treatment.
faclev: Maximum number of different numerical values an outcome variable can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.
youtype: "contin"uous => next eleven outputs; "factor" => no additional output items.
pbinout: LATE regardless of treatment by cluster.
pbinpsp: Within-Cluster Treatment Percentage = non-parametric Propensity Score.
pbinsiz: Cluster radii measure: square root of total number of patients.
symsiz: Symbol size of largest possible Snowball in a UPSivadj() plot with 1 cluster.
ivfit: lm() output for linear smooth across clusters.
ivtzero: Predicted outcome at PS percentage zero.
ivtxsde: Standard deviation of outcome prediction at PS percentage zero.
ivtdiff: Predicted outcome difference for PS percentage 100 minus that at zero.
ivtdsde: Standard deviation of outcome difference.
ivt100p: Predicted outcome at PS percentage 100.
ivt1pse: Standard deviation of outcome prediction at PS percentage 100.

Author(s)

Bob Obenchain <[email protected]>

References

Imbens GW, Angrist JD. (1994) Identification and Estimation of Local Average Treatment Effects (LATEs). Econometrica 62: 467-475.
Obenchain RL. (2004) Unsupervised Propensity Scoring: NN and IV Plots. Proceedings of the American Statistical Association (on CD) 8 pages.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.-
McClellan M, McNeil BJ, Newhouse JP. (1994) Does More Intensive Treatment of Myocardial Infarction in the Elderly Reduce Mortality?: Analysis Using Instrumental Variables. JAMA 272: 859-866.
Rosenbaum PR, Rubin RB. (1983) The Central Role of the Propensity Score in Observational Studies for Causal Effects. Biometrika 70: 41-55.

Plot the LTD distribution as a function of the number of clusters.

Description

This function creates a plot displaying the distribution of Local Treatment Differences (LTDs) as a function of the number of clusters created for all UPSnnltd objects in the provided environment. The hinges and whiskers are generated using boxplot.stats.

Usage

UPSLTDdist(envir, legloc = "bottomleft", ...)
UPSLTDdist(envir, legloc = "bottomleft", ...)

Arguments

envir

A LocalControlClassic environment containing UPSnnltd objects.

legloc

Where to place the legend in the returned plot. Defaults to "bottomleft".

...

Arguments passed on to graphics::plot.default

type

1-character string giving the type of plot desired. The following values are possible, for details, see plot: "p" for points, "l" for lines, "b" for both points and lines, "c" for empty points joined by lines, "o" for overplotted points and lines, "s" and "S" for stair steps and "h" for histogram-like vertical lines. Finally, "n" does not produce any points or lines.

xlim

the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed and leads to a ‘reversed axis’.

The default value, NULL, indicates that the range of the finite values to be plotted should be used.

ylim

the y limits of the plot.

log

a character string which contains "x" if the x axis is to be logarithmic, "y" if the y axis is to be logarithmic and "xy" or "yx" if both axes are to be logarithmic.

main

a main title for the plot, see also title.

sub

a subtitle for the plot.

xlab

a label for the x axis, defaults to a description of x.

ylab

a label for the y axis, defaults to a description of y.

ann

a logical value indicating whether the default annotation (title and x and y axis labels) should appear on the plot.

axes

a logical value indicating whether both axes should be drawn on the plot. Use graphical parameter "xaxt" or "yaxt" to suppress just one of the axes.

frame.plot

a logical indicating whether a box should be drawn around the plot.

panel.first

an ‘expression’ to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids or scatterplot smooths. Note that this works by lazy evaluation: passing this argument from other plot methods may well not work since it may be evaluated too early.

panel.last

an expression to be evaluated after plotting has taken place but before the axes, title and box are added. See the comments about panel.first.

asp

the $y/x$ aspect ratio, see plot.window.

xgap.axis,ygap.axis

the $x/y$ axis gap factors, passed as gap.axis to the two axis() calls (when axes is true, as per default).

Value

Returns the LTD distribution plot.

Adds the "ltdds" object to envir.

Examples


 data(lindner)
 cvars <- c("stent","height","female","diabetic","acutemi",
            "ejecfrac","ves1proc")
 numClusters <- c(1, 2, 10, 15, 20, 25, 30, 35, 40, 45, 50)
 results <- LocalControlClassic(data = lindner,
                                clusterVars = cvars,
                                treatmentColName = "abcix",
                                outcomeColName = "cardbill",
                                clusterCounts = numClusters)
 UPSLTDdist(results,ylim=c(-15000,15000))

data(lindner)
 cvars <- c("stent","height","female","diabetic","acutemi",
            "ejecfrac","ves1proc")
 numClusters <- c(1, 2, 10, 15, 20, 25, 30, 35, 40, 45, 50)
 results <- LocalControlClassic(data = lindner,
                                clusterVars = cvars,
                                treatmentColName = "abcix",
                                outcomeColName = "cardbill",
                                clusterCounts = numClusters)
 UPSLTDdist(results,ylim=c(-15000,15000))

Nearest Neighbor Distribution of LTDs in Unsupervised Propensiy Scoring

Description

For a given number of patient clusters in baseline X-covariate space, UPSnnltd() characterizes the distribution of Nearest Neighbor "Local Treatemnt Differences" (LTDs) on a specified Y-outcome variable.

Usage

UPSnnltd(envir, numclust)
UPSnnltd(envir, numclust)

Arguments

`envir`	name of the working local control classic environment.
`numclust`	Number of clusters in baseline X-covariate space.

Details

Multiple calls to UPSnnltd(n) for varying numbers of clusters, n, are typically made after first invoking UPShclus() to hierarchically cluster patients in X-space and then invoking UPSaccum() to specify a Y outcome variable and a two-level treatment factor t. UPSnnltd(n) then determines the LTD Distribution corresponding to n clusters and, optionally, displays this distribution in a "Snowball" plot.

Value

An output list object of class UPSnnltd:

hiclus: Name of clustering object created by UPShclus().
dframe: Name of data.frame containing X, t & Y variables.
trtm: Name of treatment factor variable.
yvar: Name of outcome Y variable.
numclust: Number of clusters requested.
actclust: Number of clusters actually produced.
scedas: Scedasticity assumption: "homo" or "hete"
PStdif: Character string describing the treatment difference.
nnhbindf: Vector containing cluster number for each patient.
rawmean: Unadjusted outcome mean by treatment group.
rawvars: Unadjusted outcome variance by treatment group.
rawfreq: Number of patients by treatment group.
ratdif: Unadjusted mean outcome difference between treatments.
ratsde: Standard error of unadjusted mean treatment difference.
binmean: Unadjusted mean outcome by cluster and treatment.
binvars: Unadjusted variance by cluster and treatment.
binfreq: Number of patients by bin and treatment.
awbdif: Across cluster average difference with cluster size weights.
awbsde: Standard error of awbdif.
wwbdif: Across cluster average difference, inverse variance weights.
wwbsde: Standard error of wwbdif.
faclev: Maximum number of different numerical values an outcome variable can assume without automatically being converted into a "factor" variable; faclev=1 causes a binary indicator to be treated as a continuous variable determining an average or proportion.
youtype: "contin"uous => only next eight outputs; "factor" => only last three outputs.
aovdiff: ANOVA summary for treatment main effect only.
form2: Formula for outcome differences due to bins and to treatment nested within bins.
bindiff: ANOVA summary for treatment nested within cluster.
sig2: Estimate of error mean square in nested model.
pbindif: Unadjusted treatment difference by cluster.
pbinsde: Standard error of the unadjusted difference by cluster.
pbinsiz: Cluster radii measure: square root of total number of patients.
symsiz: Symbol size of largest possible Snowball in a UPSnnltd() plot with 1 cluster.
factab: Marginal table of counts by Y-factor level and treatment.
cumchi: Cumulative Chi-Square statistic for interaction in the three-way, nested table.
cumdf: Degrees of-Freedom for the Cumulative Chi-Squared.

Author(s)

Bob Obenchain <[email protected]>

References

Obenchain RL. (2004) Unsupervised Propensity Scoring: NN and IV Plots. Proceedings of the American Statistical Association (on CD) 8 pages.
Obenchain RL. (2011) USPSinR.pdf USPS R-package vignette, 40 pages.
Rosenbaum PR, Rubin RB. (1983) The Central Role of the Propensity Score in Observational Studies for Causal Effects. Biometrika 70: 41–55.
Rubin DB. (1980) Bias reduction using Mahalanobis metric matching. Biometrics 36: 293-298.

Package 'LocalControl'

Help Index

Simulated cardiac medication data for survival analysis

Description

Format

Author(s)

Framingham heart study data extract on smoking and hypertension.

Description

Format

References

Lindner Center for Research and Education study on Abciximab cost-effectiveness and survival

Description

Format

References

Local Control

Description

Usage

Arguments

Value

References

Examples

Deprecated LocalControl functions

Description

Details

Local Control Classic

Description

Usage

Arguments

Value

References

Examples

Calculate confidence intervals around the cumulative incidence functions (CIFs) generated by LocalControl when outcomeType = "survival".

Description

Usage

Arguments

References

Examples

Provides a bootstrapped confidence interval estimate for LocalControl LTDs.

Description

Usage

Arguments

References

Examples

Plot cumulative incidence functions (CIFs) from Local Control.

Description

Usage

Arguments

References

Examples

Plots the local treatment difference as a function of radius for LocalControl.

Description

Usage

Arguments

References

Examples

Test for Within-Bin X-covariate Balance in Supervised Propensiy Scoring

Description

Usage

Arguments

Value

Author(s)

References

LOESS Smoothing of Outcome by Treatment in Supervised Propensiy Scoring

Description

Usage

Arguments

Details

Author(s)

References

Propensity Score prediction of Treatment Selection from Patient Baseline X-covariates

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Change the Number of Bins in Supervised Propensiy Scoring

Description