search for: mspath

I have code and documentation that don't match, but R CMD check didn't flag it. in mspath.R mspath <- function(formula, # formula with observed Markov states ~ observation times (required) qmatrix, # matrix of 1s and 0s with indices of allowed transitions (diagonal is ignored) (required) misc = FALSE, ematrix = NULL, # matri...

Now available on CRAN. Package: mspath Title: Multi-state Path-Dependent Models in Discrete Time Description: Functions for fitting path-dependent (non-Markov) multi-state models to categorical processes observed at arbitrary times, optionally with misclassified responses, and covariates on transition or misclassification rates....

Now available on CRAN. Package: mspath Title: Multi-state Path-Dependent Models in Discrete Time Description: Functions for fitting path-dependent (non-Markov) multi-state models to categorical processes observed at arbitrary times, optionally with misclassified responses, and covariates on transition or misclassification rates....

...; #include <Rinternals.h> and later #include <memory> // I think this is why I needed R_NO_REMAP I realize this is not a complete example, but I'm hoping this will ring a bell with someone. I encountered this while running R CMD check. The link line generated was g++ -shared -o mspath.so AbstractTimeStepsGenerator.o Coefficients.o CompositeHistoryComputer.o CompressedTimeStepsGenerator.o Covariates.o Data.o Environment.o Evaluator.o FixedTimeStepsGenerator.o LinearProduct.o Manager.o Model.o ModelBuilder.o Path.o PathGenerator.o PrimitiveHistoryComputer.o SimpleRecorder.o Specif...

...version 2.10.0 Are this and other packages likely to work correctly with different R's (2.7 in the case of stable)? How well are they likely to work with a backported R? The R version would then match, but I assume some of the associated libraries might be off. Ross Boylan P.S. I see the mspath package I just uploaded is already in cran2deb. Cool, and thanks to Dirk, Charles Blundell, Google, and others who made this possible.

...library(...). In particular, I don't need to figure out what lib.loc is. I have some C code as part of the package, so that (well the .so file) needs to be loaded too. 2) Others seem to just say data(..), but this doesn't work for me. I created the data with save(gold, e2, q2, file="mspath/data/inputs", compress=TRUE) and later renamed the file to inputs.RData. (check didn't think the file counted without the extension). I have tried to access it in my test script (under tests/) with both load and data (e.g., data("inputs"), data("inputs.RData"), data(i...

...em{10}{Use the model to generate a random path for each case. returning a \code{data.frame} with simulated observed states and times and all other data as observed.} }} \item{testing}{This argument is only for use by developers. Set it ## etc This comes out fine in a pdf, but ?mspath (the function) produces, in part, <quote> stepdenominator: See 'stepnumerator' just above. 1 By default, calculates a maximimum likelihood. To evaluate a single likelihood, set all parameters to fixed. 0 Count number of paths and related statistics without eval...

...pect, it is clearly preferable to create allGenerics.py from the start. If you didn't, and discover you should have, the script automates the conversion. Thanks to everyone who helped me with my packaging problems. The package finally made it to CRAN as http://cran.r-project.org/web/packages/mspath/index.html. I'll send a public notice of that to the general R list. Ross Boylan

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })