[R] Failed Convergence when using mi to generate synthetic data
I was hoping to use mi to generate a synthetic version of a database. The
strategy (see code below) was simple: use the diamonds dataset from
ggplot2, subset it focus on 3K single-color, then create a blank record
for every "real" record, and throw the new dataset at mi to see if it would
populate the blank records. I kept getting failed convergence.
I think I have simplified the dataset down to the point where either I am
doing it wrong or something is wrong (conceptually) with what I am doing. I
would welcome suggestions:
library(ggplot2)
library(mi)
data(diamonds)
#use only 2800 or so observations!
diamonds1 <-subset(diamonds, color=="J")
rm(diamonds)
#simplify the data structure
diamonds1 <-subset(diamonds1, select=-c(x, z, y, cut, clarity, depth,
table))
str(diamonds1)
#generate a blank table
emptydiamonds1 <-diamonds1
for(j in 1:dim(diamonds1)[2]) {
emptydiamonds1[,j] <- NA
}
#throw up a dummy variable for imputation
diamonds1$impute=0
emptydiamonds1$impute=1
#package the two into one dataset
d2 <-rbind(diamonds1, emptydiamonds1)
str(d2)
#run in.info
miinfo <-mi.info(d2)
#pre_process
mi_pre <-mi.preprocess(d2)
#impute
Imp1 <-mi(mi_pre, n.iter=49)
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[R] Quantile scores as dependent variables.. an R and general method question
I have a dataset that does not include native scores, but only serial quantile rankings for a set of units. Clearly these observations are dependent (in that you can't alter one observation without also altering others). Are there methods for dealing with quantile dependent variables. My atempt to find such methods has not bee successful. Any leads to theory, texts or R code would be most appeciated. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plot methods for summary of rms objects
The integration of plot methods for various outputs from rms packages is a great appreciated aspect of the rms package. I particularly like to use: plot(summary(model)) for my own purposes, but... for publication/presentation I need to modify details like variable names, or the number of signficant digits used in the figure annotations. Is there a simple way to modify the plot inputs arising from summary, or is it necessary to hack the summary object? Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] rms:fastbw variable selection differences with AIC .vs. p value methods
I want to employ a parsimonious model to draw nomograms, as the full model is too complex to draw nomograms readily (several interactions of continuous variables). However, one interesting variable stays or leaves based on whether I choose "p value" or "AIC" options to fastbw(). My question boils down to this: Is there a theoretical reason to prefer one over another? Consider: fastbw(model94c, aic=1e10) DeletedChi-Sq d.f. P Residual d.f. P AIC ToD 0.11 3 0.99030.11 3 0.9903 -5.89 Experience * ToD 2.56 3 0.46462.67 6 0.8487 -9.33 Experience * Assoc 0.45 2 0.79703.13 8 0.9262 -12.87 RatePressure 2.99 3 0.39396.11 11 0.8658 -15.89 DW_height_t 2.92 3 0.40479.03 14 0.8293 -18.97 TBV * Experience 3.46 3 0.3260 12.49 17 0.7698 -21.51 Experience * Sex 0.05 1 0.8153 12.54 18 0.8181 -23.46 Experience 0.18 1 0.67212.72 19 0.8526 -25.28 Sex 1.19 1 0.2745 13.91 20 0.8348 -26.09 Assoc6.09 2 0.0475 20.01 22 0.5826 -23.99 Experience * Pulse 10.53 3 0.0146 30.53 25 0.2049 -19.47 Sex * ToD 18.24 3 0.0004 48.77 28 0.0088 -7.23 PulsePressure 21.15 3 0.0001 69.92 31 0.00017.92 Race19.87 2 0. 89.79 33 0. 23.79 Pulse 25.31 3 0. 115.09 36 0. 43.09 Age * Experience 202.80 3 0. 317.89 39 0. 239.89 TBV282.41 3 0. 600.30 42 0. 516.30 Location 310.19 14 0. 910.50 56 0. 798.50 Age809.64 3 0. 1720.13 59 0. 1602.13 The ordering of variables is expected, and is consistent with the substantial knowledge I have about the outcome. The problematic variable is Sex * TOD . When I use p value as the rule, with an SLS of 0.01, the variable is retained, but when I use AIC , Sex*TOD is not retained. This reflects the fact that while the Sex*TOD interaction is theoretically interesting, the AIC value is negative and relatively small in magnitude, even as the p value skirts below 0.01. Is this judgement territory or are their statistical considerations that should be invoked? Caveats? Is there a theoretical reason to choose AIC over p value methods, or is either acceptable? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] When models and anova(model) disagree...
I have a situation where the parameter estimates from lrm identify a
binary predictor variable ("X") as clearly non-significant (p>0.3), but
the ANOVA of that same model gives X a chi^2-df rank of > 200, and
adjudicates X and one interaction of X and a continuous measure as
highly significant. The N is massive and X has two categories, each
with > 100,000 observations. I would expect X to have a significant
impact on the outcome.
The full model includes a large number of continuous (coded with rcs
with 3 knots) and categorical variables, as well as a plethora of
interactions between the categorical and continuous variables. Only one
of the interactions between the binary variable and the other
categorical or continuous variables is statistically significant.
Can anyone offer a suggestion on what might explain this discordance?
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[R] Removal of elements from nomograms
The rms package includes the nomogram function, which generates a list object that can be passed to plot for graphical production of nomograms. I would like to remove the "linear predictor" line in the graph, which means (I suspect) removing it from the nomogram output object. I've looked at the nomogram output object, but it is not clear to me if or how it might be edited to remove the linear predictor content. Similarly , I do not see how to coax nomogram() into not producing this output in the first place. As ever, thanks in advance are likely due to Frank Harrell, without whom many things would be much more difficult. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Nomograms from rms' fastbw output objects
There is both a technical and a theoretical element to my question... Should I be able to use the outputs which arise from the fastbw function as inputs to nomogram(). I seem to be failing at this, -- I obtain a subscript out of range error. That I can't do this may speak to technical failings, but I suspect it is because Prof Harrell thinks/knows it injudicious. However, I can't invent a reason why nomograms should be restricted to the full models, if the purpose of fastbw is to generate parsimonious models with appropriate standard errors. I'd welcome comments on either the technical or the theoretical issues. Many thanks in advance, Rob James __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Baseline terms for lrm
I should rephrase my question. When using the notation rcs(V1, N) within the lrm function in the rms package, the associated model reports out N-1 values for the associated variable. Fine. The rcs-constructed temporary variables are denoted V1, V1', V1'' when one looks at the model output, but the model output is not explicit about which values of V1 are associated with variables V1, V1', V1'' . Yes, specs() tells you what the splits are for rcs, but is there a way to explicitly generate the associations between the model outcome variables, and the associated ranges, Here's the idea: e.g: Variable LowHigh V 02 V' 36 V' 722 ... Is there existing functionality to do this? If not, it suggest it would be a helpful addition. Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Baseline terms for lrm
Dear R-help and Prof. Harrell: My question concerns the baseline state for continuous variable in lrm() within the RMS package. I have a model which can be reduced to: lrm(FT ~ rcs(V1, c(0, 1,5)) The model makes perfect sense if the baseline state is where V1>=5 but the model makes no sense if the baseline category is 0 (which I had expected). Can someone point me to a reference, or suggest a command/test, to get the model to fess up to the baseline state. The variable V1 and V1' are shown in the model output, but there is no clear association between these pseudo-variables and the ranges specified in the cut. Thus, it is seems possible to misidentify the baseline value for the term. Many thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Dealing with Latex output in Openoffice
I am making considerable use of Harrell's rms package, but I do not use Latex for writing. (I have enough trouble convincing my co-authors to use Openoffice!). rms makes copious use of Latex output for various mixed graphical and text outputs, amongst other things. Does someone have a convenient strategy for dealing with Latex output and openoffice, either within or outside of a OdfSweave environment? Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Reorder factor and address embedded escapes
I am trying to reorder a factor variable that has embedded escape
characters. The data begins as a csv file with a factor that includes
embedded new line characters. By the time read.table has rendered it
into a data frame, the variable now has an extra backslash.
e.g.
"This\nLabel" in the csv becomes "This\\nLabel" in the data frame.
So, I am trying to reorder the factor and deal with the introduction of
a secondary \ . Here's a small example:
A = c("A\\nB", "C\\nD")
test <-data.frame(A)
str(test)
test$reorderA <-factor(test$A, c("C\\nD", "A\\nB"))
str(test)
test$reorderB <-sub("n", "\n", test$reorderA)
str(test)
When sub is applied to the now-correctly ordered factor, it returns to
the default ordering.
Suggestions?
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[R] Recovering x/y coordinates from a scatterplot image
Do I recall correctly that there is an R package that can take an image, and help one estimate the x/y coordinates? I can't find the package, thought it was an R-tool, but would appreciate any leads. Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] XML getNodeSet syntax for PUBMED XML export
I am looking for the syntax to capture XML tags marked with /DescriptorName MajorTopicYN="Y"/ , but the combination of the internal space (between "Name" and "Major" and the embedded quote marks are defeating me. I can get all the "DescriptorName" tags, but these include both MajroTopicYN = "Y" and "N" variants. Any suggestions? Thanks in advance. Prototype text from PUBMED Antibodies, Monoclonal Blood Platelets immunology physiology ultrastructure [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] HMisc/rms package questions
1) How does one capture the plots from the plsmo procedure? Simply inserting a routing call to a graphical device (such as jpeg, png, etc) and then running the plsmo procedure (and then dev.off()) does not route the output to the file system. 1b) Related to above, has anyone thought of revising the plsmo procedure to use ggplot? I'd like to capture several such graphs into a faceted arrangement. 2) The 2nd issue is more about communications than software. I have developed a model using lrm() and am using plot to display the model. All that is fairly easy. However, my coauthors are used to traditional methods, where baseline categories are rather broadly defined (e.g. males, age 25-40, height 170-180cm, BP 120-140, etc) and results are reported as odds-ratios, not as probabilities of outcomes. Therefore, and understandably, they are finding the graphs which arise from lrm->Predict->plot difficult to interpret. Specifically, in one graph, the adjusted to population is defined one way, and in another graph of the same model (displaying new predictors) there will be a new "adjusted to" population. Sometimes the adjusted populations are substantially distinct, giving rise to event rates that vary dramatically across graphs. This can prove challenging when trying to present the set of graphs as parts of a whole. It all makes sense; it just adds complexity to introducing these new methods. One strategy might be to manually define the baseline population across graphs; this way I could attempt to impose some content-specific coherence to the graphs, by selecting the baseline populations. Clearly this is do-able, but I have yet to see it done. I'd welcome suggestions and comments. Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Specifying interactions in rms package... error
I am encountering an error I do not know how to debug. The error arises when I try to add an interaction term involving two continuous variables (defined using rcs functions) to an existing (and working) model. The new model reads: model5 <- lrm( B_fainting ~ gender+ rcs(exactage, 7) + rcs(DW_nadler_bv, 7) + rcs(drawtimefrom8am, 7)+ DW_firsttime+ DW_race_eth + rcs(DW_BPS, 5)+ rcs(DW_BPD, 5)+ rcs(pulse3, 5)+ locat2+ (rcs(exactage, 3) * rcs(drawtimefrom8am, 3)) ) This gives rise to the following error: Error in dimnames(X)[[2]] <- atr$colnames : length of 'dimnames' [2] not equal to array extent In addition: Warning message: In names(nmiss)[jz] <- fname[asm != 9] : number of items to replace is not a multiple of replacement length The sessionInfo() output is below, but I think relatively unremarkable. The dataset is very large (about 550K observations, although the outcome (B_fainting) is relatively sparse with only 1500 events in this sample. I do not get this error when the interaction term is replaced by two categorical variables (data not shown). I can replicate this error when there is just one continuous variable and one categorical variable. I'd welcome suggestions. Thank you in advance. sessionInfo() R version 2.11.0 (2010-04-22) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 [4] LC_COLLATE=en_CA.UTF-8 LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] gmodels_2.15.0 rms_3.0-0 Hmisc_3.8-2 survival_2.35-8 odfWeave_0.7.14 XML_3.1-0 [7] lattice_0.18-8 loaded via a namespace (and not attached): [1] cluster_1.13.1 gdata_2.8.0grid_2.11.0gtools_2.6.2 MASS_7.3-7 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fidelity of lattice graphics captured to jpeg or png... followup
Subsequent investigations (via GIMP) show that the problem is in OO, and now with the images themselves. Off to the OO forums. Original Message Subject:Fidelity of lattice graphics captured to jpeg or png Date: Thu, 29 Apr 2010 08:05:04 -0700 From: Rob James To: r-help@r-project.org I am generating images via lattice from Frank Harrell's RMS package. These images are characterized by coloured lines and grey-scale confidence intervals. I need to port them to Openoffice/etc, and have tried both png and jpeg (at high quality), but in neither format can I subsequently see the the grey scale confidence intervals. Other than moving to LaTex, does anyone have other suggestions? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fidelity of lattice graphics captured to jpeg or png
I am generating images via lattice from Frank Harrell's RMS package. These images are characterized by coloured lines and grey-scale confidence intervals. I need to port them to Openoffice/etc, and have tried both png and jpeg (at high quality), but in neither format can I subsequently see the the grey scale confidence intervals. Other than moving to LaTex, does anyone have other suggestions? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] logical(0) response from lrm
What causes the error report: logical(0) to arise in the rms function lrm? Here's my data: But both the dependent and the independent variable seem fine... > str(AABB) 'data.frame':1176425 obs. of 9 variables: $ sex : int 1 1 0 1 1 0 0 0 0 0 ... $ faint : int 0 0 0 0 0 0 0 0 0 0 ... Here's the simplified model and error AABB$model1 < lrm (faint ~ sex) logical(0) But the data seem fine > table(AABB$faint) 0 1 11734752950 > table(AABB$sex) 0 1 502551 673874 Suggestions? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] odfWeave & XML error in post-processing
Just to close out my earlier posting, I have identified and resolved the
following odfWeave/XML error:
xmlParseStartTag: invalid element name
I used odfWeave to call various logistic regression models which
included the above mentioned variable. odfWeave failed to generate the
destination file throwing multiple lines of the above error.
It happened that the dataset originated in STATA (probably irrelevant),
and included a variable which had five levels. Two of those levels had
values of
"(1)<3500" and "(5)=>5000".
So, while these codes did not appear in the source document, these codes
appear in the odfWeave destination file. The results were displayed in
the document using the following crude method:
results <-glm(..
and subsequently reported out using :
odfTable(
as.matrix(results[,c(X1, X2, X3)],)
horizontal = TRUE)
odfTableCaption("Selected Logistic Regression Results for RXN3 outcome")
@
I received xmlParseStartTag errors for each such table. Editting of the
XML file in gedit highlighted the above values as problematic.
I then removed the two problematic value for this variable, and re-ran
odfWeave, which generated the output I needed.
So, it appears that these values of this variable operated as invalid
xmlParseStartTags, and that the process of wrapping up content_1.xml
back into an ODF file failed because of the mis-recognition of these
ParseStartTags found embedded in the data. I think this is likely to
be regarded more as a feature than as a bug, but it is none-the-less a
cautionary tale.
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Re: [R] odfWeave & XML error in post-processing
Just so we complete (partially) the web-record... Some further hunting determined that the &apos was an apostrophe - obvious only in retrospect! Removal of this character has resolved the Entity errors, but not the xmlParseStartTag: invalid element name errors. I had assumed that the two errors were dependent, but they are not. odfWeave does have some ability with its translate command to address some XML/OO special characters, but I have not explored this facet of odfWeave yet, and I was a bit surprised that the use of this common grammatical mark generated an error, but.. Now, in search of a cause for the invalid element name error(s). Thanks to Duncan for his help. Duncan Temple Lang wrote: Hi Rob. Without the file content_1.xml or any information from the R call stack (e.g. options(error = recover) and then run the command and dynamically explore the state of affairs when the error occurs), there is no way for us to know what the problem might be. Somehow, the XML parser appears to be seeing a I've been happily building a file with odfWeave, and just as the hour draws nigh for it to be sent off, odfWeave or XML throws the following catastrophic error: ...this is the tail of entirely uneventful processing of input file. 31 : term xml(label=LR_Fall_Model_Results) 32 : term verbatim(label=LR_Model_Fall_graph) 33 : term xml(label=LR_OMC_tab) 'content_1.xml' has been Sweaved Removing content.xml Post-processing the contents xmlParseStartTag: invalid element name Entity 'apos' not defined Entity 'apos' not defined This triplet of errors XMLParse, and duplicate "Entity" lines is reported several times, then XML or odfWeave packs up its toys, and goes home without an output file. I'd (desperately) love any insights anyone might have. Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] odfWeave & XML error in post-processing
I've been happily building a file with odfWeave, and just as the hour draws nigh for it to be sent off, odfWeave or XML throws the following catastrophic error: ...this is the tail of entirely uneventful processing of input file. 31 : term xml(label=LR_Fall_Model_Results) 32 : term verbatim(label=LR_Model_Fall_graph) 33 : term xml(label=LR_OMC_tab) 'content_1.xml' has been Sweaved Removing content.xml Post-processing the contents xmlParseStartTag: invalid element name Entity 'apos' not defined Entity 'apos' not defined This triplet of errors XMLParse, and duplicate "Entity" lines is reported several times, then XML or odfWeave packs up its toys, and goes home without an output file. I'd (desperately) love any insights anyone might have. Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dependencies for binaries install of R 2.8.2 under Ubuntu 648.1 (Intrepid)
Problem resolved. This error occurred because of a mixture of hardy and intrepid sources in my sources.list . Thanks to Phil Spector, Dirk Eddelbuettel and others for their input. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Dependencies for binaries install of R 2.8.2 under Ubuntu 64 8.1 (Intrepid)
BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; }I
can't seem to perform an install from CRAN (stat.sfu.ca, specifically)
for Ubuntu 64 8.1 (Intrepid) and 2.8.2 of R. Here is the log:
Looks like some dependencies cannot be satisfied.
Suggestions? Thanks in advance.
sudo apt-get install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
Since you only requested a single operation it is extremely likely
that
the package is simply not installable and a bug report against
that package should be filed.
The following information may help resolve the situation:
The following packages have unmet dependencies:
r-base: Depends: r-base-core (>= 2.8.1-1intrepid0) but it is not
going to be installed
Depends: r-recommended (= 2.8.1-1intrepid0) but it is not
going to be installed
E: Broken packages
r...@u8:~$
r...@u8:~$ sudo apt-get install r-base-core
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
Since you only requested a single operation it is extremely likely
that
the package is simply not installable and a bug report against
that package should be filed.
The following information may help resolve the situation:
The following packages have unmet dependencies:
r-base-core: Depends: libc6 (>= 2.8~20080505) but 2.7-10ubuntu4 is
to be installed
Depends: libgfortran3 (>= 4.3) but it is not
installable
Depends: libpango1.0-0 (>= 1.21.6) but
1.20.5-0ubuntu1 is to be installed
E: Broken packages
r...@u8:~$
r...@u8:~$
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[R] Graphics for proportion within factor
BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; }I
am looking to draw what I hoped was a simple plot of proportion WITHIN
a strata, save % males by site. I seem to be able to get proportion of
males, by
site, where the proportion is across the whole dataset, but not the
proportion within each site.
thanks in advance,
Rob
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[R] odfWeave error
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odfWeave is throwing up a cryptic error, after successfully processing a
file with a large number of figures (~30) and many \Sexpr{} calls. The
error is (at least to me) cryptic. I am not sure where to look to
correct this problem.
Here's the error:
Post-processing the contents
Error in .Call("RS_XML_Parse", file, handlers, endElementHandlers,
as.logical(addContext), :
attempt to apply non-function
Is there any way to figure out what this means, or where I might look
for the error in the source?
Here's a capture of the associated log. I am running R 2.8 under Ubuntu
8.04.
Thanks,
> odfWeave("/home/rob/Trauma/Report_2_draft.odt",
"/home/rob/Trauma/Report_2_draft_out.odt")
Copying /home/rob/Trauma/Report_2_draft.odt
Setting wd to /tmp/Rtmp2tlRz0/odfWeave23115040235
Unzipping ODF file using unzip -o Report_2_draft.odt
Archive: Report_2_draft.odt
extracting: mimetype
creating: Configurations2/statusbar/
inflating: Configurations2/accelerator/current.xml
creating: Configurations2/floater/
creating: Configurations2/popupmenu/
creating: Configurations2/progressbar/
creating: Configurations2/menubar/
creating: Configurations2/toolbar/
creating: Configurations2/images/Bitmaps/
inflating: layout-cache
inflating: content.xml
inflating: styles.xml
extracting: meta.xml
inflating: Thumbnails/thumbnail.png
inflating: settings.xml
inflating: META-INF/manifest.xml
Removing Report_2_draft.odt
Creating a Pictures directory
Pre-processing the contents
Sweaving content.Rnw
Writing to file content_1.xml
Processing code chunks ...
1 : term hide(label=loadData)
d2 : term verbatim(label=SiteHist)
ate()
3 : term verbatim(label=AgeSex)
4 : term verbatim(label=Sitesex)
5 : term verbatim(label=SiteHeadNeck)
6 : term verbatim(label=SiteFace)
7 : term verbatim(label=SiteChest)
8 : term verbatim(label=SiteAbdomnen)
9 : term verbatim(label=SiteGCS_Eyes)
10 : term verbatim(label=SiteGCS_Verbal)
11 : term verbatim(label=SiteGCS_Motor)
12 : term verbatim(label=SiteGCS_total)
13 : term verbatim(label=SBP)
14 : term verbatim(label=DBP)
15 : term verbatim(label=HR)
16 : term verbatim(label=RESPIRATION)
17 : term verbatim(label=PF_ADMIT)
18 : term verbatim(label=O2_admit)
19 : term verbatim(label=Ph_admit)
20 : term verbatim(label=DEFICIT)
21 : term verbatim(label=lactic_acid)
'content_1.xml' has been Sweaved
Removing content.xml
Post-processing the contents
Error in .Call("RS_XML_Parse", file, handlers, endElementHandlers,
as.logical(addContext), :
attempt to apply non-function
In addition: There were 50 or more warnings (use warnings() to see the
first 50)
> date()
[1] "Thu Oct 23 12:18:18 2008"
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--- End Message ---
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] odfWeave error
odfWeave is throwing up a cryptic error, after successfully processing a
file with a large number of figures (~30) and many \Sexpr{} calls. The
error is (at least to me) cryptic. I am not sure where to look to
correct this problem.
Here's the error:
Post-processing the contents
Error in .Call("RS_XML_Parse", file, handlers, endElementHandlers,
as.logical(addContext), :
attempt to apply non-function
Is there any way to figure out what this means, or where I might look
for the error in the source?
Here's a capture of the associated log. I am running R 2.8 under Ubuntu
8.04.
Thanks,
> odfWeave("/home/rob/Trauma/Report_2_draft.odt",
"/home/rob/Trauma/Report_2_draft_out.odt")
Copying /home/rob/Trauma/Report_2_draft.odt
Setting wd to /tmp/Rtmp2tlRz0/odfWeave23115040235
Unzipping ODF file using unzip -o Report_2_draft.odt
Archive: Report_2_draft.odt
extracting: mimetype
creating: Configurations2/statusbar/
inflating: Configurations2/accelerator/current.xml
creating: Configurations2/floater/
creating: Configurations2/popupmenu/
creating: Configurations2/progressbar/
creating: Configurations2/menubar/
creating: Configurations2/toolbar/
creating: Configurations2/images/Bitmaps/
inflating: layout-cache
inflating: content.xml
inflating: styles.xml
extracting: meta.xml
inflating: Thumbnails/thumbnail.png
inflating: settings.xml
inflating: META-INF/manifest.xml
Removing Report_2_draft.odt
Creating a Pictures directory
Pre-processing the contents
Sweaving content.Rnw
Writing to file content_1.xml
Processing code chunks ...
1 : term hide(label=loadData)
d2 : term verbatim(label=SiteHist)
ate()
3 : term verbatim(label=AgeSex)
4 : term verbatim(label=Sitesex)
5 : term verbatim(label=SiteHeadNeck)
6 : term verbatim(label=SiteFace)
7 : term verbatim(label=SiteChest)
8 : term verbatim(label=SiteAbdomnen)
9 : term verbatim(label=SiteGCS_Eyes)
10 : term verbatim(label=SiteGCS_Verbal)
11 : term verbatim(label=SiteGCS_Motor)
12 : term verbatim(label=SiteGCS_total)
13 : term verbatim(label=SBP)
14 : term verbatim(label=DBP)
15 : term verbatim(label=HR)
16 : term verbatim(label=RESPIRATION)
17 : term verbatim(label=PF_ADMIT)
18 : term verbatim(label=O2_admit)
19 : term verbatim(label=Ph_admit)
20 : term verbatim(label=DEFICIT)
21 : term verbatim(label=lactic_acid)
'content_1.xml' has been Sweaved
Removing content.xml
Post-processing the contents
Error in .Call("RS_XML_Parse", file, handlers, endElementHandlers,
as.logical(addContext), :
attempt to apply non-function
In addition: There were 50 or more warnings (use warnings() to see the
first 50)
> date()
[1] "Thu Oct 23 12:18:18 2008"
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
