The changes, as already discussed in the population-level estimation workgroup, are the following:
Adding inverse probability weighting: see inversePtWeighting argument in the fitOutcomeModel function. This is also described in the single studies vignette.
Adding interaction terms: see interactionCovariateIds argument in the fitOutcomeModel function. This is also described in the single studies vignette.
Adding summary statistics to plots: see show... arguments in the plotPs and plotCovariateBalanceScatterPlot functions.
Enforcing consistency in language: for example, createDrugComparatorOutcome has become createTargetComparatorOutcome. There are many small changes, and unfortunately it probably means your old code wonât work anymore.
Relative instead of absolute paths: the result of runCmAnalyses used to have absolute paths to the various files. Now these are relative to whatever was the outputFolder. Note that the summarizeAnalyses function now requires the outputFolder as argument.
Compression of intermediate results: see compress argument in the saveCohortMethodData function and the compressCohortMethodData argument in the runCmAnalyses function.
In addition, there are many improvements in speed that will likely only matter if you run millions of analyses (which few people seem to do).
If you still require the old version of CohortMethod, please run:
Just a heads up that a late minute change introduced an annoying bug in v3.0.0 (stratified population files were not being generated.). Please use v3.0.1 instead.
I feel like Iâm the only one having trouble of installing v3.0.1.Iâve tried many different ways, but none of those worked out. Am I supposed to get rid of the old version first? Iâm trying to installing it in the server thatâs not connected to internet. Could it be the reason of the error?
the error message says:
cannot open compressed file âCohortMethod/DESCRIPTIONâ, probable reason âNo such file or directoryâ
Error in install.packages : cannot open the connection.
by the way, I used the code
install.packages() with the option repos=NULL, type=âbinaryâ
Any help or comment would be appreciated. Thank you.
Thank you very much for your reply.
I tried those codes and it had another issue.
tools::install_github(âohdsi/CohortMethodâ)
Error in curl::curl_fetch_memory(url, handle = h) :
Failed to connect to api.github.com port 80: Timed out
Thank you for your reply! Actually Iâve tried that, but had another issue. â
Below is the code I used to install CohortMethod. filename<-"CohortMethod-master.zip" install.packages(filename,type="binary",repos=NULL)
and I could see âCohortMethod-masterâ folder(not .zip) newly created,
but when I tried to load package by running library(CohortMethod), (Iâve also tried âCohortMethod-masterâ)
it didnât really work. there is no package called âCohortMethod'
I think Iâm missing something, but have no idea how I could fix this.
Could you try to clone the git repo to local repo of yours (using âgit cloneâ in command) and then launch the .Rproj object in that repo? Then, click the âbuild and reinstallâ button in the RStudio. I think this would be the easiest way.
Hello,
I have a question. (with CohortMethod 2.6.4)
I am running R code for population-level estimation, which Atlas gives automatically.
Everytime I do propensity score matching, the data slightly changes. but what if I want to have the exactly same matching? Is there any argument that makes it possible? I walked through the CohortMethod.pdf but couldnât find any solutions.
(Is it saving the data of matched target to comparator persons would be the only way to see the ouput of that anlaysis? Is there any way I could replicate the match?)
and I have one more question.
I am looking at the readRDS, but I donât see the data of the data of matched target to comparator persons(the output of the matchOnPs()). Is it not saved automatically as .rds, or am I doing something wrong?
Hi @JUNGEUN_PARK. The next step (the one that fails) is a call to FeatureExtraction. Most likely the DiabetesTxPath study requires a different version of the FeatureExtraction package than youâre running. I donât see a mention of which version you should use. @rohitv: do you know?