benoslab / causalmgm Goto Github PK

Hi,

I'm using the mgm_init() in R 3.6 on mac, and got the following error message, would you please help to understand why and how to fix it? Thank you!

trying URL 'https://cdn.rawgit.com/benoslab/tetradLite/7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar'
Error in download.file(url = file_url, mode = "wb", destfile = jarPath) :
cannot open URL 'https://cdn.rawgit.com/benoslab/tetradLite/7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar'
In addition: Warning message:
In download.file(url = file_url, mode = "wb", destfile = jarPath) :
URL 'https://cdn.rawgit.com/benoslab/tetradLite/7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar': status was 'Peer certificate cannot be authenticated with given CA certificates'

When I run mgm_init on Ubuntu 18 (GCP VM)

library(causalMGM)
mgm_init()

I get the following error message.

https://cdn.rawgit.com/benoslab/tetradLite/7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar
Resolving cdn.rawgit.com (cdn.rawgit.com)... IPaddress
Connecting to cdn.rawgit.com (cdn.rawgit.com)| IPaddress|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://cdn.jsdelivr.net/gh/benoslab/tetradLite@7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar [following]
--2022-08-09 12:28:21--  https://cdn.jsdelivr.net/gh/benoslab/tetradLite@7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar
Resolving cdn.jsdelivr.net (cdn.jsdelivr.net)...  IPaddress,  IPaddress,  IPaddress, ...
Connecting to cdn.jsdelivr.net (cdn.jsdelivr.net)| IPaddress|:443... connected.
HTTP request sent, awaiting response... 403 Forbidden
2022-08-09 12:28:21 ERROR 403: Forbidden.

Its also forbidden to access the page directly:

https://cdn.jsdelivr.net/gh/benoslab/tetradLite@7c16abbd/out/artifacts/tetradLite_jar/tetradLite.jar

When installing the package on Windows, mgm_init() returns the following error:

> Sys.setenv(JAVA_HOME="c:/Program Files/AdoptOpenJDK/jdk-11.0.3.7-hotspot/")
> library(causalMGM)
> setwd("c:/Temp")
> mgm_init()
[1] "Error: tetrad.jar not loaded"

Notwithstanding this error, the package works but it is confusing. The reason is that
.jclassPath() on windows uses escaped slashes "\" as a path separator rather .Platform$file.sep and this causes the comparison to fail. See:

> .jclassPath()
[1] "C:\\Users\\davidn\\R_library\\rJava\\java"
[2] "c:\\Temp\\tetradLite.jar"           

The attached patch should address the issue.

mgm_init_windows.txt

Hi there,

I have a mixed dataset that consists of numerical (continuous and discrete values) variables and categorical variables (with max 3 different categories per variable). Some values, in both types of variables, are missing. Thus, they are represented by an *. According to the User Guide, missing values are not accepted, but it does not make sense to replace my missing values with any other value. As a result, missing values have to be retained. In that case, is Causal-MGM an appropriate tool? What should I do?

I have another dataset that consists of only numerical (continuous values) variables. According to the User Guide, Causal-MGM needs a mixed dataset (numerical and categorical variables). In that case, is Causal-MGM an appropriate tool? What should I do, in order to use the tool?

Thank you in advance!