I am trying to use interaction terms with psem in the piecewiseSEM package but I get the following error:
Error in names(B) <- numVars :
'names' attribute [3] must be the same length as the vector [2]
lme(response1 ~ predictor1 * predictor2, data),
lme(response2 ~ predictor1 * predictor2, data),
...)```
lme is in the nlme package
predictor1 is an integer of 7 levels
predictor2 is a factor of 2 levels
The model alone runs fine outside of psem, though. I could not find a reference as to why interaction terms will not work in the function psem.
I appreciate any insights on this. Thanks!
Update:
this SEM only worked if predictor2 is an integer
Related
I am trying to improve my loop computation speed by using foreach, but there is a simple Rcpp function I defined inside of this loop. I saved the Rcpp function as mproduct.cpp, and I call out the function simply using
sourceCpp("mproduct.cpp")
and the Rcpp function is a simple one, which is to perform matrix product in C++:
// [[Rcpp::depends(RcppArmadillo, RcppEigen)]]
#include <RcppArmadillo.h>
#include <RcppEigen.h>
// [[Rcpp::export]]
SEXP MP(const Eigen::Map<Eigen::MatrixXd> A, Eigen::Map<Eigen::MatrixXd> B){
Eigen::MatrixXd C = A * B;
return Rcpp::wrap(C);
}
So, the function in the Rcpp file is MP, referring to matrix product. I need to perform the following foreach loop (I have simplified the code for illustration):
foreach(j=1:n, .package='Rcpp',.noexport= c("mproduct.cpp"),.combine=rbind)%dopar%{
n=1000000
A<-matrix(rnorm(n,1000,1000))
B<-matrix(rnorm(n,1000,1000))
S<-MP(A,B)
return(S)
}
Since the size of matrix A and B are large, it is why I want to use foreach to alleviate the computational cost.
However, the above code does not work, since it provides me error message:
task 1 failed - "NULL value passed as symbol address"
The reason I added .noexport= c("mproduct.cpp") is to follow some suggestions from people who solved similar issues (Can't run Rcpp function in foreach - "NULL value passed as symbol address"). But somehow this does not solve my issue.
So I tried to install my Rcpp function as a library. I used the following code:
Rcpp.package.skeleton('mp',cpp_files = "<my working directory>")
but it returns me a warning message:
The following packages are referenced using Rcpp::depends attributes however are not listed in the Depends, Imports or LinkingTo fields of the package DESCRIPTION file: RcppArmadillo, RcppEigen
so when I tried to install my package using
install.packages("<my working directory>",repos = NULL,type='source')
I got the warning message:
Error in untar2(tarfile, files, list, exdir, restore_times) :
incomplete block on file
In R CMD INSTALL
Warning in install.packages :
installation of package ‘C:/Users/Lenovo/Documents/mproduct.cpp’ had non-zero exit status
So can someone help me out how to solve 1) using foreach with Rcpp function MP, or 2) install the Rcpp file as a package?
Thank you all very much.
The first step would be making sure that you are optimizing the right thing. For me, this would not be the case as this simple benchmark shows:
set.seed(42)
n <- 1000
A<-matrix(rnorm(n*n), n, n)
B<-matrix(rnorm(n*n), n, n)
MP <- Rcpp::cppFunction("SEXP MP(const Eigen::Map<Eigen::MatrixXd> A, Eigen::Map<Eigen::MatrixXd> B){
Eigen::MatrixXd C = A * B;
return Rcpp::wrap(C);
}", depends = "RcppEigen")
bench::mark(MP(A, B), A %*% B)[1:5]
#> # A tibble: 2 x 5
#> expression min median `itr/sec` mem_alloc
#> <bch:expr> <bch:tm> <bch:tm> <dbl> <bch:byt>
#> 1 MP(A, B) 277.8ms 278ms 3.60 7.63MB
#> 2 A %*% B 37.4ms 39ms 22.8 7.63MB
So for me the matrix product via %*% is several times faster than the one via RcppEigen. However, I am using Linux with OpenBLAS for matrix operations while you are on Windows, which often means reference BLAS for matrix operations. It might be that RcppEigen is faster on your system. I am not sure how difficult it is for Windows user to get a faster BLAS implementation (https://csgillespie.github.io/efficientR/set-up.html#blas-and-alternative-r-interpreters might contain some pointers), but I would suggest spending some time on investigating this.
Now if you come to the conclusion that you do need RcppEigen or RcppArmadillo in your code and want to put that code into a package, you can do the following. Instead of Rcpp::Rcpp.package.skeleton() use RcppEigen::RcppEigen.package.skeleton() or RcppArmadillo::RcppArmadillo.package.skeleton() to create a starting point for a package based on RcppEigen or RcppArmadillo, respectively.
I was trying to implement a Deedle solution for the little challenge from #migueldeicaza to achieve in F# what was done in http://t.co/4YFXk8PQaU with python and R. The csv source data is available from the link.
The start is simple but now, while trying to order based upon a column series of float values I'm struggling to understand the syntax for the IndexRows type annotation.
#I "../packages/FSharp.Charting.0.90.5"
#I "../packages/Deedle.0.9.12"
#load "FSharp.Charting.fsx"
#load "Deedle.fsx"
open System
open Deedle
open FSharp.Charting
let bodyCountData = Frame.ReadCsv(__SOURCE_DIRECTORY__ + "/film_death_counts.csv")
bodyCountData?DeathsPerMinute <- bodyCountData?Body_Count / bodyCountData?Length_Minutes
// select top 3 rows based upon default ordinal indexer
bodyCountData.Rows.[0..3]
// create a new frame indexed and ordered by descending number of screen deaths per minute
let bodyCountDataOrdered =
bodyCountData
|> Frame.indexRows <float>"DeathsPerMinute" // uh oh error here - I'm confused
And because I can't figure that syntax out... various messages like:
Error 1 The type '('a -> Frame<'c,Frame<int,string>>)' does not support the 'comparison' constraint. For example, it does not support the 'System.IComparable' interface. See also c:\wd\RPythonFSharpDFChallenge\RPythonFSharpDFChallenge\EvilMovieQuery.fsx(18,4)-(19,22). c:\wd\RPythonFSharpDFChallenge\RPythonFSharpDFChallenge\EvilMovieQuery.fsx 19 8 RPythonFSharpDFChallenge
Error 2 Type mismatch. Expecting a
'a -> Frame<'c,Frame<int,string>>
but given a
'a -> float
The type 'Frame<'a,Frame<int,string>>' does not match the type 'float' c:\wd\RPythonFSharpDFChallenge\RPythonFSharpDFChallenge\EvilMovieQuery.fsx 19 25 RPythonFSharpDFChallenge
Error 3 This expression was expected to have type
bool
but here has type
string c:\wd\RPythonFSharpDFChallenge\RPythonFSharpDFChallenge\EvilMovieQuery.fsx 19 31 RPythonFSharpDFChallenge
Edit: Just thinking about this... indexing on a measured float is a silly thing to do anyway - duplicates and missing values in real world data. So, I wonder what a more sensible approach to this would be. I still need to find the 25 max values... Maybe I can work this out for myself...
With Deedle 1.0, you can sort on an arbitrary column.
See: http://bluemountaincapital.github.io/Deedle/reference/deedle-framemodule.html#section7
I'm actually using Z3py for scheduling solving problems and I'm trying to represent a 2 processors system where 4 process of different execution time must be done.
My actual data are :
Process 1 : Arrival at 0 and execution time of 4
Process 2 : Arrival at 1 and execution time of 3
Process 3 : Arrival at 3 and execution time of 5
Process 4 : Arrival at 1 and execution time of 2
I'm actually trying to represent each process while decomposing each in subprocess of equal time so my datatypes are like this :
Pn = Datatype('Pn')
Pn.declare('1')
Pn.declare('2')
Pn.declare('3')
Pn.declare('4')
Pt = Datatype('Pt')
Pt.declare('1')
Pt.declare('2')
Pt.declare('3')
Pt.declare('4')
Pt.declare('5')
Process = Datatype('Process')
Process.declare('cons' , ('name',Pn) , ('time', Pt))
Process.declare('idle')
where pn and pt are the process name and the part of the process (process 1 is in 4 parts, ...)
But now I don't know how I can represent my processors to add 3 rules I need : unicity (each sub process must be done 1 and only 1 time by only 1 processor) check arrival (the first part of a process can't be processed before it arrived) and order (each part of a process must be processed after the precedent)
So I was thinking of using arrays to represent my 2 processors with this kind of declaration :
P = Array('P', IntSort() , Process)
But when I tried to execute it I got an error message saying :
Traceback (most recent call last):
File "C:\Users\Alexis\Desktop\test.py", line 16, in <module>
P = Array('P', IntSort() , Process)
File "src/api/python\z3.py", line 3887, in Array
File "src/api/python\z3.py", line 3873, in ArraySort
File "src/api/python\z3.py", line 56, in _z3_assert
Z3Exception: 'Z3 sort expected'
And know I don't know how handle it... must I create a new datatype and figure a way to add my rules ? or Is there a way to add datatypes to array which would let me create rules like this :
unicity = ForAll([x,y] , (Implies(x!=y,P[x]!=P[y])))
Thanks in advance
There is a tutorial on using Datatypes from the Python API. A link to the tutorial is:
http://rise4fun.com/Z3Py/tutorialcontent/advanced#h22
It shows how to create a list data-type and use the "create()" method to instantiate a Sort object from the object used when declaring the data-type. For your example, it suffices to add calls to "create()" in the places where you want to use the declared type as a sort.
See: http://rise4fun.com/Z3Py/rQ7t
Regarding the rest of the case study you are looking at: it is certainly possible to express the constrsaints you describe using quantifiers and arrays. You could also consider somewhat more efficient encodings:
Instead of using an array, use a function declaration. So P would be declared as a unary function:
P = Function('P', IntSort(), Process.create()).
Using quantifiers for small finite domain problems may be more of an overhead than a benefit. Writing down the constraints directly as a finite conjunction saves the overhead of instantiating quantifiers possibly repeatedly. That said, some quantified axioms can also be optimized. Z3 automatically compiles axioms of the form: ForAll([x,y], Implies(x != y, P(x) != P(y))) into
an axioms of the form Forall([x], Pinv(P(x)) == x), where "Pinv" is a fresh function. The new axiom still enforces that P is injective but requires only a linear number of instantiations, linear in the number of occurrences of P(t) for some term 't'.
Have fun!
my question now is :
I have the variavle M which contains : 37.5 (as you see is integer)
I want to convert M in order to be string "37.5"
so 37.5 should became "37.5"
I try with function :
M2=integer_to_list(M)
but when I execute this function it displays this error :
** exception error: bad argument
in function integer_to_list/1
called as integer_to_list(37.5)
integer_to_list wont work in that situation because 37.5 is a float and not an integer. Erlang does have float_to_list, but the output is usually pretty unusable.
Instead, I would recommend looking into mochiweb project for pretty conversion of floats to lists. In particular, the mochinum module:
> M = 37.5,
> mochinum:digits(M).
"37.5"
#chops has a great answer, IMO (using mochinum:digits/1), but you might also get something out of looking at the io_lib module. For example:
8> io_lib:format("~.2f",[37.5]).
["37.50"]
9> io_lib:format("~.1f",[37.5]).
["37.5"]
I realize this might not be exactly what you are looking for, and in this case I think looking at/using the mochinum module is an efficient way to go, but io_lib is often overlooked and provides a really useful set of functions for formatting lists / strings
I have to partition a multiset into two sets who sums are equal. For example, given the multiset:
1 3 5 1 3 -1 2 0
I would output the two sets:
1) 1 3 3
2) 5 -1 2 1 0
both of which sum to 7.
I need to do this using Z3 (smt2 input format) and "Linear Arithmetic Logic", which is defined as:
formula : formula /\ formula | (formula) | atom
atom : sum op sum
op : = | <= | <
sum : term | sum + term
term : identifier | constant | constant identifier
I honestly don't know where to begin with this and any advice at all would be appreciated.
Regards.
Here is an idea:
1- Create a 0-1 integer variable c_i for each element. The idea is c_i is zero if element is in the first set, and 1 if it is in the second set. You can accomplish that by saying that 0 <= c_i and c_i <= 1.
2- The sum of the elements in the first set can be written as 1*(1 - c_1) + 3*(1 - c_2) + ... +
3- The sum of the elements in the second set can be written as 1*c1 + 3*c2 + ...
While SMT-Lib2 is quite expressive, it's not the easiest language to program in. Unless you have a hard requirement that you have to code directly in SMTLib2, I'd recommend looking into other languages that have higher-level bindings to SMT solvers. For instance, both Haskell and Scala have libraries that allow you to script SMT solvers at a much higher level. Here's how to solve your problem using the Haskell, for instance: https://gist.github.com/1701881.
The idea is that these libraries allow you to code at a much higher level, and then perform the necessary translation and querying of the SMT solver for you behind the scenes. (If you really need to get your hands onto the SMTLib encoding of your problem, you can use these libraries as well, as they typically come with the necessary API to dump the SMTLib they generate before querying the solver.)
While these libraries may not offer everything that Z3 gives you access to via SMTLib, they are much easier to use for most practical problems of interest.