Flow function in qgraph error edgeConnectPoints #51
Comments
|
Hi! Could you provide a reproducible example of the error? |
|
Thank you for your answer Mr Epskamp,
I used data from our cohort , subjets who answered sf36 questionnaire, and try to replicate what you have done in the article Kossakowski and all (2016) “The application of a network approach to Health-Related Quality of Life (HRQoL): introducing a new method for assessing HRQoL in healthy adults and cancer patients”. I use the R progam associated to the article. I have to modify the program because when running the cor_auto function alone I get an error for the qgraph.
corMat_test <- cor_auto(Datan)
… other lines for lables and groups
gcorMat_n <- qgraph(corMat_test, graph = "glasso", sampleSize = nrow(Datan), esize = 20, cut = 0.1,
minimum = 0, maximum = 1, groups = groups1,
color = c("red", "yellow", "orange", "cornflowerblue", "green", "purple", "grey", "maroon1", "chocolate3"),
borders = FALSE, vsize= 10, labels = labels1, legend = FALSE)
I get this error
Error in EBICglassoCore(S = S, n = n, gamma = gamma, penalize.diagonal = penalize.diagonal, :
'S' is not positive definite
I don’t get this error if I take out the yes/no questions (questions 4a-d and 5a-c), but to replicate the analysis using all sf36 questions, I found the function forcePD
So I change for
corMat_test <- cor_auto(Datan,forcePD =TRUE)
get this warning
In cor_auto(Datan, forcePD = TRUE) :
Correlation matrix is not positive definite. Finding nearest positive definite matrix
Then run
gcorMat_test <- qgraph(corMat_test, graph = "glasso", sampleSize = nrow(Datan), esize = 20, cut = 0.1,
minimum = 0, maximum = 1, groups = groups1,
color = c("red", "yellow", "orange", "cornflowerblue", "green", "purple", "grey", "maroon1", "chocolate3"),
borders = FALSE, vsize= 10, labels = labels1, legend = FALSE)
get this warning
Warning message:
In EBICglassoCore(S = S, n = n, gamma = gamma, penalize.diagonal = penalize.diagonal, :
A dense regularized network was selected (lambda < 0.1 * lambda.max). Recent work indicates a possible drop in specificity. Interpret the presence of the smallest edges with care. Setting threshold = TRUE will enforce higher specificity, at the cost of sensitivity.
Then run the flow
flow(gcorMat_test, "02", vsize = 4)
and get this error
Error in qgraph(object, layout = Layout, curve = Curve, edgeConnectPoints = ECP, :
Number of rows in 'edgeConnectPoints' do not match number of edges
Should I send you dataset corMat_test?
Thanks a lot for your help
Lyne
…________________________________
De : Sacha Epskamp <notifications@github.com>
Envoyé : 17 février 2021 06:16
À : SachaEpskamp/qgraph <qgraph@noreply.github.com>
Cc : Lyne Nadeau, Mlle <lyne.nadeau@mcgill.ca>; Author <author@noreply.github.com>
Objet : Re: [SachaEpskamp/qgraph] Flow function in qgraph error edgeConnectPoints (#51)
Hi! Could you provide a reproducible example of the error?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#51 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AS2P4GZ23BBGTKTCJSV3KYDS7OQRJANCNFSM4XQ36KAQ>.
|
|
I meant perhaps you can try to make a minimal reproducible example. See for some details here. For example, this code runs for me: If you can extend that code to the point where it reproduces your error we can figure out the problem. |
|
I was not sure how to do it with my dataset. I use the one available on line - bfi - data and replicated the example from https://www.rdocumentation.org/packages/qgraph/versions/1.6.9/topics/flow
I get the same error message as with my dataset.
Let me know if this is not a good way of doing it, I will try to make my own dataset as minimal reproducible example.
This is the information on my Rstudio version (from console)
R version 4.0.3 Patched (2020-11-24 r79490) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
with those notes
Registered S3 methods overwritten by 'BDgraph':
method from
plot.sim huge
print.sim huge
------------------------
Program I run
library("qgraph")
library("psych")
bdata<-read.csv("bfi.csv")
bdata2 <- bdata[,2:26] # Select only variables
bcorMat <- cor_auto(bdata2) # Correlate data
# Glasso network:
g2 <- qgraph(bcorMat, cut = 0, graph = "glasso", sampleSize = nrow(bdata2),
threshold = TRUE)
# Flow from A2:
flow(g2, "A2", horizontal = TRUE)
# }
----------------------------
information on the console
library("qgraph")
library("psych")
bdata<-read.csv("bfi.csv")
bdata2 <- bdata[,2:26] # Select only variables
bcorMat <- cor_auto(bdata2) # Correlate data
Variables detected as ordinal: A1; A2; A3; A4; A5; C1; C2; C3; C4; C5; E1; E2; E3; E4; E5; N1; N2; N3; N4; N5; O1; O2; O3; O4; O5
# Glasso network:
g2 <- qgraph(bcorMat, cut = 0, graph = "glasso", sampleSize = nrow(bdata2),
+ threshold = TRUE)
# Flow from A2:
flow(g2, "A2", horizontal = TRUE)
Error in qgraph(object, layout = Layout, curve = Curve, edgeConnectPoints = ECP, :
Number of rows in 'edgeConnectPoints' do not match number of edges
# }
thank you
Lyne
…________________________________
De : Sacha Epskamp <notifications@github.com>
Envoyé : 22 février 2021 05:19
À : SachaEpskamp/qgraph <qgraph@noreply.github.com>
Cc : Lyne Nadeau, Mlle <lyne.nadeau@mcgill.ca>; Author <author@noreply.github.com>
Objet : Re: [SachaEpskamp/qgraph] Flow function in qgraph error edgeConnectPoints (#51)
I meant perhaps you can try to make a minimal reproducible example. See for some details here<https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example>. For example, this code runs for me:
library("qgraph")
corMat_n <- matrix(0.1,6,6)
diag(corMat_n) <- 1
qgraph(corMat_n, graph = "glasso", sampleSize = 1000,
esize = 20, cut = 0.1,
minimum = 0, maximum = 1,
borders = FALSE, vsize= 10, legend = FALSE)
If you can extend that code to the point where it reproduces your error we can figure out the problem.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#51 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AS2P4G7CNGGH2N7SOGZICNDTAIVTDANCNFSM4XQ36KAQ>.
|
|
I'm adding more information
about rstudio
rstudioapi::versionInfo()
$citation
To cite RStudio in publications use:
RStudio Team (2020). RStudio: Integrated Development Environment for R. RStudio, PBC, Boston,
MA URL http://www.rstudio.com/.
A BibTeX entry for LaTeX users is
@Manual{,
title = {RStudio: Integrated Development Environment for R},
author = {{RStudio Team}},
organization = {RStudio, PBC},
address = {Boston, MA},
year = {2020},
url = {http://www.rstudio.com/},
}
$mode
[1] "desktop"
$version
[1] ‘1.3.1093’
$release_name
[1] "Apricot Nasturtium"
Version of qgraph
packageVersion("qgraph")[1] ‘1.6.9’
The 4th first observation of the bfi dataset that I used
dput(bdata2[1:4,])
structure(list(A1 = c(2L, 2L, 5L, 4L), A2 = c(4L, 4L, 4L, 4L),
A3 = c(3L, 5L, 5L, 6L), A4 = c(4L, 2L, 4L, 5L), A5 = c(4L,
5L, 4L, 5L), C1 = c(2L, 5L, 4L, 4L), C2 = c(3L, 4L, 5L, 4L
), C3 = c(3L, 4L, 4L, 3L), C4 = c(4L, 3L, 2L, 5L), C5 = c(4L,
4L, 5L, 5L), E1 = c(3L, 1L, 2L, 5L), E2 = c(3L, 1L, 4L, 3L
), E3 = c(3L, 6L, 4L, 4L), E4 = c(4L, 4L, 4L, 4L), E5 = c(4L,
3L, 5L, 4L), N1 = c(3L, 3L, 4L, 2L), N2 = c(4L, 3L, 5L, 5L
), N3 = c(2L, 3L, 4L, 2L), N4 = c(2L, 5L, 2L, 4L), N5 = c(3L,
5L, 3L, 1L), O1 = c(3L, 4L, 4L, 3L), O2 = c(6L, 2L, 2L, 3L
), O3 = c(3L, 4L, 5L, 4L), O4 = c(4L, 3L, 5L, 3L), O5 = c(3L,
3L, 2L, 5L)), row.names = c(NA, 4L), class = "data.frame")
and the Compute polychoric correlations:
dput(btcorMat)
structure(c(1, -0.40845072522919, -0.322534994540207, -0.17542796138817,
-0.227855906050576, 0.00338022290150531, 0.00823880135729777,
-0.0237128310819885, 0.153609897117526, 0.0605073445905763, 0.11767782718733,
0.111200375720246, -0.0668774340982724, -0.0770524730485401,
-0.0250110827451967, 0.184071495565574, 0.157599819692691, 0.113338093728924,
0.0600922819398693, 0.0111411434049144, -0.00219488973357894,
0.083692047355312, -0.0906601520904744, -0.100352540936164, 0.136195610802798,
-0.40845072522919, 1, 0.555458433280261, 0.389699147545801, 0.448824736349496,
0.115382706160093, 0.159706117954993, 0.22711675884859, -0.193306871055427,
-0.156377359988479, -0.239529718194745, -0.272060735509787, 0.294978016229907,
0.317504381982443, 0.322790487934583, -0.11486872579201, -0.0671192334374541,
-0.0471702253803139, -0.115519634667437, 0.0214067106371493,
0.16408541462196, -0.00180427164421131, 0.190845330418667, 0.112458354316386,
-0.114857214482796, -0.322534994540207, 0.555458433280261, 1,
0.408057129570504, 0.572841645684758, 0.124207732100454, 0.158770048552652,
0.161416932547041, -0.164154431450698, -0.187689330001194, -0.250216018040367,
-0.333326092646584, 0.452752024998062, 0.420595998812892, 0.293967656352481,
-0.110530507000048, -0.0958025687224147, -0.0603045180873399,
-0.147088009827957, -0.0452410037197774, 0.18624086622624, -0.0271008137322305,
0.26494986247808, 0.0607321562285621, -0.0770999453679185, -0.17542796138817,
0.389699147545801, 0.408057129570504, 1, 0.355267948545011, 0.109176678920492,
0.270532273610431, 0.168347639312913, -0.196338150517947, -0.283203470518255,
-0.13716252513638, -0.211291698359744, 0.221329218777118, 0.348034229886854,
0.190651559709163, -0.120599235542214, -0.154978830874735, -0.0745425939596536,
-0.191082468778672, -0.00660292698843281, 0.0760936866435515,
0.0346575925820618, 0.0806668189704019, -0.0448093920361592,
0.0242631908961083, -0.227855906050576, 0.448824736349496, 0.572841645684758,
0.355267948545011, 1, 0.157211860455217, 0.140696598254073, 0.154719689004687,
-0.165191395738391, -0.199942406645241, -0.275418931444304, -0.383660053640273,
0.478069660797655, 0.525996557240064, 0.302470841001335, -0.225949355413018,
-0.211263879021032, -0.156089938397737, -0.220998805924937, -0.0877815064050865,
0.201359904514984, -0.0111162392340621, 0.271712977242795, 0.0238985806744179,
-0.0659686354034993, 0.00338022290150531, 0.115382706160093,
0.124207732100454, 0.109176678920492, 0.157211860455217, 1, 0.483160927402407,
0.34456226530737, -0.402339113671263, -0.292630121851316, -0.0285972172000304,
-0.107860347201659, 0.142365375183762, 0.154628821270497, 0.279858226306097,
-0.0832969138392508, -0.0469044417559331, -0.0382695114130622,
-0.108102603475262, -0.0683571462272784, 0.210569960837643, -0.144615929627244,
0.221971284747031, 0.135686975847761, -0.163197323146781, 0.00823880135729777,
0.159706117954993, 0.158770048552652, 0.270532273610431, 0.140696598254073,
0.483160927402407, 1, 0.397221246166351, -0.432183922232435,
-0.330938053154251, 0.0119741037365558, -0.0712302715943209,
0.183744832398228, 0.140657156179685, 0.292842957386705, -0.0193654400527341,
0.000590838071767851, 0.00566391481101162, -0.0391143260057959,
0.0527107787170832, 0.200962510836073, -0.0605274709906444, 0.222135991038895,
0.0735101720105925, -0.0921981096961722, -0.0237128310819885,
0.22711675884859, 0.161416932547041, 0.168347639312913, 0.154719689004687,
0.34456226530737, 0.397221246166351, 1, -0.381005823879698, -0.381436705731882,
0.00305539480973744, -0.0856654880557203, 0.103854643049832,
0.107854040583036, 0.246888609176707, -0.0749751637260222, -0.0638829038208722,
-0.0752908621495415, -0.116987437914303, -0.0177219278664302,
0.110338843990225, -0.0384221836101039, 0.0730129442770303, 0.0319204817135418,
-0.019539241600808, 0.153609897117526, -0.193306871055427, -0.164154431450698,
-0.196338150517947, -0.165191395738391, -0.402339113671263, -0.432183922232435,
-0.381005823879698, 1, 0.529978444609527, 0.10405173069964, 0.233822505292174,
-0.104851026181364, -0.13335533998431, -0.280135976323902, 0.245662859811112,
0.183714441397665, 0.23981646514717, 0.293293561029336, 0.226530891052251,
-0.112554195015304, 0.245451100257727, -0.104672555186331, 0.0595153507740293,
0.230574396375704, 0.0605073445905763, -0.156377359988479, -0.187689330001194,
-0.283203470518255, -0.199942406645241, -0.292630121851316, -0.330938053154251,
-0.381436705731882, 0.529978444609527, 1, 0.067641346273511,
0.292018438271398, -0.179069037663231, -0.223875003511747, -0.269440509846196,
0.232112062142674, 0.274947540551155, 0.269678324813815, 0.375258658823781,
0.203651718648595, -0.0989963516851542, 0.169077230473407, -0.0982043516949346,
0.1642848661326, 0.0672082576310994, 0.11767782718733, -0.239529718194745,
-0.250216018040367, -0.13716252513638, -0.275418931444304, -0.0285972172000304,
0.0119741037365558, 0.00305539480973744, 0.10405173069964, 0.067641346273511,
1, 0.515381315679346, -0.350352525773296, -0.481359099349233,
-0.333572381642719, 0.0218784236077433, 0.0129728412697728, 0.052083416035722,
0.249966764948959, 0.0537029642790918, -0.118369302888363, 0.0526701665049232,
-0.241064055857597, 0.089463449755998, 0.098650598311229, 0.111200375720246,
-0.272060735509787, -0.333326092646584, -0.211291698359744, -0.383660053640273,
-0.107860347201659, -0.0712302715943209, -0.0856654880557203,
0.233822505292174, 0.292018438271398, 0.515381315679346, 1, -0.421881255671979,
-0.57463815512736, -0.420829955348233, 0.183650392761085, 0.205665630017704,
0.214339195750653, 0.379065849381506, 0.280809372501722, -0.187173911773421,
0.0988177272353197, -0.257126223757293, 0.207665904495383, 0.0880322333218724,
-0.0668774340982724, 0.294978016229907, 0.452752024998062, 0.221329218777118,
0.478069660797655, 0.142365375183762, 0.183744832398228, 0.103854643049832,
-0.104851026181364, -0.179069037663231, -0.350352525773296, -0.421881255671979,
1, 0.461276200359194, 0.432050918643011, -0.0585814741969427,
-0.0684634378868069, -0.0208668996880158, -0.158543459408106,
-0.0921454780873075, 0.379052473257295, -0.0933632147288152,
0.437349449642628, 0.0753847166425374, -0.14552888239251, -0.0770524730485401,
0.317504381982443, 0.420595998812892, 0.348034229886854, 0.525996557240064,
0.154628821270497, 0.140657156179685, 0.107854040583036, -0.13335533998431,
-0.223875003511747, -0.481359099349233, -0.57463815512736, 0.461276200359194,
1, 0.347710170518931, -0.152514236354274, -0.153680911892982,
-0.117717014995973, -0.320638790074835, -0.113144285050686, 0.164907733034766,
0.0539450152903843, 0.233987220966304, -0.115926407530645, 0.05688165432528,
-0.0250110827451967, 0.322790487934583, 0.293967656352481, 0.190651559709163,
0.302470841001335, 0.279858226306097, 0.292842957386705, 0.246888609176707,
-0.280135976323902, -0.269440509846196, -0.333572381642719, -0.420829955348233,
0.432050918643011, 0.347710170518931, 1, 0.0471440901624641,
0.0482691834114875, -0.064328087917546, -0.22733628080631, -0.153845444866445,
0.347865909832072, -0.111390659663326, 0.332201519831562, 0.0016826142135295,
-0.149222864183199, 0.184071495565574, -0.11486872579201, -0.110530507000048,
-0.120599235542214, -0.225949355413018, -0.0832969138392508,
-0.0193654400527341, -0.0749751637260222, 0.245662859811112,
0.232112062142674, 0.0218784236077433, 0.183650392761085, -0.0585814741969427,
-0.152514236354274, 0.0471440901624641, 1, 0.764239678401427,
0.607521418319414, 0.436947241879599, 0.419607352895156, -0.0641105219890962,
0.14179538541356, -0.0598205713331517, 0.0947598379644517, 0.119132297501362,
0.157599819692691, -0.0671192334374541, -0.0958025687224147,
-0.154978830874735, -0.211263879021032, -0.0469044417559331,
0.000590838071767851, -0.0638829038208722, 0.183714441397665,
0.274947540551155, 0.0129728412697728, 0.205665630017704, -0.0684634378868069,
-0.153680911892982, 0.0482691834114875, 0.764239678401427, 1,
0.597040600057271, 0.429125507329192, 0.384852492275484, -0.0497347196645301,
0.142594249822546, -0.0325178310794009, 0.155396976052107, 0.0371820189769119,
0.113338093728924, -0.0471702253803139, -0.0603045180873399,
-0.0745425939596536, -0.156089938397737, -0.0382695114130622,
0.00566391481101162, -0.0752908621495415, 0.23981646514717, 0.269678324813815,
0.052083416035722, 0.214339195750653, -0.0208668996880158, -0.117717014995973,
-0.064328087917546, 0.607521418319414, 0.597040600057271, 1,
0.564343522038429, 0.470359484018177, -0.0432686311411292, 0.116193719735181,
-0.0302359472886761, 0.205388672250946, 0.058764594419129, 0.0600922819398693,
-0.115519634667437, -0.147088009827957, -0.191082468778672, -0.220998805924937,
-0.108102603475262, -0.0391143260057959, -0.116987437914303,
0.293293561029336, 0.375258658823781, 0.249966764948959, 0.379065849381506,
-0.158543459408106, -0.320638790074835, -0.22733628080631, 0.436947241879599,
0.429125507329192, 0.564343522038429, 1, 0.440264983841415, -0.0487660921641979,
0.0917193169852136, -0.0679346108592007, 0.259582600182191, 0.0415705078826088,
0.0111411434049144, 0.0214067106371493, -0.0452410037197774,
-0.00660292698843281, -0.0877815064050865, -0.0683571462272784,
0.0527107787170832, -0.0177219278664302, 0.226530891052251, 0.203651718648595,
0.0537029642790918, 0.280809372501722, -0.0921454780873075, -0.113144285050686,
-0.153845444866445, 0.419607352895156, 0.384852492275484, 0.470359484018177,
0.440264983841415, 1, -0.141952896999538, 0.227930486874359,
-0.0982829265746635, 0.140549331793399, 0.155971125676953, -0.00219488973357894,
0.16408541462196, 0.18624086622624, 0.0760936866435515, 0.201359904514984,
0.210569960837643, 0.200962510836073, 0.110338843990225, -0.112554195015304,
-0.0989963516851542, -0.118369302888363, -0.187173911773421,
0.379052473257295, 0.164907733034766, 0.347865909832072, -0.0641105219890962,
-0.0497347196645301, -0.0432686311411292, -0.0487660921641979,
-0.141952896999538, 1, -0.262773054342946, 0.450229538431314,
0.248793031658823, -0.301046830481263, 0.083692047355312, -0.00180427164421131,
-0.0271008137322305, 0.0346575925820618, -0.0111162392340621,
-0.144615929627244, -0.0605274709906444, -0.0384221836101039,
0.245451100257727, 0.169077230473407, 0.0526701665049232, 0.0988177272353197,
-0.0933632147288152, 0.0539450152903843, -0.111390659663326,
0.14179538541356, 0.142594249822546, 0.116193719735181, 0.0917193169852136,
0.227930486874359, -0.262773054342946, 1, -0.317558477268609,
-0.0972905182407821, 0.373605684506686, -0.0906601520904744,
0.190845330418667, 0.26494986247808, 0.0806668189704019, 0.271712977242795,
0.221971284747031, 0.222135991038895, 0.0730129442770303, -0.104672555186331,
-0.0982043516949346, -0.241064055857597, -0.257126223757293,
0.437349449642628, 0.233987220966304, 0.332201519831562, -0.0598205713331517,
-0.0325178310794009, -0.0302359472886761, -0.0679346108592007,
-0.0982829265746635, 0.450229538431314, -0.317558477268609, 1,
0.253009579729775, -0.375930709348172, -0.100352540936164, 0.112458354316386,
0.0607321562285621, -0.0448093920361592, 0.0238985806744179,
0.135686975847761, 0.0735101720105925, 0.0319204817135418, 0.0595153507740293,
0.1642848661326, 0.089463449755998, 0.207665904495383, 0.0753847166425374,
-0.115926407530645, 0.0016826142135295, 0.0947598379644517, 0.155396976052107,
0.205388672250946, 0.259582600182191, 0.140549331793399, 0.248793031658823,
-0.0972905182407821, 0.253009579729775, 1, -0.243858200693562,
0.136195610802798, -0.114857214482796, -0.0770999453679185, 0.0242631908961083,
-0.0659686354034993, -0.163197323146781, -0.0921981096961722,
-0.019539241600808, 0.230574396375704, 0.0672082576310994, 0.098650598311229,
0.0880322333218724, -0.14552888239251, 0.05688165432528, -0.149222864183199,
0.119132297501362, 0.0371820189769119, 0.058764594419129, 0.0415705078826088,
0.155971125676953, -0.301046830481263, 0.373605684506686, -0.375930709348172,
-0.243858200693562, 1), .Dim = c(25L, 25L), .Dimnames = list(
c("A1", "A2", "A3", "A4", "A5", "C1", "C2", "C3", "C4", "C5",
"E1", "E2", "E3", "E4", "E5", "N1", "N2", "N3", "N4", "N5",
"O1", "O2", "O3", "O4", "O5"), c("A1", "A2", "A3", "A4",
"A5", "C1", "C2", "C3", "C4", "C5", "E1", "E2", "E3", "E4",
"E5", "N1", "N2", "N3", "N4", "N5", "O1", "O2", "O3", "O4",
"O5")))
thank you
Lyne
…________________________________
De : Sacha Epskamp <notifications@github.com>
Envoyé : 22 février 2021 05:19
À : SachaEpskamp/qgraph <qgraph@noreply.github.com>
Cc : Lyne Nadeau, Mlle <lyne.nadeau@mcgill.ca>; Author <author@noreply.github.com>
Objet : Re: [SachaEpskamp/qgraph] Flow function in qgraph error edgeConnectPoints (#51)
I meant perhaps you can try to make a minimal reproducible example. See for some details here<https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example>. For example, this code runs for me:
library("qgraph")
corMat_n <- matrix(0.1,6,6)
diag(corMat_n) <- 1
qgraph(corMat_n, graph = "glasso", sampleSize = 1000,
esize = 20, cut = 0.1,
minimum = 0, maximum = 1,
borders = FALSE, vsize= 10, legend = FALSE)
If you can extend that code to the point where it reproduces your error we can figure out the problem.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#51 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AS2P4G7CNGGH2N7SOGZICNDTAIVTDANCNFSM4XQ36KAQ>.
|
|
Thanks! I can replicate this. Can you try with the new devel version? |
|
Hello,
I'm not sure i'm doing it right or in the right order. Maybe i should uninstall everything.
Below are steps I did but I think I was unable to update qgraph. I still get the same error.
Thanks a lot for your help.
I first ran library("devtools") and got this
library(devtools)
Loading required package: usethis
library("devtools")
bdata<-read.csv("bfi.csv")
bdata2 <- bdata[,2:26] # Select only variables
bcorMat <- cor_auto(bdata2) # Correlate data
Variables detected as ordinal: A1; A2; A3; A4; A5; C1; C2; C3; C4; C5; E1; E2; E3; E4; E5; N1; N2; N3; N4; N5; O1; O2; O3; O4; O5
# Glasso network:
g2 <- qgraph(bcorMat, cut = 0, graph = "glasso", sampleSize = nrow(bdata2),
+ threshold = TRUE)
# Flow from A2:
flow(g2, "A2", horizontal = TRUE)
Error in qgraph(object, layout = Layout, curve = Curve, edgeConnectPoints = ECP, :
Number of rows in 'edgeConnectPoints' do not match number of edges
# }
So I run the installation you suggest
install_github("sachaepskamp/qgraph")
WARNING: Rtools is required to build R packages, but is not currently installed.
Please download and install Rtools 4.0 from https://cran.r-project.org/bin/windows/Rtools/.
Downloading GitHub repo sachaepskamp/qgraph@HEAD
WARNING: Rtools is required to build R packages, but is not currently installed.
Please download and install Rtools 4.0 from https://cran.r-project.org/bin/windows/Rtools/.
trying URL 'https://cran.rstudio.com/bin/windows/Rtools/rtools40-x86_64.exe'
Content type 'application/x-msdownload' length 132205064 bytes (126.1 MB)
downloaded 126.1 MB
Error: Failed to install 'qgraph' from GitHub:
Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.
detach("package:devtools", unload = TRUE)
detach("package:psych", unload = TRUE)
Warning message:
‘psych’ namespace cannot be unloaded:
namespace ‘psych’ is imported by ‘qgraph’, ‘NetworkToolbox’, ‘networktools’ so cannot be unloaded
detach("package:qgraph", unload = TRUE)
Warning message:
‘qgraph’ namespace cannot be unloaded:
namespace ‘qgraph’ is imported by ‘IsingFit’, ‘bootnet’, ‘mgm’ so cannot be unloaded
detach("package:sas7bdat", unload = TRUE)
install.packages("Rtools")
Installing package into ‘C:/Users/Nancy Mayo/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘Rtools’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Then I tried those lines. I'm not sure what I'm doing exactly.
pkgbuild::check_build_tools(debug = TRUE)
Scanning R CMD config CC...
cc_path:
'' does not exist
Scanning path...
Scanning registry...
Found C:/RBuildTools/4.0 for 4.0
Your system is ready to build packages!
install.packages("Rtools")
Installing package into ‘C:/Users/Nancy Mayo/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘Rtools’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
library("devtools")
install_github("sachaepskamp/qgraph")
Downloading GitHub repo sachaepskamp/qgraph@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: pillar (1.4.7 -> 1.5.0 ) [CRAN]
5: lifecycle (0.2.0 -> 1.0.0 ) [CRAN]
6: crayon (1.4.0 -> 1.4.1 ) [CRAN]
7: waldo (0.2.3 -> 0.2.4 ) [CRAN]
8: pkgload (1.1.0 -> 1.2.0 ) [CRAN]
9: testthat (3.0.1 -> 3.0.2 ) [CRAN]
10: mime (0.9 -> 0.10 ) [CRAN]
11: xfun (0.20 -> 0.21 ) [CRAN]
12: backports (1.2.0 -> 1.2.1 ) [CRAN]
13: data.table (1.13.6 -> 1.14.0) [CRAN]
14: dplyr (1.0.3 -> 1.0.4 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:1
pillar (1.4.7 -> 1.5.0 ) [CRAN]
lifecycle (0.2.0 -> 1.0.0 ) [CRAN]
crayon (1.4.0 -> 1.4.1 ) [CRAN]
waldo (0.2.3 -> 0.2.4 ) [CRAN]
pkgload (1.1.0 -> 1.2.0 ) [CRAN]
testthat (3.0.1 -> 3.0.2 ) [CRAN]
mime (0.9 -> 0.10 ) [CRAN]
xfun (0.20 -> 0.21 ) [CRAN]
backports (1.2.0 -> 1.2.1 ) [CRAN]
data.table (1.13.6 -> 1.14.0) [CRAN]
dplyr (1.0.3 -> 1.0.4 ) [CRAN]
Installing 11 packages: pillar, lifecycle, crayon, waldo, pkgload, testthat, mime, xfun, backports, data.table, dplyr
Installing packages into ‘C:/Users/Nancy Mayo/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
There are binary versions available but the source versions are later:
binary source needs_compilation
pillar 1.4.7 1.5.0 FALSE
pkgload 1.1.0 1.2.0 TRUE
data.table 1.13.6 1.14.0 TRUE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/lifecycle_1.0.0.zip'
Content type 'application/zip' length 111193 bytes (108 KB)
downloaded 108 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/crayon_1.4.1.zip'
Content type 'application/zip' length 142313 bytes (138 KB)
downloaded 138 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/waldo_0.2.4.zip'
Content type 'application/zip' length 72194 bytes (70 KB)
downloaded 70 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/testthat_3.0.2.zip'
Content type 'application/zip' length 2496093 bytes (2.4 MB)
downloaded 2.4 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/mime_0.10.zip'
Content type 'application/zip' length 48442 bytes (47 KB)
downloaded 47 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/xfun_0.21.zip'
Content type 'application/zip' length 319389 bytes (311 KB)
downloaded 311 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/backports_1.2.1.zip'
Content type 'application/zip' length 98506 bytes (96 KB)
downloaded 96 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/dplyr_1.0.4.zip'
Content type 'application/zip' length 1329695 bytes (1.3 MB)
downloaded 1.3 MB
package ‘lifecycle’ successfully unpacked and MD5 sums checked
package ‘crayon’ successfully unpacked and MD5 sums checked
package ‘waldo’ successfully unpacked and MD5 sums checked
package ‘testthat’ successfully unpacked and MD5 sums checked
Error: Failed to install 'qgraph' from GitHub:
(converted from warning) cannot remove prior installation of package ‘testthat’
…________________________________
De : Sacha Epskamp <notifications@github.com>
Envoyé : 23 février 2021 09:29
À : SachaEpskamp/qgraph <qgraph@noreply.github.com>
Cc : Lyne Nadeau, Mlle <lyne.nadeau@mcgill.ca>; Author <author@noreply.github.com>
Objet : Re: [SachaEpskamp/qgraph] Flow function in qgraph error edgeConnectPoints (#51)
Thanks! I can replicate this. Can you try with the new devel version?
library("devtools")
install_github("sachaepskamp/qgraph")
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#51 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AS2P4G4SM42BVPHWBAER4JDTAO3WPANCNFSM4XQ36KAQ>.
|
|
You need to install Rtools to compile from source: https://cran.r-project.org/bin/windows/Rtools/. When asked about installing any other package from source, say "no". |
|
Hello,
1: All then I selected 1 to install ALL and got this Enter one or more numbers, or an empty line to skip updates:1 There are binary versions available but the source versions are later: trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/tibble_3.1.0.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/mime_0.10.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/xfun_0.21.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/backports_1.2.1.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/data.table_1.14.0.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/Hmisc_4.5-0.zip' package ‘tibble’ successfully unpacked and MD5 sums checked Should I uninstall qgraph before running this |
|
Sorry I missed this. You can select none when asked which packages should be updated. I think this is fixed now so I will close the issue. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hello I'm new with R and start to learn network analysis using qgraph with a data cohort that have sf36 questionnaire.
I try to do a flow diagram from one of the item and I get this error below. I don't find references about this error.
I did a qgraph call g2
g2 <- qgraph(corMat_n, graph = "glasso", layout = L2, sampleSize = nrow(Datan),
esize = 20, cut = 0.1,
minimum = 0, maximum = 1, groups = groups1,
color = c("red", "yellow", "orange", "cornflowerblue", "green", "purple", "grey", "maroon1", "chocolate3"),
borders = FALSE, vsize= 10, labels = labels1, legend = FALSE)
mtext("(b)", cex = 1.25, side = 1, line = 8.7, las = 1)
then run the flow and get an error
I don't know where to look for that type of error.
Am I giving enough information?
thank you
Lyne
The text was updated successfully, but these errors were encountered: