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JClavel / mvMORPH

mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data
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Error in svd(B, nu = 0) : infinite or missing values in 'x' for mvgls #15

Open MKeao opened 9 months ago

MKeao commented 9 months ago

Hi,

Not sure if this is a bug since the package is new or just an error on my end. I'm trying to use function mvgls to fit a pgls model but get the error "Error in svd(B, nu = 0) : infinite or missing values in 'x'" when I run the following. I'm attempting to make my data match the simulation data in your example but am failing to do so. 

df5 <- Bacteria_dat3 %>% mutate_at(1:21, as.numeric)
df6 <- as.matrix(df5) 
data=list(df6=df6)
fit1 <- mvgls(df6~1, data=data, tree2, model="BM", penalty="RidgeArch")

Bacteria_dat3 is a data frame with microbiome community occurrence data.

Family, Genus, Species, Acinetobacter,Apilactobacillus,Bacillus,Citrobacter,Enterococcus,Erwinia,Fructobacillus,Gilliamella,Lactobacillus,Pantoea,Phaseolibacter,Pleosporaceae,Pseudomonas,Rhodococcus,Rosenbergiella,Saccharibacter,Shigella,Stephania,Streptomyces,Weissella,Wolbachia Apidae, Apis,Apis_mellifera,17,24,0,0,0,0,3,0,18,2,0,0,0,0,25,9,0,0,0,4,0 Apidae, Ceratina,Ceratina_calcarata,2,1,0,39,3,4,0,6,0,10,0,0,0,3,0,0,5,0,0,0,6 Megachilidae, Heriades,Heriades_truncorum,4,0,4,0,0,0,0,0,6,5,2,0,28,0,0,0,0,0,19,0,0 Megachilidae, Megachile,Megachile_ligniseca,0,0,0,0,0,0,2,0,0,1,2,1,2,0,0,0,0,0,2,0,0 Megachilidae, Megachile,Megachile_rotundata,0,0,0,0,0,0,2,0,0,1,2,1,0,0,0,0,0,0,0,0,0 Halictidae, Nomia,Nomia_irridescens,1,16,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_caerulescens,2,0,3,0,0,1,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_leaiana,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,1 Megachilidae, Osmia,Osmia_lignaria,30,0,0,2,0,0,0,0,5,1,0,0,1,0,0,1,0,3,0,0,0

After trying to make my data match the simulation data this is the output for str() and class().

num [1:9, 1:21] 2 17 30 0 2 4 0 0 1 1 ...

[1] "matrix" "array"

Any idea what might be going on here? Thanks for the help!

Makaylee

JClavel commented 9 months ago

Hi Makaylee,

Send me your data or a working example to replicate the issue. I'll look at it ASAP.

Regards,

Julien

De : Makaylee Crone @.> Envoyé : mercredi 24 janvier 2024 19:55 À : JClavel/mvMORPH @.> Cc : Subscribed @.***> Objet : [JClavel/mvMORPH] Error in svd(B, nu = 0) : infinite or missing values in 'x' for mvgls (Issue #15)

Hi,

Not sure if this is a bug since the package is new or just an error on my end. I'm trying to use function mvgls to fit a pgls model but get the error "Error in svd(B, nu = 0) : infinite or missing values in 'x'" when I run the following. I'm attempting to make my data match the simulation data in your example but am failing to do so.

df5 <- Bacteria_dat3 %>% mutate_at(1:21, as.numeric) df6 <- as.matrix(df5) data=list(df6=df6) fit1 <- mvgls(df6~1, data=data, tree2, model="BM", penalty="RidgeArch")

Bacteria_dat3 is a data frame with microbiome community occurrence data.

Family, Genus, Species, Acinetobacter,Apilactobacillus,Bacillus,Citrobacter,Enterococcus,Erwinia,Fructobacillus,Gilliamella,Lactobacillus,Pantoea,Phaseolibacter,Pleosporaceae,Pseudomonas,Rhodococcus,Rosenbergiella,Saccharibacter,Shigella,Stephania,Streptomyces,Weissella,Wolbachia Apidae, Apis,Apis_mellifera,17,24,0,0,0,0,3,0,18,2,0,0,0,0,25,9,0,0,0,4,0 Apidae, Ceratina,Ceratina_calcarata,2,1,0,39,3,4,0,6,0,10,0,0,0,3,0,0,5,0,0,0,6 Megachilidae, Heriades,Heriades_truncorum,4,0,4,0,0,0,0,0,6,5,2,0,28,0,0,0,0,0,19,0,0 Megachilidae, Megachile,Megachile_ligniseca,0,0,0,0,0,0,2,0,0,1,2,1,2,0,0,0,0,0,2,0,0 Megachilidae, Megachile,Megachile_rotundata,0,0,0,0,0,0,2,0,0,1,2,1,0,0,0,0,0,0,0,0,0 Halictidae, Nomia,Nomia_irridescens,1,16,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_caerulescens,2,0,3,0,0,1,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_leaiana,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,1 Megachilidae, Osmia,Osmia_lignaria,30,0,0,2,0,0,0,0,5,1,0,0,1,0,0,1,0,3,0,0,0

After trying to make my data match the simulation data this is the output for str() and class().

num [1:9, 1:21] 2 17 30 0 2 4 0 0 1 1 ...

[1] "matrix" "array"

Any idea what might be going on here? Thanks for the help!

Makaylee

— Reply to this email directly, view it on GitHubhttps://github.com/JClavel/mvMORPH/issues/15, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACSCJSN5FQXZFNO3TP42HYTYQFKIJAVCNFSM6AAAAABCJIJ6FCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4TQOBYHAYTSMA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

MKeao commented 9 months ago

Hi Julien,

Thanks so much for looking into this. My data frame and tree are attached for you. The data file is the original before using any code to prepare it for analysis. The code I used to do this was:

load data

tree <- read.tree("tree.txt") data <- read.csv("data_Julien.csv", header=TRUE)

remove columns and make species the row name

rownames(data) <- data[,3] data <- data[-c(1:3)]

reorder rows to match tree

data <- data[tree$tip.label,]

make data numeric and transform to matrix

df5 <- data %>% mutate_at(1:21, as.numeric) df6 <- as.matrix(df5)

code used for pgls model

data=list(df6=df6) fit1 <- mvgls(df6~1, data=data, tree2, model="BM", penalty="RidgeArch")

I'm new to phylogenetic analyses so I'm not entirely sure that options BM and RidgeArch are best for my data, but I figure that the code should work for any of these options and I can find the best one later.

Thanks again,

Makaylee

On Wed, Jan 24, 2024 at 8:54 PM JClavel @.***> wrote:

Hi Makaylee,

Send me your data or a working example to replicate the issue. I'll look at it ASAP.

Regards,

Julien

De : Makaylee Crone @.> Envoyé : mercredi 24 janvier 2024 19:55 À : JClavel/mvMORPH @.> Cc : Subscribed @.***> Objet : [JClavel/mvMORPH] Error in svd(B, nu = 0) : infinite or missing values in 'x' for mvgls (Issue #15)

Hi,

Not sure if this is a bug since the package is new or just an error on my end. I'm trying to use function mvgls to fit a pgls model but get the error "Error in svd(B, nu = 0) : infinite or missing values in 'x'" when I run the following. I'm attempting to make my data match the simulation data in your example but am failing to do so.

df5 <- Bacteria_dat3 %>% mutate_at(1:21, as.numeric) df6 <- as.matrix(df5) data=list(df6=df6) fit1 <- mvgls(df6~1, data=data, tree2, model="BM", penalty="RidgeArch")

Bacteria_dat3 is a data frame with microbiome community occurrence data.

Family, Genus, Species, Acinetobacter,Apilactobacillus,Bacillus,Citrobacter,Enterococcus,Erwinia,Fructobacillus,Gilliamella,Lactobacillus,Pantoea,Phaseolibacter,Pleosporaceae,Pseudomonas,Rhodococcus,Rosenbergiella,Saccharibacter,Shigella,Stephania,Streptomyces,Weissella,Wolbachia

Apidae, Apis,Apis_mellifera,17,24,0,0,0,0,3,0,18,2,0,0,0,0,25,9,0,0,0,4,0 Apidae, Ceratina,Ceratina_calcarata,2,1,0,39,3,4,0,6,0,10,0,0,0,3,0,0,5,0,0,0,6 Megachilidae, Heriades,Heriades_truncorum,4,0,4,0,0,0,0,0,6,5,2,0,28,0,0,0,0,0,19,0,0 Megachilidae, Megachile,Megachile_ligniseca,0,0,0,0,0,0,2,0,0,1,2,1,2,0,0,0,0,0,2,0,0 Megachilidae, Megachile,Megachile_rotundata,0,0,0,0,0,0,2,0,0,1,2,1,0,0,0,0,0,0,0,0,0 Halictidae, Nomia,Nomia_irridescens,1,16,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_caerulescens,2,0,3,0,0,1,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_leaiana,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,1 Megachilidae, Osmia,Osmia_lignaria,30,0,0,2,0,0,0,0,5,1,0,0,1,0,0,1,0,3,0,0,0

After trying to make my data match the simulation data this is the output for str() and class().

num [1:9, 1:21] 2 17 30 0 2 4 0 0 1 1 ...

  • attr(*, "dimnames")=List of 2 ..$ : chr [1:9] "Ceratina_calcarata" "Apis_mellifera" "Osmia_lignaria" "Osmia_leaiana" ... ..$ : chr [1:21] "V4" "V5" "V6" "V7" ...

[1] "matrix" "array"

Any idea what might be going on here? Thanks for the help!

Makaylee

— Reply to this email directly, view it on GitHub< https://github.com/JClavel/mvMORPH/issues/15>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ACSCJSN5FQXZFNO3TP42HYTYQFKIJAVCNFSM6AAAAABCJIJ6FCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4TQOBYHAYTSMA>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

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(Ceratina_calcarata:0.1321524803,Apis_mellifera:0.1091336779,(((((Osmia_lignaria:0.0492390593,Osmia_leaiana:0.0638433515):0.0230248572,Osmia_caerulescens:0.0550472058):0.0950060555,Heriades_truncorum:0.0788141759):0.0487930055,(Megachile_rotundata:0.0328941804,Megachile_ligniseca:0.1551547559):0.0769495053):0.0183938387,Nomia_irridescens:0.295023156):0.0091878868);

JClavel commented 9 months ago

Hi Makaylee,

Sorry I did not get the data in your last email (only got the tree in text format). Can you send them directly to my email address ? Maybe you simply save your R session with data.

Regards,

Julien

De : Makaylee Crone @.> Envoyé : jeudi 25 janvier 2024 03:26 À : JClavel/mvMORPH @.> Cc : JClavel @.>; Comment @.> Objet : Re: [JClavel/mvMORPH] Error in svd(B, nu = 0) : infinite or missing values in 'x' for mvgls (Issue #15)

Hi Julien,

Thanks so much for looking into this. My data frame and tree are attached for you. The data file is the original before using any code to prepare it for analysis. The code I used to do this was:

load data

tree <- read.tree("tree.txt") data <- read.csv("data_Julien.csv", header=TRUE)

remove columns and make species the row name

rownames(data) <- data[,3] data <- data[-c(1:3)]

reorder rows to match tree

data <- data[tree$tip.label,]

make data numeric and transform to matrix

df5 <- data %>% mutate_at(1:21, as.numeric) df6 <- as.matrix(df5)

code used for pgls model

data=list(df6=df6) fit1 <- mvgls(df6~1, data=data, tree2, model="BM", penalty="RidgeArch")

I'm new to phylogenetic analyses so I'm not entirely sure that options BM and RidgeArch are best for my data, but I figure that the code should work for any of these options and I can find the best one later.

Thanks again,

Makaylee

On Wed, Jan 24, 2024 at 8:54 PM JClavel @.***> wrote:

Hi Makaylee,

Send me your data or a working example to replicate the issue. I'll look at it ASAP.

Regards,

Julien

De : Makaylee Crone @.> Envoyé : mercredi 24 janvier 2024 19:55 À : JClavel/mvMORPH @.> Cc : Subscribed @.***> Objet : [JClavel/mvMORPH] Error in svd(B, nu = 0) : infinite or missing values in 'x' for mvgls (Issue #15)

Hi,

Not sure if this is a bug since the package is new or just an error on my end. I'm trying to use function mvgls to fit a pgls model but get the error "Error in svd(B, nu = 0) : infinite or missing values in 'x'" when I run the following. I'm attempting to make my data match the simulation data in your example but am failing to do so.

df5 <- Bacteria_dat3 %>% mutate_at(1:21, as.numeric) df6 <- as.matrix(df5) data=list(df6=df6) fit1 <- mvgls(df6~1, data=data, tree2, model="BM", penalty="RidgeArch")

Bacteria_dat3 is a data frame with microbiome community occurrence data.

Family, Genus, Species, Acinetobacter,Apilactobacillus,Bacillus,Citrobacter,Enterococcus,Erwinia,Fructobacillus,Gilliamella,Lactobacillus,Pantoea,Phaseolibacter,Pleosporaceae,Pseudomonas,Rhodococcus,Rosenbergiella,Saccharibacter,Shigella,Stephania,Streptomyces,Weissella,Wolbachia

Apidae, Apis,Apis_mellifera,17,24,0,0,0,0,3,0,18,2,0,0,0,0,25,9,0,0,0,4,0 Apidae, Ceratina,Ceratina_calcarata,2,1,0,39,3,4,0,6,0,10,0,0,0,3,0,0,5,0,0,0,6 Megachilidae, Heriades,Heriades_truncorum,4,0,4,0,0,0,0,0,6,5,2,0,28,0,0,0,0,0,19,0,0 Megachilidae, Megachile,Megachile_ligniseca,0,0,0,0,0,0,2,0,0,1,2,1,2,0,0,0,0,0,2,0,0 Megachilidae, Megachile,Megachile_rotundata,0,0,0,0,0,0,2,0,0,1,2,1,0,0,0,0,0,0,0,0,0 Halictidae, Nomia,Nomia_irridescens,1,16,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_caerulescens,2,0,3,0,0,1,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_leaiana,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,1 Megachilidae, Osmia,Osmia_lignaria,30,0,0,2,0,0,0,0,5,1,0,0,1,0,0,1,0,3,0,0,0

After trying to make my data match the simulation data this is the output for str() and class().

num [1:9, 1:21] 2 17 30 0 2 4 0 0 1 1 ...

  • attr(*, "dimnames")=List of 2 ..$ : chr [1:9] "Ceratina_calcarata" "Apis_mellifera" "Osmia_lignaria" "Osmia_leaiana" ... ..$ : chr [1:21] "V4" "V5" "V6" "V7" ...

[1] "matrix" "array"

Any idea what might be going on here? Thanks for the help!

Makaylee

— Reply to this email directly, view it on GitHub< https://github.com/JClavel/mvMORPH/issues/15>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ACSCJSN5FQXZFNO3TP42HYTYQFKIJAVCNFSM6AAAAABCJIJ6FCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4TQOBYHAYTSMA>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

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(Ceratina_calcarata:0.1321524803,Apis_mellifera:0.1091336779,(((((Osmia_lignaria:0.0492390593,Osmia_leaiana:0.0638433515):0.0230248572,Osmia_caerulescens:0.0550472058):0.0950060555,Heriades_truncorum:0.0788141759):0.0487930055,(Megachile_rotundata:0.0328941804,Megachile_ligniseca:0.1551547559):0.0769495053):0.0183938387,Nomia_irridescens:0.295023156):0.0091878868);

— Reply to this email directly, view it on GitHubhttps://github.com/JClavel/mvMORPH/issues/15#issuecomment-1909240382, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACSCJSJT4AVA2MFLGUEJWLLYQG7EVAVCNFSM6AAAAABCJIJ6FCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBZGI2DAMZYGI. You are receiving this because you commented.Message ID: @.***>

MKeao commented 9 months ago

Got it, just sent to your uni lyon email address.

Makaylee

On Thu, Jan 25, 2024 at 8:34 AM JClavel @.***> wrote:

Hi Makaylee,

Sorry I did not get the data in your last email. Can you send them directly to my email address ? Maybe you simply save your R session with data.

Regards,

Julien

De : Makaylee Crone @.> Envoyé : jeudi 25 janvier 2024 03:26 À : JClavel/mvMORPH @.> Cc : JClavel @.>; Comment @.> Objet : Re: [JClavel/mvMORPH] Error in svd(B, nu = 0) : infinite or missing values in 'x' for mvgls (Issue #15)

Hi Julien,

Thanks so much for looking into this. My data frame and tree are attached for you. The data file is the original before using any code to prepare it for analysis. The code I used to do this was:

load data

tree <- read.tree("tree.txt") data <- read.csv("data_Julien.csv", header=TRUE)

remove columns and make species the row name

rownames(data) <- data[,3] data <- data[-c(1:3)]

reorder rows to match tree

data <- data[tree$tip.label,]

make data numeric and transform to matrix

df5 <- data %>% mutate_at(1:21, as.numeric) df6 <- as.matrix(df5)

code used for pgls model

data=list(df6=df6) fit1 <- mvgls(df6~1, data=data, tree2, model="BM", penalty="RidgeArch")

I'm new to phylogenetic analyses so I'm not entirely sure that options BM and RidgeArch are best for my data, but I figure that the code should work for any of these options and I can find the best one later.

Thanks again,

Makaylee

On Wed, Jan 24, 2024 at 8:54 PM JClavel @.***> wrote:

Hi Makaylee,

Send me your data or a working example to replicate the issue. I'll look at it ASAP.

Regards,

Julien

De : Makaylee Crone @.> Envoyé : mercredi 24 janvier 2024 19:55 À : JClavel/mvMORPH @.> Cc : Subscribed @.***> Objet : [JClavel/mvMORPH] Error in svd(B, nu = 0) : infinite or missing values in 'x' for mvgls (Issue #15)

Hi,

Not sure if this is a bug since the package is new or just an error on my end. I'm trying to use function mvgls to fit a pgls model but get the error "Error in svd(B, nu = 0) : infinite or missing values in 'x'" when I run the following. I'm attempting to make my data match the simulation data in your example but am failing to do so.

df5 <- Bacteria_dat3 %>% mutate_at(1:21, as.numeric) df6 <- as.matrix(df5) data=list(df6=df6) fit1 <- mvgls(df6~1, data=data, tree2, model="BM", penalty="RidgeArch")

Bacteria_dat3 is a data frame with microbiome community occurrence data.

Family, Genus, Species,

Acinetobacter,Apilactobacillus,Bacillus,Citrobacter,Enterococcus,Erwinia,Fructobacillus,Gilliamella,Lactobacillus,Pantoea,Phaseolibacter,Pleosporaceae,Pseudomonas,Rhodococcus,Rosenbergiella,Saccharibacter,Shigella,Stephania,Streptomyces,Weissella,Wolbachia

Apidae, Apis,Apis_mellifera,17,24,0,0,0,0,3,0,18,2,0,0,0,0,25,9,0,0,0,4,0 Apidae, Ceratina,Ceratina_calcarata,2,1,0,39,3,4,0,6,0,10,0,0,0,3,0,0,5,0,0,0,6 Megachilidae, Heriades,Heriades_truncorum,4,0,4,0,0,0,0,0,6,5,2,0,28,0,0,0,0,0,19,0,0 Megachilidae, Megachile,Megachile_ligniseca,0,0,0,0,0,0,2,0,0,1,2,1,2,0,0,0,0,0,2,0,0 Megachilidae, Megachile,Megachile_rotundata,0,0,0,0,0,0,2,0,0,1,2,1,0,0,0,0,0,0,0,0,0 Halictidae, Nomia,Nomia_irridescens,1,16,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_caerulescens,2,0,3,0,0,1,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0 Megachilidae, Osmia,Osmia_leaiana,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,1 Megachilidae, Osmia,Osmia_lignaria,30,0,0,2,0,0,0,0,5,1,0,0,1,0,0,1,0,3,0,0,0

After trying to make my data match the simulation data this is the output for str() and class().

num [1:9, 1:21] 2 17 30 0 2 4 0 0 1 1 ...

  • attr(*, "dimnames")=List of 2 ..$ : chr [1:9] "Ceratina_calcarata" "Apis_mellifera" "Osmia_lignaria" "Osmia_leaiana" ... ..$ : chr [1:21] "V4" "V5" "V6" "V7" ...

[1] "matrix" "array"

Any idea what might be going on here? Thanks for the help!

Makaylee

— Reply to this email directly, view it on GitHub< https://github.com/JClavel/mvMORPH/issues/15>, or unsubscribe<

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(Ceratina_calcarata:0.1321524803,Apis_mellifera:0.1091336779,(((((Osmia_lignaria:0.0492390593,Osmia_leaiana:0.0638433515):0.0230248572,Osmia_caerulescens:0.0550472058):0.0950060555,Heriades_truncorum:0.0788141759):0.0487930055,(Megachile_rotundata:0.0328941804,Megachile_ligniseca:0.1551547559):0.0769495053):0.0183938387,Nomia_irridescens:0.295023156):0.0091878868);

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