From a5d64f237d64020fb545fdf0fba789b661fb5a75 Mon Sep 17 00:00:00 2001
From: Rmomal <rmomaleisenring@gmail.com>
Date: Fri, 13 Dec 2024 17:20:16 +0100
Subject: [PATCH] Fix for incompatibility with PLNmodels latest release
---
.Rprofile | 2 +-
.gitignore | 1 +
DESCRIPTION | 26 +++++++----
R/F_inference.R | 4 +-
README.Rmd | 6 +--
README.md | 6 +--
cran-comments.md | 15 +++---
dev_history.R | 7 +--
docs/.DS_Store | Bin 8196 -> 8196 bytes
tests/.DS_Store | Bin 8196 -> 8196 bytes
tests/testthat/test-F_Graphs.R | 2 -
tests/testthat/test-F_inference.R | 2 -
tests/testthat/test-test_gener_data.R | 1 -
vignettes/.DS_Store | Bin 0 -> 6148 bytes
vignettes/Fatala_Net.Rmd | 3 --
vignettes/Partial_correlations.Rmd | 65 ++++++++++++++++++++++++++
16 files changed, 105 insertions(+), 35 deletions(-)
create mode 100644 vignettes/.DS_Store
create mode 100644 vignettes/Partial_correlations.Rmd
diff --git a/.Rprofile b/.Rprofile
index cae50de..a9fbfb2 100644
--- a/.Rprofile
+++ b/.Rprofile
@@ -1 +1 @@
-options(repos=structure(c(CRAN="http://cran.us.r-project.org")))
+options(repos=structure(c(CRAN="https://cloud.r-project.org/")))
diff --git a/.gitignore b/.gitignore
index 138866d..44ac001 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,4 @@
.Ruserdata
inst/doc
docs
+dev_history.R
diff --git a/DESCRIPTION b/DESCRIPTION
index edaacc3..45db86c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,37 +2,45 @@ Type: Package
Package: EMtree
Title: Infers Direct Species Association Networks using Tree Averaging
Version: 1.1.0
-Author: Raphaelle Momal <rmomaleisenring@gmail.com>
-Maintainer: Raphaelle Momal <rmomaleisenring@gmail.com>
-Description: Uses averages over spanning trees within an Expectation Maximization algorithm to infer conditional dependence networks. Involves plotting functionalities.
+Authors@R: c(
+ person("Raphaëlle", "Momal", role = c("aut", "cre","cph"), email = "rmomaleisenring@gmail.com",
+ comment = c(ORCID = "0000-0002-1550-4530")))
+Description: The spanning tree averaging within an Expectation-Maximization algorithm
+ (Momal, Robin and Ambroise, 2020 <doi:10.1111/2041-210X.13380>) leverages the
+ Matrix Tree Theorem to infer conditional dependence networks, such as direct species association
+ networks.
License: GPL-3
Imports:
dplyr,
ggplot2,
ggraph,
huge,
- influenceR,
magrittr,
Matrix,
mvtnorm,
parallel,
PLNmodels,
- purrr,
tibble,
tidygraph,
- tidyr,
vegan,
+ gridExtra,
+ pillar,
ade4,
- gridExtra
+ viridis,
+ gmp
Suggests:
testthat (>= 2.1.0),
knitr,
rmarkdown,
networkD3,
+ pROC,
+ tidyr,
RColorBrewer
Encoding: UTF-8
-LazyData: false
-RoxygenNote: 7.1.1
+LazyData: true
+RoxygenNote: 7.3.2
+Depends: R (>= 3.5)
VignetteBuilder: knitr
URL: https://rmomal.github.io/EMtree/
BugReports: https://github.com/Rmomal/EMtree/issues
+Language: en-US
diff --git a/R/F_inference.R b/R/F_inference.R
index 378e80c..7141f64 100644
--- a/R/F_inference.R
+++ b/R/F_inference.R
@@ -410,8 +410,8 @@ ResampleEMtree <- function(counts,covar_matrix=NULL, unlinked=NULL,
#- parallel computation of S fits of new_EMtree
if(is.null(user_covariance_estimation)){
suppressWarnings(
- PLNfit <- PLNmodels::PLN(counts ~ -1 + offset(log(O)) + .,
- data=data.frame(X),control=list("trace"=0))
+ PLNfit <- PLNmodels::PLN(formula=counts ~ -1 + offset(log(O)) + .,
+ data=data.frame(X),control=PLN_param(trace=0))
)}
obj<-parallel::mclapply(1:S,function(b){
if(init){
diff --git a/README.Rmd b/README.Rmd
index 23f9080..bbf01b0 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -28,9 +28,9 @@ By default, it uses the Poisson log-Normal Model ([PLNmodels](https://github.com
### CRAN dependencies
```{r,eval=FALSE}
-required_CRAN <- c("Matrix", "purrr","parallel", "mvtnorm", "vegan","huge",
- "ggplot2", "magrittr", "dplyr","tidyr", "tibble",
- "PLNmodels","ggraph", "tidygraph", "ade4")
+required_CRAN <- c("Matrix", "parallel", "mvtnorm", "vegan",
+ "ggplot2", "magrittr", "dplyr", "tibble",
+ "PLNmodels","ggraph", "tidygraph","huge")
not_installed_CRAN <- setdiff(required_CRAN, rownames(installed.packages()))
if (length(not_installed_CRAN) > 0) install.packages(not_installed_CRAN)
```
diff --git a/README.md b/README.md
index 205e588..b8e6b64 100644
--- a/README.md
+++ b/README.md
@@ -31,9 +31,9 @@ copulas, or Gaussian data transformations.
### CRAN dependencies
``` r
-required_CRAN <- c("Matrix", "purrr","parallel", "mvtnorm", "vegan","huge",
- "ggplot2", "magrittr", "dplyr","tidyr", "tibble",
- "PLNmodels","ggraph", "tidygraph", "ade4")
+required_CRAN <- c("Matrix", "parallel", "mvtnorm", "vegan",
+ "ggplot2", "magrittr", "dplyr", "tibble",
+ "PLNmodels","ggraph", "tidygraph","huge")
not_installed_CRAN <- setdiff(required_CRAN, rownames(installed.packages()))
if (length(not_installed_CRAN) > 0) install.packages(not_installed_CRAN)
```
diff --git a/cran-comments.md b/cran-comments.md
index aee4e45..a2e7020 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,10 +1,13 @@
## Test environments
-* local R installation, R 4.0.2
-* ubuntu 16.04 (on travis-ci), R 4.0.2
-* win-builder (devel)
+- R-hub fedora-clang-devel (r-devel)
+- R-hub windows-x86_64-devel (r-devel)
+- R-hub macos-highsierra-release (r-release)
## R CMD check results
+> On fedora-clang-devel (r-devel), windows-x86_64-devel (r-devel)
+ checking CRAN incoming feasibility ... NOTE
+ Maintainer: ‘Raphaelle Momal <rmomaleisenring@gmail.com>’
+
+ New submission
-0 errors | 0 warnings | 1 note
-
-* This is a new release.
+0 errors ✓ | 0 warnings ✓ | 1 note x
diff --git a/dev_history.R b/dev_history.R
index a070827..cc5d078 100644
--- a/dev_history.R
+++ b/dev_history.R
@@ -13,6 +13,7 @@ attachment::att_to_description()
use_build_ignore("dev_history.R")
usethis::use_vignette("Fatala_Net","Fatala fishes")
+usethis::use_vignette("Partial_correlations","Partial correlations")
pkgdown::build_site()
# workflow
@@ -44,14 +45,14 @@ covr::report()
results <- rhub::check_for_cran(platforms=c("fedora-clang-devel",
"windows-x86_64-devel",
"macos-highsierra-release"))
-
+results2 <- rhub::check_for_cran()
# Get the summary of your results
-results$cran_summary()
+results2$cran_summary()
# Generate your cran-comments.md, then you copy-paste the output from the function above
usethis::use_cran_comments()
devtools::check_win_devel()
usethis::use_news_md(open = rlang::is_interactive())
-
+devtools::release()
diff --git a/docs/.DS_Store b/docs/.DS_Store
index 2adaebd44dd0132e82dc41dcfb866a092674d638..d6253b8153e26b98e45a5e0424fcb2d6f1130ad9 100644
GIT binary patch
delta 195
zcmZp1XmQveD#)zRRy}#6u=r+uK_ynUhH?(U!;V0{$mDD>J|wO{L55*)a(-?B0|+P<
yFo4x;7t?1}_J1__rI-q9Lm^P>WFc`?D9c7%g-K<?#KNVU*(JQ#kc^_5$%_DK06M?`
delta 195
zcmZp1XmQveD#$GC**JNlu=r+uK_yl;2K!$bha7=?k;&O&d`Mh@f(*mp<ow(M1`rT#
wU;wMxE~d{cX1!qYOEDEzu-3^!;;K-VjkpSvxWdH3rJLC$yx5S8qMFHz0Ac(+SO5S3
diff --git a/tests/.DS_Store b/tests/.DS_Store
index 6930394dd13dc9e9de40837b7596bb1f7600e83b..7ca28c76a1ed5e4e9724f889e0bddab1265914d6 100644
GIT binary patch
delta 121
zcmZp1XmQveCdj07dh$kL@y+^zN~~-Qf(OJ7I|BJ4le5M6S>Zf^f(*mp<ow(M1~4dK
Q04dqLU2GOR$y$6F0i|XmZ~y=R
delta 121
zcmZp1XmQveCdi~5IeDY7_-1`UC04eE$G0;MIRg12le5M6SzB*Gc>)C)hQZ1CxdjYh
TkiY;^vU$7MEOwH$_%Z?j)*C1f
diff --git a/tests/testthat/test-F_Graphs.R b/tests/testthat/test-F_Graphs.R
index d6c54f1..6283a30 100644
--- a/tests/testthat/test-F_Graphs.R
+++ b/tests/testthat/test-F_Graphs.R
@@ -4,9 +4,7 @@ library(PLNmodels)
library(parallel)
library(tidygraph)
library(ggraph)
-library(purrr)
library(dplyr)
-library(tidyr)
library(gridExtra)
##########################
n<-30
diff --git a/tests/testthat/test-F_inference.R b/tests/testthat/test-F_inference.R
index 73bdb0f..53c78f2 100644
--- a/tests/testthat/test-F_inference.R
+++ b/tests/testthat/test-F_inference.R
@@ -6,8 +6,6 @@ library(dplyr)
library(vegan)
library(Matrix)
library(mvtnorm)
-library(tidyr)
-library(EMtree)
##########################
n<-30
p<-10
diff --git a/tests/testthat/test-test_gener_data.R b/tests/testthat/test-test_gener_data.R
index 065372a..15a435a 100644
--- a/tests/testthat/test-test_gener_data.R
+++ b/tests/testthat/test-test_gener_data.R
@@ -6,7 +6,6 @@ library(dplyr)
library(vegan)
library(Matrix)
library(mvtnorm)
-library(tidyr)
library(EMtree)
##########################
n<-100
diff --git a/vignettes/.DS_Store b/vignettes/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..0b4ac769b968835370123433edcab35788f6392e
GIT binary patch
literal 6148
zcmeHK!AiqG5S^{1M7+eC$NWP5f>@$QFFi}OX=;Up6s%s|pV1%jNBj^EzS$W<W2^=R
z5t)J6m(0$~X5K<3OGIvRw-^(}L=?dp2m2U4FrH`c*gzvZ>B2Kgx}q7KQ$d?fwgvv8
z0<!sM*tZRQd;eyXBa+jKit>6q&Fg9{1za2hWBP(q)mb(#>p60Hjr-{E`J^9j@h#qZ
zwf&ABOYMBeCEcLXf^J)Njh-I+aNgDR@EU(wSF=`Cx9aN6Yt=P+;kwLB0aL&f_^ATu
z*=*5)ppB-0DPRgT3h?(KfitFxUNC$*FoYujaENd)T=Q9iIf-Jb=mjwYb3z3Q)#(w#
z2_5l7^HN1GD0Fgq_;9+i(-VpdtK<1eNGF#H+Gq-x0&NBM<TmF1f4ckp-zM3eDPRix
zD+Syzn`RS~q`kFM9QWD;ehFveJTKT#a1mNDa=8^B!Gj^5@C7hc^n!@M>_;HTV1p^}
Hs|vgUpHyPn
literal 0
HcmV?d00001
diff --git a/vignettes/Fatala_Net.Rmd b/vignettes/Fatala_Net.Rmd
index 8434edc..f3bed38 100644
--- a/vignettes/Fatala_Net.Rmd
+++ b/vignettes/Fatala_Net.Rmd
@@ -208,6 +208,3 @@ forceNetwork(Links = graph_d3$links, Nodes =graph_d3$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'group',opacity = 1,fontSize = 15, legend=TRUE)
```
-
-
-
diff --git a/vignettes/Partial_correlations.Rmd b/vignettes/Partial_correlations.Rmd
new file mode 100644
index 0000000..c6788c7
--- /dev/null
+++ b/vignettes/Partial_correlations.Rmd
@@ -0,0 +1,65 @@
+---
+title: "Partial correlations"
+output: rmarkdown::html_vignette
+vignette: >
+ %\VignetteIndexEntry{Partial correlations}
+ %\VignetteEngine{knitr::rmarkdown}
+ %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+ collapse = TRUE,
+ comment = "#>",
+ cache=TRUE
+)
+library(ggplot2)
+library(dplyr)
+library(tidyr)
+library(magrittr)
+```
+
+```{r setup}
+library(EMtree)
+```
+
+# Partial correlations simulation
+
+```{r}
+set.seed(1)
+p=300
+n=400
+simulation<-data_from_scratch(type="erdos",p=p,n=n,signed=TRUE, dens=3/p)
+G=1*(simulation$omega!=0) ; diag(G) = 0
+draw_network(G, remove_isolated = TRUE, pal_edges = "gray70",pal_nodes = "steelblue",btw_rank = 1)$G
+```
+simulated partial correlation matrix :
+```{r}
+ParCor <- - cov2cor(simulation$omega)
+```
+
+```{r}
+ParCor %>% ToVec() %>% as_tibble() %>% filter(value!=0) %>%
+ ggplot(aes(value))+geom_histogram(alpha=0.8)+
+ theme_light()+labs(title="Repartition of non-nul partial correlations",
+ x="Partial correlation values")
+
+```
+
+
+# Inference
+
+```{r}
+EMtreefit<-ResampleEMtree(simulation$data,S = 30,cores = 3)
+stab_selection=StATS(EMtreefit$Pmat, nlambda=50, stab.thresh=0.8,plot=TRUE)
+```
+
+```{r}
+net90=ToSym(1*(stab_selection$freqs_opt>0.95))
+table(net90, G)
+library(PRROC)
+pr<-pr.curve(scores.class0 = stab_selection$freqs_opt,
+ scores.class1 = ToVec(G))
+pr
+```
+