From a203c88c250d6cee435df508cfa1bac76f55018e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=B6nig?= <ye87zine@usr.idiv.de>
Date: Fri, 31 Jan 2025 09:14:25 +0100
Subject: [PATCH] msdm finally learn species embeddings
---
R/04_02_modelling_msdm_embed.R | 39 ++-
R/05_02_publication_analysis.R | 44 +--
renv.lock | 500 ++++++++++++++++++++++++++-------
3 files changed, 445 insertions(+), 138 deletions(-)
diff --git a/R/04_02_modelling_msdm_embed.R b/R/04_02_modelling_msdm_embed.R
index 8257a3a..dd991f5 100644
--- a/R/04_02_modelling_msdm_embed.R
+++ b/R/04_02_modelling_msdm_embed.R
@@ -15,7 +15,7 @@ model_data = model_data %>%
# Train model ####
# ----------------------------------------------------------------------#
predictors = c("bio6", "bio17", "cmi", "rsds", "igfc", "dtfw", "igsw", "roughness")
-formula = as.formula(paste0("present ~ ", paste(predictors, collapse = '+'), " + ", "e(species, dim = 30, train = T, lambda = 0.0001)"))
+formula = as.formula(paste0("present ~ ", paste(predictors, collapse = '+'), " + ", "e(species, dim = 10)"))
# 1. Cross validation
for(fold in 1:5){
@@ -27,24 +27,21 @@ for(fold in 1:5){
while(!converged){
msdm_embed_fit = dnn(
formula,
- data = train_data,
- hidden = c(400L, 400L, 400L),
+ data = model_data,
+ hidden = c(200L, 200L, 200L),
loss = "binomial",
- activation = c("sigmoid", "leaky_relu", "leaky_relu"),
- epochs = 25000,
- lr = 0.01,
- baseloss = 1,
- batchsize = nrow(train_data),
- dropout = 0.3,
- burnin = 500,
- optimizer = config_optimizer("adam", weight_decay = 0.001),
- lr_scheduler = config_lr_scheduler("reduce_on_plateau", patience = 100, factor = 0.7),
- early_stopping = 300,
+ epochs = 2500,
+ lr = 0.001,
+ batchsize = 4096,
+ dropout = 0.25,
+ burnin = 50,
+ optimizer = config_optimizer("adam"),
+ early_stopping = 200,
validation = 0.2,
device = "cuda"
)
- if(sum(!is.na(msdm_embed_fit$losses$valid_l)) > 5000){
+ if(min(msdm_embed_fit$losses$valid_l) < 0.4){
converged = T
}
}
@@ -56,17 +53,15 @@ for(fold in 1:5){
msdm_embed_fit = dnn(
formula,
data = model_data,
- hidden = c(400L, 400L, 400L),
+ hidden = c(200L, 200L, 200L),
loss = "binomial",
- activation = c("sigmoid", "leaky_relu", "leaky_relu"),
- epochs = 25000,
- lr = 0.01,
+ epochs = 2500,
+ lr = 0.001,
baseloss = 1,
- batchsize = nrow(model_data),
- dropout = 0.3,
+ batchsize = 4096,
+ dropout = 0.25,
burnin = 500,
- optimizer = config_optimizer("adam", weight_decay = 0.001),
- lr_scheduler = config_lr_scheduler("reduce_on_plateau", patience = 100, factor = 0.7),
+ optimizer = config_optimizer("adam"),
early_stopping = 300,
validation = 0.2,
device = "cuda"
diff --git a/R/05_02_publication_analysis.R b/R/05_02_publication_analysis.R
index babf048..19856d7 100644
--- a/R/05_02_publication_analysis.R
+++ b/R/05_02_publication_analysis.R
@@ -144,6 +144,12 @@ ggsave("plots/publication/model_performance_vs_functional_groups.pdf",
# ------------------------------------------------------------------ #
# 3. Range predictions ####
# ------------------------------------------------------------------ #
+library(caret)
+library(gam)
+library(gbm)
+library(cito)
+library(randomForest)
+
# Define plotting function
plot_predictions = function(spec, model_data, raster_data, algorithms = c("gam", "gbm", "rf", "nn", "msdm")){
# Species data
@@ -170,7 +176,7 @@ plot_predictions = function(spec, model_data, raster_data, algorithms = c("gam",
# Load model
tryCatch({
if(algorithm == "msdm"){
- load("data/r_objects/msdm_embed_results/msdm_embed_fit_full.RData")
+ load("data/r_objects/msdm_embed_results/msdm_embed_fit_test.RData")
probabilities = predict(msdm_embed_fit, new_data, type = "response")[,1]
predictions = factor(round(probabilities), levels = c("0", "1"), labels = c("A", "P"))
} else if(algorithm == "nn") {
@@ -184,7 +190,7 @@ plot_predictions = function(spec, model_data, raster_data, algorithms = c("gam",
}, error = function(e){
warning(toupper(algorithm), ": Model could not be loaded.")
})
-
+
raster_pred = terra::rast(raster_crop, nlyrs = 1)
values(raster_pred)[as.integer(rownames(new_data))] <- predictions
@@ -205,19 +211,19 @@ raster_data = terra::rast(raster_filepaths) %>%
terra::crop(sf::st_bbox(sa_polygon)) %>%
terra::project(sf::st_crs(model_data)$input)
-spec = "Thyroptera tricolor"
+spec = "Abrothrix andinus"
pdf(file = paste0("plots/range_predictions/", spec, ".pdf"))
plot_predictions(spec, model_data, raster_data, algorithms = c("gam", "gbm", "rf", "msdm"))
dev.off()
# ------------------------------------------------------------------ #
-# 5. Compare msdm predictions ####
+# 4. Compare msdm predictions ####
# ------------------------------------------------------------------ #
# Check predictions for different species
-load("data/r_objects/msdm_embed_results/msdm_embed_fit.RData")
+load("data/r_objects/msdm_embed_results/msdm_embed_fit_test.RData")
specs = sample(unique(model_data$species), size = 2, replace = F)
-new_data = spatSample(raster_data, 1000, replace = F, as.df = T) %>%
+new_data = spatSample(raster_data, 10, replace = F, as.df = T) %>%
drop_na()
new_data1 = dplyr::mutate(new_data, species = specs[1])
@@ -226,7 +232,8 @@ new_data2 = dplyr::mutate(new_data, species = specs[2])
pred1 = predict(msdm_embed_fit, new_data1, type = "response")
pred2 = predict(msdm_embed_fit, new_data2, type = "response")
-pred1 == pred2
+pred1
+pred2
# ---> identical predictions
@@ -237,7 +244,7 @@ msdm_embed_fit$net$e_1$parameters$weight$set_data(torch::torch_tensor(embeddings
# ---> Invalid external pointer
# ------------------------------------------------------------------ #
-# 6. Compare species embeddings ####
+# 5. Compare species embeddings ####
# ------------------------------------------------------------------ #
all_embeddings = lapply(1:5, function(fold){
load(paste0("data/r_objects/msdm_embed_results/msdm_embed_fit_fold", fold, ".RData"))
@@ -260,14 +267,15 @@ for(i in seq_along(pairs)){
}
# ------------------------------------------------------------------ #
-# 7. Analyse species embeddings ####
+# 6. Analyse species embeddings ####
# ------------------------------------------------------------------ #
-embeddings = coef(msdm_fit_embedding_raw)[[1]][[1]]
-species_lookup = msdm_fit_embedding_raw$data$data[,c("species", "species_int")] %>%
- distinct() %>%
- mutate(genus = stringr::str_extract(rownames(embeddings), "([a-zA-Z]+) (.*)", group = 1))
+embeddings = coef(msdm_embed_fit)[[1]][[1]]
+rownames(embeddings) = levels(species_lookup$species)
-rownames(embeddings) = species_lookup$species
+species_lookup = data.frame(species = levels(model_data$species)) %>%
+ dplyr::mutate(
+ genus = stringr::str_extract(species, "([a-zA-Z]+) (.*)", group = 1)
+ )
## Dimensionality reduction ####
### PCA ####
@@ -290,7 +298,6 @@ ggplot(df_plot, aes(x = X, y = Y, col = functional_group, label=genus)) +
geom_text(hjust=0, vjust=0) +
guides(col="none")
-# --> PCA not informative on 2 dimensions either
### TSNE ####
tsne_result <- Rtsne(embeddings, verbose = FALSE)
@@ -306,14 +313,11 @@ ggplot(df_plot, aes(x = X, y = Y, col = functional_group, label=genus)) +
geom_text(hjust=0, vjust=0) +
guides(col="none")
-# --> TSNE not informative on 2 dimensions either
-
-
### KNN ####
embeddings_dist = as.matrix(dist(embeddings))
k = 9
-knn_results = sapply(as.character(species_lookup$species), FUN = function(spec){
+knn_results = sapply(as.integer(species_lookup$species), FUN = function(spec){
return(sort(embeddings_dist[spec,])[2:(k+1)])
}, USE.NAMES = T, simplify = F)
@@ -344,7 +348,7 @@ plot_knn_ranges(sample(species_lookup$species, 1)) # Repeat this line to plot ra
# Clustering
embeddings_dist = dist(embeddings, method = "euclidean")
-hclust_complete = hclust(dist_matrix, method = "complete")
+hclust_complete = hclust(embeddings_dist, method = "complete")
plot(hclust_complete, main = "Complete Linkage", xlab = "", sub = "", labels = FALSE)
# Phylo Correlation
diff --git a/renv.lock b/renv.lock
index 7f13630..f26410c 100644
--- a/renv.lock
+++ b/renv.lock
@@ -112,6 +112,54 @@
],
"Hash": "64ff3427f559ce3f2597a4fe13255cb6"
},
+ "Deriv": {
+ "Package": "Deriv",
+ "Version": "4.1.6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "methods"
+ ],
+ "Hash": "cd52c065c9e687c60c56b51f10f7bcd3"
+ },
+ "FactoMineR": {
+ "Package": "FactoMineR",
+ "Version": "2.11",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "DT",
+ "MASS",
+ "R",
+ "car",
+ "cluster",
+ "ellipse",
+ "emmeans",
+ "flashClust",
+ "ggplot2",
+ "ggrepel",
+ "grDevices",
+ "graphics",
+ "lattice",
+ "leaps",
+ "multcompView",
+ "scatterplot3d",
+ "stats",
+ "utils"
+ ],
+ "Hash": "54fc333adf872599b177a62d5759892a"
+ },
+ "Formula": {
+ "Package": "Formula",
+ "Version": "1.2-5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats"
+ ],
+ "Hash": "7a29697b75e027767a53fde6c903eca7"
+ },
"KernSmooth": {
"Package": "KernSmooth",
"Version": "2.23-20",
@@ -140,11 +188,12 @@
},
"Matrix": {
"Package": "Matrix",
- "Version": "1.5-4",
+ "Version": "1.6-5",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
+ "grDevices",
"graphics",
"grid",
"lattice",
@@ -152,7 +201,20 @@
"stats",
"utils"
],
- "Hash": "e779c7d9f35cc364438578f334cffee2"
+ "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
+ },
+ "MatrixModels": {
+ "Package": "MatrixModels",
+ "Version": "0.5-3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Matrix",
+ "R",
+ "methods",
+ "stats"
+ ],
+ "Hash": "0776bf7526869e0286b0463cb72fb211"
},
"ModelMetrics": {
"Package": "ModelMetrics",
@@ -188,14 +250,14 @@
},
"Rcpp": {
"Package": "Rcpp",
- "Version": "1.0.13",
+ "Version": "1.0.14",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"methods",
"utils"
],
- "Hash": "f27411eb6d9c3dada5edd444b8416675"
+ "Hash": "e7bdd9ee90e96921ca8a0f1972d66682"
},
"RcppArmadillo": {
"Package": "RcppArmadillo",
@@ -261,6 +323,20 @@
],
"Hash": "75b4a36aeeed440ad03b996081190703"
},
+ "Rdpack": {
+ "Package": "Rdpack",
+ "Version": "2.6.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "methods",
+ "rbibutils",
+ "tools",
+ "utils"
+ ],
+ "Hash": "a9e2118c664c2cd694f03de074e8d4b3"
+ },
"Rfast": {
"Package": "Rfast",
"Version": "2.1.0",
@@ -275,6 +351,17 @@
],
"Hash": "79e8394e1fa06a4ae954b70ca9b16e8f"
},
+ "Rtsne": {
+ "Package": "Rtsne",
+ "Version": "0.17",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Rcpp",
+ "stats"
+ ],
+ "Hash": "f81f7764a3c3e310b1d40e1a8acee19e"
+ },
"SQUAREM": {
"Package": "SQUAREM",
"Version": "2021.1",
@@ -285,6 +372,20 @@
],
"Hash": "0cf10dab0d023d5b46a5a14387556891"
},
+ "SparseM": {
+ "Package": "SparseM",
+ "Version": "1.84-2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "graphics",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "e78499cbcbbca98200254bd171379165"
+ },
"Symobio": {
"Package": "Symobio",
"Version": "0.0.0.9000",
@@ -422,27 +523,28 @@
},
"bit": {
"Package": "bit",
- "Version": "4.5.0",
+ "Version": "4.5.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R"
],
- "Hash": "5dc7b2677d65d0e874fc4aaf0e879987"
+ "Hash": "f89f074e0e49bf1dbe3eba0a15a91476"
},
"bit64": {
"Package": "bit64",
- "Version": "4.5.2",
+ "Version": "4.6.0-1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"bit",
+ "graphics",
"methods",
"stats",
"utils"
],
- "Hash": "e84984bf5f12a18628d9a02322128dfd"
+ "Hash": "4f572fbc586294afff277db583b9060f"
},
"blob": {
"Package": "blob",
@@ -546,6 +648,41 @@
],
"Hash": "d7e13f49c19103ece9e58ad2d83a7354"
},
+ "car": {
+ "Package": "car",
+ "Version": "3.1-3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Formula",
+ "MASS",
+ "R",
+ "abind",
+ "carData",
+ "grDevices",
+ "graphics",
+ "lme4",
+ "mgcv",
+ "nlme",
+ "nnet",
+ "pbkrtest",
+ "quantreg",
+ "scales",
+ "stats",
+ "utils"
+ ],
+ "Hash": "82067bf302d1440b730437693a86406a"
+ },
+ "carData": {
+ "Package": "carData",
+ "Version": "3.0-5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "ac6cdb8552c61bd36b0e54d07cf2aab7"
+ },
"caret": {
"Package": "caret",
"Version": "7.0-1",
@@ -598,9 +735,13 @@
},
"cito": {
"Package": "cito",
- "Version": "1.1",
- "Source": "Repository",
- "Repository": "CRAN",
+ "Version": "1.1.1",
+ "Source": "GitHub",
+ "RemoteType": "github",
+ "RemoteHost": "api.github.com",
+ "RemoteRepo": "cito",
+ "RemoteUsername": "citoverse",
+ "RemoteSha": "46ee5c209e1241d7daa8262fdaf3904c841c36c7",
"Requirements": [
"R",
"abind",
@@ -611,11 +752,12 @@
"lme4",
"parabar",
"progress",
+ "rlang",
"tibble",
"torch",
"torchvision"
],
- "Hash": "087adef61576c3153598bc3859b17969"
+ "Hash": "2886d012c57d81f96151e8ed41af3ed3"
},
"class": {
"Package": "class",
@@ -750,13 +892,6 @@
"Repository": "CRAN",
"Hash": "f0acb9dcb71a9cd9d5ae233c5035b1c5"
},
- "commonmark": {
- "Package": "commonmark",
- "Version": "1.9.2",
- "Source": "Repository",
- "Repository": "CRAN",
- "Hash": "14eb0596f987c71535d07c3aff814742"
- },
"conflicted": {
"Package": "conflicted",
"Version": "1.2.0",
@@ -772,14 +907,31 @@
},
"coro": {
"Package": "coro",
- "Version": "1.0.4",
+ "Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"rlang"
],
- "Hash": "4b224d10f3b10ce791c6a4afd50abce3"
+ "Hash": "4998c8836ff95c90993a4eb8d853df71"
+ },
+ "cowplot": {
+ "Package": "cowplot",
+ "Version": "1.1.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "ggplot2",
+ "grDevices",
+ "grid",
+ "gtable",
+ "methods",
+ "rlang",
+ "scales"
+ ],
+ "Hash": "8ef2084dd7d28847b374e55440e4f8cb"
},
"cpp11": {
"Package": "cpp11",
@@ -932,6 +1084,30 @@
],
"Hash": "5c8646b40ba69146afc070aaea9f893c"
},
+ "doBy": {
+ "Package": "doBy",
+ "Version": "4.6.24",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Deriv",
+ "MASS",
+ "Matrix",
+ "R",
+ "boot",
+ "broom",
+ "cowplot",
+ "dplyr",
+ "ggplot2",
+ "methods",
+ "microbenchmark",
+ "modelr",
+ "rlang",
+ "tibble",
+ "tidyr"
+ ],
+ "Hash": "8ddf795104defe53c5392a588888ec68"
+ },
"doParallel": {
"Package": "doParallel",
"Version": "1.0.17",
@@ -1017,6 +1193,18 @@
],
"Hash": "27a09ca40266a1066d62ef5402dd51d6"
},
+ "ellipse": {
+ "Package": "ellipse",
+ "Version": "0.5.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "graphics",
+ "stats"
+ ],
+ "Hash": "4aa52573ccedf7dc635a0eb471944a36"
+ },
"ellipsis": {
"Package": "ellipsis",
"Version": "0.3.2",
@@ -1028,6 +1216,34 @@
],
"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
},
+ "emmeans": {
+ "Package": "emmeans",
+ "Version": "1.10.6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "estimability",
+ "graphics",
+ "methods",
+ "mvtnorm",
+ "numDeriv",
+ "stats",
+ "utils"
+ ],
+ "Hash": "6b0c6fcbdbefe525d2ee713f95880f90"
+ },
+ "estimability": {
+ "Package": "estimability",
+ "Version": "1.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats"
+ ],
+ "Hash": "21ec52af13afbcab1cb317567b639b0a"
+ },
"evaluate": {
"Package": "evaluate",
"Version": "1.0.0",
@@ -1109,6 +1325,16 @@
],
"Hash": "192053c276525c8495ccfd523aa8f2d1"
},
+ "flashClust": {
+ "Package": "flashClust",
+ "Version": "1.01-2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "09fb526c49460c4933bc077db6eba924"
+ },
"fontawesome": {
"Package": "fontawesome",
"Version": "0.5.2",
@@ -1152,14 +1378,14 @@
},
"fs": {
"Package": "fs",
- "Version": "1.6.4",
+ "Version": "1.6.5",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"methods"
],
- "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
+ "Hash": "7f48af39fa27711ea5fbd183b399920d"
},
"furrr": {
"Package": "furrr",
@@ -1287,6 +1513,22 @@
],
"Hash": "44c6a2f8202d5b7e878ea274b1092426"
},
+ "ggrepel": {
+ "Package": "ggrepel",
+ "Version": "0.9.6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp",
+ "ggplot2",
+ "grid",
+ "rlang",
+ "scales",
+ "withr"
+ ],
+ "Hash": "bc7c0d607038ae9cb4f539b47cbdbda7"
+ },
"globals": {
"Package": "globals",
"Version": "0.16.3",
@@ -1385,7 +1627,7 @@
},
"gtable": {
"Package": "gtable",
- "Version": "0.3.5",
+ "Version": "0.3.6",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -1394,9 +1636,10 @@
"glue",
"grid",
"lifecycle",
- "rlang"
+ "rlang",
+ "stats"
],
- "Hash": "e18861963cbc65a27736e02b3cd3c4a0"
+ "Hash": "de949855009e2d4d0e52a844e30617ae"
},
"hardhat": {
"Package": "hardhat",
@@ -1734,6 +1977,13 @@
],
"Hash": "d908914ae53b04d4c0c0fd72ecc35370"
},
+ "leaps": {
+ "Package": "leaps",
+ "Version": "3.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "06ddb0b69b0714ae929b1b6029d6faf0"
+ },
"libgeos": {
"Package": "libgeos",
"Version": "3.11.1-2",
@@ -1766,7 +2016,7 @@
},
"lme4": {
"Package": "lme4",
- "Version": "1.1-35.5",
+ "Version": "1.1-36",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -1784,11 +2034,12 @@
"nlme",
"nloptr",
"parallel",
+ "reformulas",
"splines",
"stats",
"utils"
],
- "Hash": "16a08fc75007da0d08e0c0388c7c33e6"
+ "Hash": "5f0e0456cdabdc82fbf1e4a7dcb5885e"
},
"lubridate": {
"Package": "lubridate",
@@ -1853,6 +2104,18 @@
],
"Hash": "3460beba7ccc8946249ba35327ba902a"
},
+ "microbenchmark": {
+ "Package": "microbenchmark",
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+ "R",
+ "graphics",
+ "stats"
+ ],
+ "Hash": "f9d226d88d4087d817d4e616626ce8e5"
+ },
"mime": {
"Package": "mime",
"Version": "0.12",
@@ -1901,6 +2164,16 @@
],
"Hash": "4f50122dc256b1b6996a4703fecea821"
},
+ "multcompView": {
+ "Package": "multcompView",
+ "Version": "0.1-10",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "grid"
+ ],
+ "Hash": "bd174e328b679e9a1ce589422002c72b"
+ },
"munsell": {
"Package": "munsell",
"Version": "0.5.1",
@@ -1912,6 +2185,17 @@
],
"Hash": "4fd8900853b746af55b81fda99da7695"
},
+ "mvtnorm": {
+ "Package": "mvtnorm",
+ "Version": "1.3-3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats"
+ ],
+ "Hash": "c7241e6be9d6df551a2e539a50f5c875"
+ },
"nlme": {
"Package": "nlme",
"Version": "3.1-162",
@@ -2006,7 +2290,7 @@
},
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- "Version": "1.1.1",
+ "Version": "1.4.2",
"Source": "Repository",
"Repository": "CRAN",
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@@ -2017,7 +2301,7 @@
"progress",
"utils"
],
- "Hash": "9f6ea158c643fb9fbbf096c958b51fdf"
+ "Hash": "9b5d3243600f0e70472ec4b376765f9c"
},
"parallelly": {
"Package": "parallelly",
@@ -2031,6 +2315,43 @@
],
"Hash": "6e8b139c1904f5e9e14c69db64453bbe"
},
+ "patchwork": {
+ "Package": "patchwork",
+ "Version": "1.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "cli",
+ "farver",
+ "ggplot2",
+ "grDevices",
+ "graphics",
+ "grid",
+ "gtable",
+ "rlang",
+ "stats",
+ "utils"
+ ],
+ "Hash": "e23fb9ecb1258207bcb763d78d513439"
+ },
+ "pbkrtest": {
+ "Package": "pbkrtest",
+ "Version": "0.5.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "MASS",
+ "Matrix",
+ "R",
+ "broom",
+ "doBy",
+ "dplyr",
+ "lme4",
+ "methods",
+ "numDeriv"
+ ],
+ "Hash": "938e6bbc4ac57534f8b43224506a8966"
+ },
"permute": {
"Package": "permute",
"Version": "0.9-7",
@@ -2100,12 +2421,11 @@
},
"pillar": {
"Package": "pillar",
- "Version": "1.9.0",
+ "Version": "1.10.1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"cli",
- "fansi",
"glue",
"lifecycle",
"rlang",
@@ -2113,7 +2433,7 @@
"utils",
"vctrs"
],
- "Hash": "15da5a8412f317beeee6175fbc76f4bb"
+ "Hash": "8b16b6097daef84cd3c40a6a7c5c9d86"
},
"pkgconfig": {
"Package": "pkgconfig",
@@ -2190,7 +2510,7 @@
},
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+ "Version": "3.8.5",
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"Repository": "CRAN",
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@@ -2199,7 +2519,7 @@
"ps",
"utils"
],
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+ "Hash": "790b1edafbd9980aeb8c3d77e3b0ba33"
},
"prodlim": {
"Package": "prodlim",
@@ -2276,14 +2596,14 @@
},
"ps": {
"Package": "ps",
- "Version": "1.8.0",
+ "Version": "1.8.1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"utils"
],
- "Hash": "4b9c8485b0c7eecdf0a9ba5132a45576"
+ "Hash": "b4404b1de13758dea1c0484ad0d48563"
},
"purrr": {
"Package": "purrr",
@@ -2310,6 +2630,24 @@
],
"Hash": "5f919ae5e7f83a6f91dcf2288943370d"
},
+ "quantreg": {
+ "Package": "quantreg",
+ "Version": "5.99.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "MASS",
+ "Matrix",
+ "MatrixModels",
+ "R",
+ "SparseM",
+ "graphics",
+ "methods",
+ "stats",
+ "survival"
+ ],
+ "Hash": "c48844cd7961de506a1b4d22b2e082c7"
+ },
"ragg": {
"Package": "ragg",
"Version": "1.3.3",
@@ -2345,6 +2683,18 @@
],
"Hash": "0e2829df8cb74a98179c886b023ffea8"
},
+ "rbibutils": {
+ "Package": "rbibutils",
+ "Version": "2.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "tools",
+ "utils"
+ ],
+ "Hash": "dfc034a172fd88fc66b1a703894c4185"
+ },
"readr": {
"Package": "readr",
"Version": "2.1.5",
@@ -2415,6 +2765,19 @@
],
"Hash": "fc6672e55fcd1b5c461a3529ff6b1b08"
},
+ "reformulas": {
+ "Package": "reformulas",
+ "Version": "0.4.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Matrix",
+ "Rdpack",
+ "methods",
+ "stats"
+ ],
+ "Hash": "d23beb08dca526d22ff47ce399260ba4"
+ },
"rematch": {
"Package": "rematch",
"Version": "2.0.0",
@@ -2501,14 +2864,14 @@
},
"rlang": {
"Package": "rlang",
- "Version": "1.1.4",
+ "Version": "1.1.5",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"utils"
],
- "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
+ "Hash": "724dcc1490cd7071ee75ca2994a5446e"
},
"rmarkdown": {
"Package": "rmarkdown",
@@ -2718,49 +3081,6 @@
],
"Hash": "5c47e84dc0a3ca761ae1d307889e796d"
},
- "shiny": {
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- "Version": "1.9.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "R6",
- "bslib",
- "cachem",
- "commonmark",
- "crayon",
- "fastmap",
- "fontawesome",
- "glue",
- "grDevices",
- "htmltools",
- "httpuv",
- "jsonlite",
- "later",
- "lifecycle",
- "methods",
- "mime",
- "promises",
- "rlang",
- "sourcetools",
- "tools",
- "utils",
- "withr",
- "xtable"
- ],
- "Hash": "6a293995a66e12c48d13aa1f957d09c7"
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- "sourcetools": {
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- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
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- "Hash": "5f5a7629f956619d519205ec475fe647"
- },
"sp": {
"Package": "sp",
"Version": "2.1-4",
@@ -3273,7 +3593,7 @@
},
"withr": {
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- "Version": "3.0.1",
+ "Version": "3.0.2",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -3281,7 +3601,7 @@
"grDevices",
"graphics"
],
- "Hash": "07909200e8bbe90426fbfeb73e1e27aa"
+ "Hash": "cc2d62c76458d425210d1eb1478b30b4"
},
"wk": {
"Package": "wk",
@@ -3319,18 +3639,6 @@
],
"Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61"
},
- "xtable": {
- "Package": "xtable",
- "Version": "1.8-4",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "stats",
- "utils"
- ],
- "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
- },
"yaml": {
"Package": "yaml",
"Version": "2.3.10",
--
GitLab