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inst/doc/examples.R
In slouch: Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses
## ----setup, cache=FALSE, include=FALSE----------------------------------------
library(knitr)
knitr::opts_knit$set(global.par = TRUE)
#output <- opts_knit$get("rmarkdown.pandoc.to")
#if (output=="html") opts_chunk$set(fig.width=11, fig.height=11)
#if (output=="docx") opts_chunk$set(fig.width=6, fig.height=6)
opts_chunk$set(collapse = TRUE, results = 'markup')
par(mar = rep(0,4))
## ----eval = FALSE-------------------------------------------------------------
# install.packages("slouch")
## ---- warning=FALSE, echo = TRUE, message = FALSE, highlight = TRUE, fig.width = 7, fig.height = 5----
# Load necessary packages
library(ape)
library(slouch)
## Load the phylogenetic tree with annotation data
data(artiodactyla)
phy <- artiodactyla
## Load the neocortex dataset
data(neocortex)
## Plot the tree
plot(ladderize(phy), cex = 0.6)
## ----include = FALSE----------------------------------------------------------
par(mar = c(5.1, 4.1, 4.1, 2.1))
## ---- fig.width=7, fig.height = 4, highlight = TRUE---------------------------
## Check whether they are lined up correctly
neocortex$species == phy$tip.label
## ---- highlight = TRUE--------------------------------------------------------
neocortex <- neocortex[match(phy$tip.label, neocortex$species), ]
## Check if they line up again
neocortex$species == phy$tip.label
## ---- fig.show='hold', highlight = TRUE, fig.width=7, fig.height = 4, fig.cap = "Scatter plot of mean log neocortex area (mm$^2$) on mean log brain mass (g).", fig.pos = "H", out.extra = ""----
braincentered <- neocortex$brain_mass_g_log_mean - mean(neocortex$brain_mass_g_log_mean)
plot(x = braincentered,
y = neocortex$neocortex_area_mm2_log_mean,
xlab = "Mean log brain mass (g)",
ylab = "Mean log neocortex area (mm2)")
## ---- highlight = TRUE, fig.width=7, fig.height = 4, fig.cap="The path-trajectory of the L-BFGS-B hillclimber algorithm.", fig.pos = "H"----
model0 <- slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean)
## ---- hightlight = TRUE-------------------------------------------------------
print(model0)
## ---- hightlight = TRUE-------------------------------------------------------
summary(model0)
## ---- highlight=TRUE, fig.pos = "H"-------------------------------------------
model3 <- slouch.fit(phy = phy,
hl_values = 1,
vy_values = 0.05,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
random.cov = braincentered)
model3
## ---- highlight=TRUE, fig.pos = "H"-------------------------------------------
model3 <- slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
random.cov = braincentered,
mv.random.cov = neocortex$brain_se_squared)
## ---- fig.show='asis', highlight = TRUE, fig.width=7, fig.height = 4, fig.cap = "The evolutionary (black) and optimal (orange) regression lines for the model of mean log neocortex area (mm$^2$) on mean log brain mass (g), both corrected for bias due to measurement error in mean log brain mass.", fig.pos = "H", out.extra=""----
plot(x = braincentered,
y = neocortex$neocortex_area_mm2_log_mean,
xlab = "Mean log brain mass (g)",
ylab = "Mean log neocortex area (mm2)")
abline(model3$beta_evolutionary$coefficients_bias_corr[,1],
col = "black", lwd = 2)
abline(model3$beta_primary$coefficients_bias_corr[,1],
col = "orange", lwd = 2)
## ---- highlight = TRUE, fig.width=7, fig.height = 4, fig.pos = "H", out.extra=""----
bodycentered <- neocortex$body_mass_g_log_mean - mean(neocortex$body_mass_g_log_mean)
model4 <-
slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
random.cov = cbind(braincentered,
bodycentered),
mv.random.cov = cbind(neocortex$brain_se_squared,
neocortex$body_se_squared))
model4
## ---- highlight = TRUE, fig.width=7, fig.height = 4, eval=F, fig.pos = "H", out.extra=""----
# model5 <- slouch.fit(phy = phy,
# species = neocortex$species,
# response = neocortex$neocortex_area_mm2_log_mean,
# mv.response = neocortex$neocortex_se_squared,
# random.cov = braincentered,
# mv.random.cov = neocortex$brain_se_squared,
# estimate.Ya = TRUE,
# estimate.bXa = TRUE)
## ----include = FALSE, fig.pos = "H"-------------------------------------------
par(mar = rep(0, 4))
## ---- fig.width=7, fig.height = 4, highlight = TRUE---------------------------
## Inspect the internal node regimes
## These have order n+1, n+2, n+3 ...
internal_regimes <- factor(phy$node.label)
## Concatenate tip and internal regimes. These will have order 1,2,3 ...
regimes <- c(neocortex$diet, internal_regimes)
## Pick out the regimes of the edges, in the order of phy$edge
edge_regimes <- factor(regimes[phy$edge[,2]])
plot(phy,
edge.color = c("Black", "Orange", "blue")[edge_regimes],
edge.width = 3, cex = 0.6)
## ----include = FALSE----------------------------------------------------------
par(mar = c(5.1, 4.1, 4.1, 2.1))
## ---- highlight = TRUE, fig.pos = "H"-----------------------------------------
model6 <- slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
direct.cov = neocortex$brain_mass_g_log_mean,
fixed.fact = neocortex$diet)
model6
## ---- fig.width = 7, fig.height = 4, highlight = TRUE, fig.pos = "H", out.extra=""----
model7 <- slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
direct.cov = neocortex$brain_mass_g_log_mean,
mv.direct.cov = neocortex$brain_se_squared)
model7
## ---- fig.width = 7, fig.height = 4, highlight = TRUE, fig.pos = "H"----------
model8 <- brown.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared)
model8
## ---- fig.width = 7, fig.height = 4, highlight = TRUE, fig.pos = "H"----------
model9 <- brown.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
fixed.fact = neocortex$diet)
model9
## -----------------------------------------------------------------------------
model9$beta_primary$trend_diff
## ---- fig.width = 7, fig.height = 4, highlight = TRUE, fig.pos = "H"----------
model10 <- brown.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
random.cov = braincentered,
mv.random.cov = neocortex$brain_se_squared)
model10
## -----------------------------------------------------------------------------
model10$beta_evolutionary$coefficients
## -----------------------------------------------------------------------------
## The manual way
h <- c(0.01, 0.1, 1, 5, 10, 15, 20, 100)
vy <- h
## Using the seq function
h <- seq(from = 0.001, to = 100, length.out = 15)
vy <- seq(from = 0.001, to = 5, length.out = 15)
## Using a seq function with logarithmically spaced steps
h <- lseq(from = 0.001, to = 100, length.out = 15)
vy <- lseq(from = 0.001, to = 5, length.out = 15)
## ---- fig.show='asis', fig.width=6, fig.height = 4, fig.cap = "Three-dimensional joint support region for the estimates of half-lives and stationary variances, for the single-optimum model.", highlight = TRUE, warning=FALSE, fig.pos = "H", out.extra=""----
model_grid_0 <- slouch.fit(phy = phy,
hl_values = seq(0.001, 12, length.out = 20),
vy_values = seq(0.1, 1, length.out = 20),
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
hillclimb = FALSE)
plot(model_grid_0)
## ---- fig.show='asis', fig.width=6, fig.height = 4, fig.cap = "Another slice of the log likelihood surface for the same single-optimum model", highlight = TRUE, warning=FALSE, fig.pos = "H", out.extra=""----
model_grid_1 <- slouch.fit(phy = phy,
hl_values = seq(0.001, 150, length.out = 20),
vy_values = seq(0.1, 2.5, length.out = 20),
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
hillclimb = FALSE)
plot(model_grid_1)
## ---- highlight = TRUE, eval = FALSE, fig.width=7, fig.height = 4, fig.pos = "H", out.extra=""----
# library(plotly)
# p <- plot_ly(x = model0$supportplot$hl,
# y = model0$supportplot$vy,
# z = model0$supportplot$z) %>%
# add_surface() %>%
# layout(title = "Grid-search",
# scene = list(xaxis = list(title = "Phylogenetic half-life"),
# yaxis = list(title = "Stationary variance"),
# zaxis = list(title = "Log-likelihood")))
#
# p
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## ----setup, cache=FALSE, include=FALSE----------------------------------------
library(knitr)
knitr::opts_knit$set(global.par = TRUE)
#output <- opts_knit$get("rmarkdown.pandoc.to")
#if (output=="html") opts_chunk$set(fig.width=11, fig.height=11)
#if (output=="docx") opts_chunk$set(fig.width=6, fig.height=6)
opts_chunk$set(collapse = TRUE, results = 'markup')
par(mar = rep(0,4))
## ----eval = FALSE-------------------------------------------------------------
# install.packages("slouch")
## ---- warning=FALSE, echo = TRUE, message = FALSE, highlight = TRUE, fig.width = 7, fig.height = 5----
# Load necessary packages
library(ape)
library(slouch)
## Load the phylogenetic tree with annotation data
data(artiodactyla)
phy <- artiodactyla
## Load the neocortex dataset
data(neocortex)
## Plot the tree
plot(ladderize(phy), cex = 0.6)
## ----include = FALSE----------------------------------------------------------
par(mar = c(5.1, 4.1, 4.1, 2.1))
## ---- fig.width=7, fig.height = 4, highlight = TRUE---------------------------
## Check whether they are lined up correctly
neocortex$species == phy$tip.label
## ---- highlight = TRUE--------------------------------------------------------
neocortex <- neocortex[match(phy$tip.label, neocortex$species), ]
## Check if they line up again
neocortex$species == phy$tip.label
## ---- fig.show='hold', highlight = TRUE, fig.width=7, fig.height = 4, fig.cap = "Scatter plot of mean log neocortex area (mm$^2$) on mean log brain mass (g).", fig.pos = "H", out.extra = ""----
braincentered <- neocortex$brain_mass_g_log_mean - mean(neocortex$brain_mass_g_log_mean)
plot(x = braincentered,
y = neocortex$neocortex_area_mm2_log_mean,
xlab = "Mean log brain mass (g)",
ylab = "Mean log neocortex area (mm2)")
## ---- highlight = TRUE, fig.width=7, fig.height = 4, fig.cap="The path-trajectory of the L-BFGS-B hillclimber algorithm.", fig.pos = "H"----
model0 <- slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean)
## ---- hightlight = TRUE-------------------------------------------------------
print(model0)
## ---- hightlight = TRUE-------------------------------------------------------
summary(model0)
## ---- highlight=TRUE, fig.pos = "H"-------------------------------------------
model3 <- slouch.fit(phy = phy,
hl_values = 1,
vy_values = 0.05,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
random.cov = braincentered)
model3
## ---- highlight=TRUE, fig.pos = "H"-------------------------------------------
model3 <- slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
random.cov = braincentered,
mv.random.cov = neocortex$brain_se_squared)
## ---- fig.show='asis', highlight = TRUE, fig.width=7, fig.height = 4, fig.cap = "The evolutionary (black) and optimal (orange) regression lines for the model of mean log neocortex area (mm$^2$) on mean log brain mass (g), both corrected for bias due to measurement error in mean log brain mass.", fig.pos = "H", out.extra=""----
plot(x = braincentered,
y = neocortex$neocortex_area_mm2_log_mean,
xlab = "Mean log brain mass (g)",
ylab = "Mean log neocortex area (mm2)")
abline(model3$beta_evolutionary$coefficients_bias_corr[,1],
col = "black", lwd = 2)
abline(model3$beta_primary$coefficients_bias_corr[,1],
col = "orange", lwd = 2)
## ---- highlight = TRUE, fig.width=7, fig.height = 4, fig.pos = "H", out.extra=""----
bodycentered <- neocortex$body_mass_g_log_mean - mean(neocortex$body_mass_g_log_mean)
model4 <-
slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
random.cov = cbind(braincentered,
bodycentered),
mv.random.cov = cbind(neocortex$brain_se_squared,
neocortex$body_se_squared))
model4
## ---- highlight = TRUE, fig.width=7, fig.height = 4, eval=F, fig.pos = "H", out.extra=""----
# model5 <- slouch.fit(phy = phy,
# species = neocortex$species,
# response = neocortex$neocortex_area_mm2_log_mean,
# mv.response = neocortex$neocortex_se_squared,
# random.cov = braincentered,
# mv.random.cov = neocortex$brain_se_squared,
# estimate.Ya = TRUE,
# estimate.bXa = TRUE)
## ----include = FALSE, fig.pos = "H"-------------------------------------------
par(mar = rep(0, 4))
## ---- fig.width=7, fig.height = 4, highlight = TRUE---------------------------
## Inspect the internal node regimes
## These have order n+1, n+2, n+3 ...
internal_regimes <- factor(phy$node.label)
## Concatenate tip and internal regimes. These will have order 1,2,3 ...
regimes <- c(neocortex$diet, internal_regimes)
## Pick out the regimes of the edges, in the order of phy$edge
edge_regimes <- factor(regimes[phy$edge[,2]])
plot(phy,
edge.color = c("Black", "Orange", "blue")[edge_regimes],
edge.width = 3, cex = 0.6)
## ----include = FALSE----------------------------------------------------------
par(mar = c(5.1, 4.1, 4.1, 2.1))
## ---- highlight = TRUE, fig.pos = "H"-----------------------------------------
model6 <- slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
direct.cov = neocortex$brain_mass_g_log_mean,
fixed.fact = neocortex$diet)
model6
## ---- fig.width = 7, fig.height = 4, highlight = TRUE, fig.pos = "H", out.extra=""----
model7 <- slouch.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
direct.cov = neocortex$brain_mass_g_log_mean,
mv.direct.cov = neocortex$brain_se_squared)
model7
## ---- fig.width = 7, fig.height = 4, highlight = TRUE, fig.pos = "H"----------
model8 <- brown.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared)
model8
## ---- fig.width = 7, fig.height = 4, highlight = TRUE, fig.pos = "H"----------
model9 <- brown.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
fixed.fact = neocortex$diet)
model9
## -----------------------------------------------------------------------------
model9$beta_primary$trend_diff
## ---- fig.width = 7, fig.height = 4, highlight = TRUE, fig.pos = "H"----------
model10 <- brown.fit(phy = phy,
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
mv.response = neocortex$neocortex_se_squared,
random.cov = braincentered,
mv.random.cov = neocortex$brain_se_squared)
model10
## -----------------------------------------------------------------------------
model10$beta_evolutionary$coefficients
## -----------------------------------------------------------------------------
## The manual way
h <- c(0.01, 0.1, 1, 5, 10, 15, 20, 100)
vy <- h
## Using the seq function
h <- seq(from = 0.001, to = 100, length.out = 15)
vy <- seq(from = 0.001, to = 5, length.out = 15)
## Using a seq function with logarithmically spaced steps
h <- lseq(from = 0.001, to = 100, length.out = 15)
vy <- lseq(from = 0.001, to = 5, length.out = 15)
## ---- fig.show='asis', fig.width=6, fig.height = 4, fig.cap = "Three-dimensional joint support region for the estimates of half-lives and stationary variances, for the single-optimum model.", highlight = TRUE, warning=FALSE, fig.pos = "H", out.extra=""----
model_grid_0 <- slouch.fit(phy = phy,
hl_values = seq(0.001, 12, length.out = 20),
vy_values = seq(0.1, 1, length.out = 20),
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
hillclimb = FALSE)
plot(model_grid_0)
## ---- fig.show='asis', fig.width=6, fig.height = 4, fig.cap = "Another slice of the log likelihood surface for the same single-optimum model", highlight = TRUE, warning=FALSE, fig.pos = "H", out.extra=""----
model_grid_1 <- slouch.fit(phy = phy,
hl_values = seq(0.001, 150, length.out = 20),
vy_values = seq(0.1, 2.5, length.out = 20),
species = neocortex$species,
response = neocortex$neocortex_area_mm2_log_mean,
hillclimb = FALSE)
plot(model_grid_1)
## ---- highlight = TRUE, eval = FALSE, fig.width=7, fig.height = 4, fig.pos = "H", out.extra=""----
# library(plotly)
# p <- plot_ly(x = model0$supportplot$hl,
# y = model0$supportplot$vy,
# z = model0$supportplot$z) %>%
# add_surface() %>%
# layout(title = "Grid-search",
# scene = list(xaxis = list(title = "Phylogenetic half-life"),
# yaxis = list(title = "Stationary variance"),
# zaxis = list(title = "Log-likelihood")))
#
# p
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R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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