diff --git a/README.Rmd b/README.Rmd
index 2d49fa1..8cc1306 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -54,7 +54,7 @@ using the package. Let's first generate some data:
library(netidmtpreg)
library(tidyverse)
-n_ind <- 1e2 # number of simulated individuals
+n_ind <- 5e2 # number of simulated individuals
# Generate exponentially distributed event times without censoring
synth_idm_data <- generate_uncensored_ind_exp_idm_data(
@@ -121,10 +121,10 @@ future::plan("sequential") # close the multisession, see future's documentation
We obtain a `TPreg` object with a dedicated plotting method using ggplot:
```{r plot}
-plot(net_estimate) + ggplot2::coord_cartesian(ylim = c(-5, 5))
+plot(net_estimate) + ggplot2::coord_cartesian(ylim = c(-5, 5), clip = "off")
```
-*Warning: note the use of `ggplot2::coord_cartesian` instead of `ggplot2::ylim`.
+*Warning: note the use of `ggplot2::coord_cartesian` with `clip="off"` instead of `ggplot2::ylim`.
The former acts as a "zoom" command, while the latter acts as a filter on input
data, and as such might prevent display of large confidence intervals.*
@@ -171,7 +171,7 @@ set the linetype accordingly.
autoplot(net_estimate, model = "Net estimate") +
autolayer(crude_estimate, model = "Crude estimate") +
autolayer(truth_estimate, model = "Ground Truth") +
- ggplot2::coord_cartesian(ylim = c(-5, 5))
+ ggplot2::coord_cartesian(ylim = c(-5, 5), xlim = c(0, 2), clip = "off")
```
These automated plotting routines are designed for quick inspection of the model.
diff --git a/README.md b/README.md
index 87b8d40..0bf50e4 100644
--- a/README.md
+++ b/README.md
@@ -56,7 +56,7 @@ library(tidyverse)
#> ✖ dplyr::lag() masks stats::lag()
#> ℹ Use the conflicted package () to force all conflicts to become errors
-n_ind <- 1e2 # number of simulated individuals
+n_ind <- 5e2 # number of simulated individuals
# Generate exponentially distributed event times without censoring
synth_idm_data <- generate_uncensored_ind_exp_idm_data(
@@ -127,17 +127,17 @@ We obtain a `TPreg` object with a dedicated plotting method using
ggplot:
``` r
-plot(net_estimate) + ggplot2::coord_cartesian(ylim = c(-5, 5))
+plot(net_estimate) + ggplot2::coord_cartesian(ylim = c(-5, 5), clip = "off")
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_line()`).
```
-*Warning: note the use of `ggplot2::coord_cartesian` instead of
-`ggplot2::ylim`. The former acts as a “zoom” command, while the latter
-acts as a filter on input data, and as such might prevent display of
-large confidence intervals.*
+*Warning: note the use of `ggplot2::coord_cartesian` with `clip="off"`
+instead of `ggplot2::ylim`. The former acts as a “zoom” command, while
+the latter acts as a filter on input data, and as such might prevent
+display of large confidence intervals.*
The obtained TPreg plots are composable ggplot objects that can be
combined. Let’s use this to compare our results with: 1) what would have
@@ -186,7 +186,7 @@ automatically set the linetype accordingly.
autoplot(net_estimate, model = "Net estimate") +
autolayer(crude_estimate, model = "Crude estimate") +
autolayer(truth_estimate, model = "Ground Truth") +
- ggplot2::coord_cartesian(ylim = c(-5, 5))
+ ggplot2::coord_cartesian(ylim = c(-5, 5), xlim = c(0, 2), clip = "off")
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_line()`).
#> Removed 1 row containing missing values or values outside the scale range
diff --git a/man/figures/README-plot-1.png b/man/figures/README-plot-1.png
index 236032e..ec2c5a7 100644
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diff --git a/man/figures/README-plot_compare-1.png b/man/figures/README-plot_compare-1.png
index 4cecd98..53b1dbf 100644
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