diff --git a/docs/src/fig/exponential.svg b/docs/src/fig/exponential.svg
deleted file mode 100644
index e56ced7..0000000
--- a/docs/src/fig/exponential.svg
+++ /dev/null
@@ -1,38 +0,0 @@
-
-
diff --git a/docs/src/fig/exponential_haz.svg b/docs/src/fig/exponential_haz.svg
new file mode 100644
index 0000000..7b5de66
--- /dev/null
+++ b/docs/src/fig/exponential_haz.svg
@@ -0,0 +1,38 @@
+
+
diff --git a/docs/src/fig/gamma.svg b/docs/src/fig/gamma.svg
deleted file mode 100644
index dcb20e5..0000000
--- a/docs/src/fig/gamma.svg
+++ /dev/null
@@ -1,38 +0,0 @@
-
-
diff --git a/docs/src/fig/gamma_haz.svg b/docs/src/fig/gamma_haz.svg
new file mode 100644
index 0000000..cd38e8f
--- /dev/null
+++ b/docs/src/fig/gamma_haz.svg
@@ -0,0 +1,40 @@
+
+
diff --git a/docs/src/fig/gengamma_haz.svg b/docs/src/fig/gengamma_haz.svg
new file mode 100644
index 0000000..9cb44a1
--- /dev/null
+++ b/docs/src/fig/gengamma_haz.svg
@@ -0,0 +1,38 @@
+
+
diff --git a/docs/src/fig/gengamma_pdf.svg b/docs/src/fig/gengamma_pdf.svg
deleted file mode 100644
index 44b4edd..0000000
--- a/docs/src/fig/gengamma_pdf.svg
+++ /dev/null
@@ -1,39 +0,0 @@
-
-
diff --git a/docs/src/fig/lognormal_haz.svg b/docs/src/fig/lognormal_haz.svg
new file mode 100644
index 0000000..27bc163
--- /dev/null
+++ b/docs/src/fig/lognormal_haz.svg
@@ -0,0 +1,39 @@
+
+
diff --git a/docs/src/fig/lognormal_pdf.svg b/docs/src/fig/lognormal_pdf.svg
deleted file mode 100644
index 0f239d0..0000000
--- a/docs/src/fig/lognormal_pdf.svg
+++ /dev/null
@@ -1,37 +0,0 @@
-
-
diff --git a/docs/src/fig/weibull_haz.svg b/docs/src/fig/weibull_haz.svg
new file mode 100644
index 0000000..9a22359
--- /dev/null
+++ b/docs/src/fig/weibull_haz.svg
@@ -0,0 +1,37 @@
+
+
diff --git a/docs/src/fig/survdist_pdf.svg b/docs/src/fig/weibull_pdf.svg
similarity index 85%
rename from docs/src/fig/survdist_pdf.svg
rename to docs/src/fig/weibull_pdf.svg
index fcee2f4..9fb2a22 100644
--- a/docs/src/fig/survdist_pdf.svg
+++ b/docs/src/fig/weibull_pdf.svg
@@ -1,39 +1,39 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/src/fig/weibull_risk.svg b/docs/src/fig/weibull_risk.svg
new file mode 100644
index 0000000..ea42f1b
--- /dev/null
+++ b/docs/src/fig/weibull_risk.svg
@@ -0,0 +1,38 @@
+
+
diff --git a/docs/src/fig/survdist_surv.svg b/docs/src/fig/weibull_surv.svg
similarity index 85%
rename from docs/src/fig/survdist_surv.svg
rename to docs/src/fig/weibull_surv.svg
index 333ef48..466e8ea 100644
--- a/docs/src/fig/survdist_surv.svg
+++ b/docs/src/fig/weibull_surv.svg
@@ -1,38 +1,38 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/src/parametric.md b/docs/src/parametric.md
index e12340c..44480f8 100644
--- a/docs/src/parametric.md
+++ b/docs/src/parametric.md
@@ -89,36 +89,53 @@ using Plots
aftdist(weibullfit, label="X=0, Z1=0, Z2=0", title="Weibull distribution")
# for specific covariate levels, include a 1.0 for the intercept
aftdist!(weibullfit, covlevels=[1.0, 1.0, 1.0, 1.0], color="red", label="X=1, Z1=1, Z2=1", npoints=300)
-savefig("survdist_pdf.svg")
+savefig("weibull_pdf.svg")
```
-
+
## Visualizing the distributions, survival distribution
```julia
-using Plots
-
aftdist(weibullfit, type="surv", label="X=0, Z1=0, Z2=0", title="Weibull distribution")
# for specific covariate levels, include a 1.0 for the intercept
aftdist!(weibullfit, type="surv", covlevels=[1.0, 1.0, 1.0, 1.0], color="red", label="X=1, Z1=1, Z2=1")
-savefig("survdist_surv.svg")
+savefig("weibull_surv.svg")
+```
+
+
+## Visualizing the distributions, hazard function
+```julia
+aftdist(weibullfit, type="haz", label="X=0, Z1=0, Z2=0", title="Weibull distribution")
+# for specific covariate levels, include a 1.0 for the intercept
+aftdist!(weibullfit, type="haz", covlevels=[1.0, 1.0, 1.0, 1.0], color="red", label="X=1, Z1=1, Z2=1", npoints=300)
+savefig("weibull_haz.svg")
```
-
+
+
+## Visualizing the distributions, risk function
+```julia
+aftdist(weibullfit, type="risk", label="X=0, Z1=0, Z2=0", title="Weibull distribution")
+# for specific covariate levels, include a 1.0 for the intercept
+aftdist!(weibullfit, type="risk", covlevels=[1.0, 1.0, 1.0, 1.0], color="red", label="X=1, Z1=1, Z2=1", npoints=300)
+savefig("weibull_risk.svg")
+```
+
+
## Other distributions
### Exponential
-Note that the exponential fit looks a lot like the Weibull fit. The log-scale parameter in the Weibull fit is close to zero. When it is exactly zero, then the Weibull distribution and exponential distribution are identical.
+Note that the exponential fit assumes a constant hazard.
```julia
expfit = survreg(@formula(Surv(in, out, d)~x+z1+z2), tab, wts=tab.wts, dist=LSurvival.Exponential())
-aftdist(expfit, type="surv", label="X=0, Z1=0, Z2=0", title="Exponential distribution")
+aftdist(expfit, type="haz", label="X=0, Z1=0, Z2=0", title="Exponential distribution")
# for specific covariate levels, include a 1.0 for the intercept
-aftdist!(expfit, type="surv", covlevels=[1.0, 1.0, 1.0, 1.0], color="red", label="X=1, Z1=1, Z2=1")
-savefig("exponential.svg")
+aftdist!(expfit, type="haz", covlevels=[1.0, 1.0, 1.0, 1.0], color="red", label="X=1, Z1=1, Z2=1")
+savefig("exponential_haz.svg")
```
-
+
Output:
@@ -149,11 +166,11 @@ Solver iterations: 14
# Here are results from a simpler model
dat1 = (time = [1, 1, 6, 6, 8, 9], status = [1, 0, 1, 1, 0, 1], x = [1, 1, 1, 0, 0, 0])
lognormalfit = survreg(@formula(Surv( time, status)~x), dat1, dist=LSurvival.Lognormal())
-aftdist(lognormalfit, label="X=0", title="Log-normal distribution")
-aftdist!(lognormalfit, covlevels=[1.0], color="red", label="X=1")
-savefig("lognormal_pdf.svg")
+aftdist(lognormalfit, type="haz", label="X=0", title="Log-normal distribution")
+aftdist!(lognormalfit, type="haz", covlevels=[1.0], color="red", label="X=1")
+savefig("lognormal_haz.svg")
```
-
+
```output
Maximum likelihood estimates (alpha=0.05):
@@ -175,12 +192,12 @@ Solver iterations: 9
### Gamma
```julia
gammafit = survreg(@formula(Surv(in, out, d)~x+z1+z2), tab, wts=tab.wts, dist=LSurvival.Gamma())
-aftdist(gammafit, type="surv", label="X=0, Z1=0, Z2=0", title="Gamma distribution")
+aftdist(gammafit, type="haz", label="X=0, Z1=0, Z2=0", title="Gamma distribution")
# for specific covariate levels, include a 1.0 for the intercept
-aftdist!(gammafit, type="surv", covlevels=[1.0, 1.0, 1.0, 1.0], color="red", label="X=1, Z1=1, Z2=1")
-savefig("gamma.svg")
+aftdist!(gammafit, type="haz", covlevels=[1.0, 1.0, 1.0, 1.0], color="red", label="X=1, Z1=1, Z2=1")
+savefig("gamma_haz.svg")
```
-
+
@@ -221,11 +238,11 @@ ggammafit2 = survreg(@formula(Surv(in, out, d)~x+z1+z2), tab, wts=tab.wts, dist=
)
ggammafit2 = survreg(@formula(Surv(t, d)~x), wtab, dist=LSurvival.GGamma())
-aftdist(ggammafit2, label="X=0", title="Generalized gamma distribution")
-aftdist!(ggammafit2, covlevels=[1.0], color="red", label="X=1")
-savefig("gengamma_pdf.svg")
+aftdist(ggammafit2, type="haz", label="X=0", title="Generalized gamma distribution")
+aftdist!(ggammafit2, type="haz", covlevels=[1.0], color="red", label="X=1")
+savefig("gengamma_haz.svg")
```
-
+
```output
┌ Warning: Optimizer reports model did not converge. Gradient: [-0.30185255746883194, -92.76305273476676, -12.51874622578631]
diff --git a/src/plot_recipes.jl b/src/plot_recipes.jl
index 003db1b..dac3c8a 100644
--- a/src/plot_recipes.jl
+++ b/src/plot_recipes.jl
@@ -368,9 +368,22 @@ dat2 = (
)
fte = survreg(@formula(Surv(enter, exit, status)~x), dat2)
+# density function
aftdist(fte, label="X=0")
aftdist!(fte, covlevels=[1.0, 2.0], color="red", label="X=1")
+# Survival function
+aftdist(fte, type="surv", label="X=0")
+aftdist!(fte, type="surv", covlevels=[1.0, 2.0], color="red", label="X=1")
+
+# hazard function
+aftdist(fte, type="haz", label="X=0")
+aftdist!(fte, type="haz", covlevels=[1.0, 2.0], color="red", label="X=1")
+
+# Cumulative incidence/risk function
+aftdist(fte, type="risk", label="X=0")
+aftdist!(fte, type="risk", covlevels=[1.0, 2.0], color="red", label="X=1")
+
```
"""
@recipe function f(h::AFTdist; type = "pdf", covlevels = nothing, npoints = 100)
@@ -389,14 +402,22 @@ aftdist!(fte, covlevels=[1.0, 2.0], color="red", label="X=1")
end
plotdist = name(typeof(dist))(sum(coefs .* covlevels), ft.P._S...)
times = range(timeminmax[1], timeminmax[2], npoints)
- if type == "pdf"
+ if type[1:3] == "pdf"
dist = [exp(lpdf(plotdist, t)) for t in times]
ylab --> "Density"
- elseif type == "surv"
+ elseif type[1:3] == "sur"
dist = [exp(lsurv(plotdist, t)) for t in times]
ylab --> "Survival"
+ elseif type[1:3] == "ris"
+ dist = 1 .- [exp(lsurv(plotdist, t)) for t in times]
+ ylab --> "Risk"
+ elseif type[1:3] == "haz"
+ S = [exp(lsurv(plotdist, t)) for t in times]
+ f = [exp(lpdf(plotdist, t)) for t in times]
+ dist = f ./ S
+ ylab --> "Hazard"
else
- throw("Type must either be 'surv' or 'pdf'")
+ throw("Type must either be 'surv', 'risk', 'haz' or 'pdf'")
end
xlab --> "Time"
grid --> false