diff --git a/man/outstandR-package.Rd b/man/outstandR-package.Rd index 1888188..a645b08 100644 --- a/man/outstandR-package.Rd +++ b/man/outstandR-package.Rd @@ -18,7 +18,7 @@ Useful links: } \author{ -\strong{Maintainer}: Nathan Green \email{n.green@ucl.ac.uk} (\href{https://orcid.org/0000-0003-2745-1736}{ORCID}) (02jx3x895) [copyright holder] +\strong{Maintainer}: Nathan Green \email{n.green@ucl.ac.uk} (\href{https://orcid.org/0000-0003-2745-1736}{ORCID}) (\href{https://ror.org/02jx3x895}{ROR}) [copyright holder] Authors: \itemize{ diff --git a/scripts/exercises2.html b/scripts/exercises2.html index 9e84347..85b25dd 100644 --- a/scripts/exercises2.html +++ b/scripts/exercises2.html @@ -315,8 +315,8 @@
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
Chain 1:
-Chain 1: Gradient evaluation took 0.000114 seconds
-Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.14 seconds.
+Chain 1: Gradient evaluation took 5.3e-05 seconds
+Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.53 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
@@ -327,15 +327,15 @@ Function Arguments
Chain 1: Iteration: 1500 / 2000 [ 75%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
-Chain 1: Elapsed Time: 0.287 seconds (Warm-up)
-Chain 1: 0.293 seconds (Sampling)
-Chain 1: 0.58 seconds (Total)
+Chain 1: Elapsed Time: 0.223 seconds (Warm-up)
+Chain 1: 0.208 seconds (Sampling)
+Chain 1: 0.431 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
Chain 2:
-Chain 2: Gradient evaluation took 2.1e-05 seconds
-Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.21 seconds.
+Chain 2: Gradient evaluation took 1.8e-05 seconds
+Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
@@ -346,9 +346,9 @@ Function Arguments
Chain 2: Iteration: 1500 / 2000 [ 75%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
-Chain 2: Elapsed Time: 0.261 seconds (Warm-up)
-Chain 2: 0.246 seconds (Sampling)
-Chain 2: 0.507 seconds (Total)
+Chain 2: Elapsed Time: 0.216 seconds (Warm-up)
+Chain 2: 0.204 seconds (Sampling)
+Chain 2: 0.42 seconds (Total)
Chain 2:
@@ -369,8 +369,8 @@
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
Chain 1:
-Chain 1: Gradient evaluation took 2.6e-05 seconds
-Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
+Chain 1: Gradient evaluation took 2.4e-05 seconds
+Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
@@ -387,15 +387,15 @@ Function Arguments
Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
-Chain 1: Elapsed Time: 0.281 seconds (Warm-up)
-Chain 1: 0.253 seconds (Sampling)
-Chain 1: 0.534 seconds (Total)
+Chain 1: Elapsed Time: 0.229 seconds (Warm-up)
+Chain 1: 0.21 seconds (Sampling)
+Chain 1: 0.439 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
Chain 2:
-Chain 2: Gradient evaluation took 2e-05 seconds
-Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds.
+Chain 2: Gradient evaluation took 1.6e-05 seconds
+Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.16 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
@@ -412,9 +412,9 @@ Function Arguments
Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
-Chain 2: Elapsed Time: 0.261 seconds (Warm-up)
-Chain 2: 0.258 seconds (Sampling)
-Chain 2: 0.519 seconds (Total)
+Chain 2: Elapsed Time: 0.211 seconds (Warm-up)
+Chain 2: 0.216 seconds (Sampling)
+Chain 2: 0.427 seconds (Total)
Chain 2:
@@ -570,8 +570,8 @@
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
Chain 1:
-Chain 1: Gradient evaluation took 2.8e-05 seconds
-Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
+Chain 1: Gradient evaluation took 2.5e-05 seconds
+Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
@@ -582,15 +582,15 @@ Function Arguments
Chain 1: Iteration: 1500 / 2000 [ 75%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
-Chain 1: Elapsed Time: 0.269 seconds (Warm-up)
-Chain 1: 0.252 seconds (Sampling)
-Chain 1: 0.521 seconds (Total)
+Chain 1: Elapsed Time: 0.225 seconds (Warm-up)
+Chain 1: 0.205 seconds (Sampling)
+Chain 1: 0.43 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
Chain 2:
-Chain 2: Gradient evaluation took 2.2e-05 seconds
-Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
+Chain 2: Gradient evaluation took 1.7e-05 seconds
+Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
@@ -601,9 +601,9 @@ Function Arguments
Chain 2: Iteration: 1500 / 2000 [ 75%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
-Chain 2: Elapsed Time: 0.278 seconds (Warm-up)
-Chain 2: 0.259 seconds (Sampling)
-Chain 2: 0.537 seconds (Total)
+Chain 2: Elapsed Time: 0.215 seconds (Warm-up)
+Chain 2: 0.204 seconds (Sampling)
+Chain 2: 0.419 seconds (Total)
Chain 2:
@@ -659,8 +659,8 @@
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
Chain 1:
-Chain 1: Gradient evaluation took 2.6e-05 seconds
-Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
+Chain 1: Gradient evaluation took 3.2e-05 seconds
+Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
@@ -677,15 +677,15 @@ Function Arguments
Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
-Chain 1: Elapsed Time: 0.283 seconds (Warm-up)
-Chain 1: 0.254 seconds (Sampling)
-Chain 1: 0.537 seconds (Total)
+Chain 1: Elapsed Time: 0.227 seconds (Warm-up)
+Chain 1: 0.209 seconds (Sampling)
+Chain 1: 0.436 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
Chain 2:
-Chain 2: Gradient evaluation took 2.2e-05 seconds
-Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
+Chain 2: Gradient evaluation took 1.7e-05 seconds
+Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
@@ -702,9 +702,9 @@ Function Arguments
Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
-Chain 2: Elapsed Time: 0.259 seconds (Warm-up)
-Chain 2: 0.264 seconds (Sampling)
-Chain 2: 0.523 seconds (Total)
+Chain 2: Elapsed Time: 0.21 seconds (Warm-up)
+Chain 2: 0.224 seconds (Sampling)
+Chain 2: 0.434 seconds (Total)
Chain 2:
@@ -1029,8 +1029,8 @@
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
-Chain 1: Gradient evaluation took 4.8e-05 seconds
-Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
+Chain 1: Gradient evaluation took 6.8e-05 seconds
+Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.68 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
@@ -1041,15 +1041,15 @@ Exercises
Chain 1: Iteration: 1500 / 2000 [ 75%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
-Chain 1: Elapsed Time: 0.09 seconds (Warm-up)
-Chain 1: 0.098 seconds (Sampling)
-Chain 1: 0.188 seconds (Total)
+Chain 1: Elapsed Time: 0.121 seconds (Warm-up)
+Chain 1: 0.14 seconds (Sampling)
+Chain 1: 0.261 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
-Chain 2: Gradient evaluation took 3.4e-05 seconds
-Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
+Chain 2: Gradient evaluation took 2.1e-05 seconds
+Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.21 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
@@ -1060,9 +1060,9 @@ Exercises
Chain 2: Iteration: 1500 / 2000 [ 75%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
-Chain 2: Elapsed Time: 0.087 seconds (Warm-up)
-Chain 2: 0.102 seconds (Sampling)
-Chain 2: 0.189 seconds (Total)
+Chain 2: Elapsed Time: 0.099 seconds (Warm-up)
+Chain 2: 0.14 seconds (Sampling)
+Chain 2: 0.239 seconds (Total)
Chain 2:
@@ -1102,15 +1102,15 @@ 3. Calculate the unadjusted (naive) estimates for comparison.
-To see exactly how much our PAIC methods moved the needle, we will calculate the naive estimators. Let \(p_A\) and \(p_{C(AC)}\) be the raw probabilities of the event in the IPD trial, and let \(p_B\) and \(p_{C(BC)}\) be the raw probabilities in the ALD trial.
+To see exactly how much our PAIC methods moved the needle, we will calculate the naive estimators. Let \(p_{A(AC)}\) and \(p_{C(AC)}\) be the raw probabilities of the event in the IPD trial, and let \(p_{B(BC)}\) and \(p_{C(BC)}\) be the raw probabilities in the ALD trial.
\[\hat{\Delta}_{AB}^{\text{naive\_anchored}} = (p_A - p_{C(AC)}) - (p_B - p_{C(BC)})\]
+\[\hat{\Delta}_{AB}^{\text{naive\_anchored}} = (p_{A(AC)} - p_{C(AC)}) - (p_{B(BC)} - p_{C(BC)})\]
\[\hat{\Delta}_{AB}^{\text{naive\_unanchored}} = p_A - p_B\]
+\[\hat{\Delta}_{AB}^{\text{naive\_unanchored}} = p_{A(AC)} - p_{B(BC)}\]