From 773923e0da9bc18f0f4e9f2bb9347f0e8490e92d Mon Sep 17 00:00:00 2001
From: Steve Phelps <sphelps@sphelps.net>
Date: Sun, 21 Jan 2024 13:55:51 +0000
Subject: [PATCH] gemeans contrast for posthoc testing

---
 environment-frozen.yml      |  4 ++++
 environment.yml             |  1 +
 jupyter-book/R-MixedModel.R | 27 +++++++++++++--------------
 3 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/environment-frozen.yml b/environment-frozen.yml
index f150183..9d55ff7 100644
--- a/environment-frozen.yml
+++ b/environment-frozen.yml
@@ -484,6 +484,7 @@ dependencies:
   - r-lme4=1.1_35.1=r43ha503ecb_0
   - r-lmtest=0.9_40=r43h61816a4_2
   - r-loo=2.6.0=r43hc72bb7e_1
+  - r-lsmeans=2.30_0=r43hc72bb7e_4
   - r-lubridate=1.9.3=r43h57805ef_0
   - r-magrittr=2.0.3=r43h57805ef_2
   - r-maptools=1.1_8=r43h57805ef_0
@@ -505,6 +506,7 @@ dependencies:
   - r-modelmetrics=1.2.2.2=r43ha503ecb_3
   - r-modelr=0.1.11=r43hc72bb7e_1
   - r-modelsummary=1.4.3=r43hc72bb7e_0
+  - r-multcomp=1.4_25=r43hc72bb7e_0
   - r-munsell=0.5.0=r43hc72bb7e_1006
   - r-mvtnorm=1.2_4=r43hd9ac46e_0
   - r-nleqslv=3.3.5=r43h61816a4_0
@@ -580,6 +582,7 @@ dependencies:
   - r-rstatix=0.7.2=r43hc72bb7e_1
   - r-rstudioapi=0.15.0=r43hc72bb7e_0
   - r-rvest=1.0.3=r43hc72bb7e_2
+  - r-sandwich=3.1_0=r43hc72bb7e_0
   - r-sass=0.4.8=r43ha503ecb_0
   - r-scales=1.3.0=r43hc72bb7e_0
   - r-selectr=0.4_2=r43hc72bb7e_3
@@ -612,6 +615,7 @@ dependencies:
   - r-tensora=0.36.2.1=r43h57805ef_0
   - r-texreg=1.39.3=r43hc72bb7e_0
   - r-textshaping=0.3.7=r43hd87b9d6_0
+  - r-th.data=1.1_2=r43hc72bb7e_1
   - r-threejs=0.3.3=r43hc72bb7e_3
   - r-tibble=3.2.1=r43h57805ef_2
   - r-tidyr=1.3.0=r43ha503ecb_1
diff --git a/environment.yml b/environment.yml
index 9b42372..2fd2d62 100644
--- a/environment.yml
+++ b/environment.yml
@@ -52,6 +52,7 @@ dependencies:
   - r-cmdstanr
   - r-languageserver
   - r-marginaleffects
+  - r-multcomp
   - pip
   - pip:
     - -e ./
diff --git a/jupyter-book/R-MixedModel.R b/jupyter-book/R-MixedModel.R
index eb7e630..01f5445 100644
--- a/jupyter-book/R-MixedModel.R
+++ b/jupyter-book/R-MixedModel.R
@@ -58,16 +58,16 @@ use_condaenv("llm-cooperation")
 llm_coop <- import("llm_cooperation.main")
 
 # %%
-config <- llm_coop$Configuration(
-  grid = dict(
-    temperature = list(0.1),
-    model = list("gpt-3.5-turbo-1106"),
-    max_tokens = list(500)
-  ),
-  experiment_names = list("dilemma"),
-  num_participant_samples = 30,
-  num_replications = 3
-)
+# config <- llm_coop$Configuration(
+#   grid = dict(
+#     temperature = list(0.1),
+#     model = list("gpt-3.5-turbo-1106"),
+#     max_tokens = list(500)
+#   ),
+#   experiment_names = list("dilemma"),
+#   num_participant_samples = 30,
+#   num_replications = 3
+# )
 
 # %%
 config <- llm_coop$Configuration(
@@ -440,8 +440,7 @@ summary(model_pd_2)
 
 # %%
 texreg(
-
-  model_pd_1,
+  model_pd_2,
   caption = "Fitted model for Prisoners Dilemma",
   label = "table:pd-estimates",
   file = "pd-estimates.tex",
@@ -461,7 +460,7 @@ texreg(
 
 # %%
 pdf("figs/ranef_hist_pd.pdf")
-hist(ranef(model_pd_1)$cond$Participant_id[, 1])
+hist(ranef(model_pd_2)$cond$Participant_id[, 1])
 dev.off()
 
 # %%
@@ -723,7 +722,7 @@ combined.plots
 options(repr.plot.height = 12)
 pdf("figs/residuals-plots.pdf")
 simulationOutput <-
-  simulateResiduals(fittedModel = model_pd_1, plot = TRUE, integerResponse = TRUE)
+  simulateResiduals(fittedModel = model_pd_2, plot = TRUE, integerResponse = TRUE)
 dev.off()
 
 # %%