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Commitf5303b7

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Merge pull request#32 from gmcmacran/add_log_normal
Add log normal
2 parentsd55b69e +883c552 commitf5303b7

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127 files changed

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‎R Code/one sample/log normal sim.R‎

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library(LRTesteR)
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library(tidyverse)
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library(stringr)
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################
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# Simulation settings
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################
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compiler::enableJIT(3)
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B<-5000
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N<-500
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################
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# Type I
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################
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mus<- seq(-4,4,2)
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variances<- c(1,3,5)
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18+
sim_results<- tibble()
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for (muinmus) {
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for (varianceinvariances) {
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for (altin c("two.sided","less","greater")) {
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stats<- vector(mode="numeric",length=B)
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pvalues<- vector(mode="numeric",length=B)
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alts<- vector(mode="character",length=B)
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CI_LBs<- vector(mode="numeric",length=B)
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CI_UBs<- vector(mode="numeric",length=B)
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testName<-"log_normal_mu_one_sample"
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for (iin1:B) {
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set.seed(i)
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x<- rlnorm(n=N,mean=mu,sd=variance^.5)
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test<- log_normal_mu_one_sample(x,mu,alt)
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stats[i]<-test$statistic
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pvalues[i]<-test$p.value
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alts[i]<-test$alternative
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CI_LBs[i]<-test$conf.int[1]
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CI_UBs[i]<-test$conf.int[2]
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}
38+
temp<- tibble(test=testName,mu=mu,variance=variance,stat=stats,pvalue=pvalues,alt=alts,CI_LB=CI_LBs,CI_UB=CI_UBs)
39+
sim_results<-sim_results %>% bind_rows(temp)
40+
rm(stats,pvalues,alts,testName,temp,i)
41+
}
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43+
for (altin c("two.sided","less","greater")) {
44+
stats<- vector(mode="numeric",length=B)
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pvalues<- vector(mode="numeric",length=B)
46+
alts<- vector(mode="character",length=B)
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CI_LBs<- vector(mode="numeric",length=B)
48+
CI_UBs<- vector(mode="numeric",length=B)
49+
testName<-"log_normal_variance_one_sample"
50+
for (iin1:B) {
51+
set.seed(i)
52+
x<- rlnorm(n=N,mean=mu,sd=variance^.5)
53+
test<- log_normal_variance_one_sample(x,variance,alt)
54+
stats[i]<-test$statistic
55+
pvalues[i]<-test$p.value
56+
alts[i]<-test$alternative
57+
CI_LBs[i]<-test$conf.int[1]
58+
CI_UBs[i]<-test$conf.int[2]
59+
}
60+
temp<- tibble(test=testName,mu=mu,variance=variance,stat=stats,pvalue=pvalues,alt=alts,CI_LB=CI_LBs,CI_UB=CI_UBs)
61+
sim_results<-sim_results %>% bind_rows(temp)
62+
rm(stats,pvalues,alts,testName,temp,i)
63+
}
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}
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}
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# Check structure
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sim_results %>%
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distinct(test) %>%
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nrow()==2
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sim_results %>%
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distinct(mu) %>%
74+
nrow()== length(mus)
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76+
sim_results %>%
77+
distinct(variance) %>%
78+
nrow()== length(variances)
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sim_results %>%
81+
distinct(alt) %>%
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nrow()==3
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sim_results %>%
85+
pull(pvalue) %>%
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min(na.rm=TRUE)>=0
87+
88+
sim_results %>%
89+
pull(pvalue) %>%
90+
max(na.rm=TRUE)<=1
91+
92+
all(sim_results$CI_LB<sim_results$CI_UB)
93+
94+
# save
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sim_results %>%
96+
saveRDS("results/log_normal_type_one.rds")
97+
98+
rm(x,test,alt,mu,mus,variance,variances)
99+
100+
################
101+
# Type II
102+
################
103+
104+
mu0<-0
105+
variance0<-1
106+
muEffectSizes<- seq(-.20,.20,.05) %>%
107+
round(2) %>%
108+
setdiff(0)
109+
110+
sim_results<- tibble()
111+
for (muEffectSizeinmuEffectSizes) {
112+
if (muEffectSize<0) {
113+
for (altin c("two.sided","less")) {
114+
stats<- vector(mode="numeric",length=B)
115+
pvalues<- vector(mode="numeric",length=B)
116+
alts<- vector(mode="character",length=B)
117+
testName<-"log_normal_mu_one_sample"
118+
for (iin1:B) {
119+
set.seed(i)
120+
x<- rlnorm(n=N,mean=mu0+muEffectSize,sd=variance0^.5)
121+
test<- log_normal_mu_one_sample(x,mu0,alt)
122+
stats[i]<-test$statistic
123+
pvalues[i]<-test$p.value
124+
alts[i]<-test$alternative
125+
}
126+
temp<- tibble(test=testName,effectSize=muEffectSize,stat=stats,pvalue=pvalues,alt=alts)
127+
sim_results<-sim_results %>% bind_rows(temp)
128+
rm(stats,pvalues,alts,testName,temp,i)
129+
}
130+
}else {
131+
for (altin c("two.sided","greater")) {
132+
stats<- vector(mode="numeric",length=B)
133+
pvalues<- vector(mode="numeric",length=B)
134+
alts<- vector(mode="character",length=B)
135+
testName<-"log_normal_mu_one_sample"
136+
for (iin1:B) {
137+
set.seed(i)
138+
x<- rlnorm(n=N,mean=mu0+muEffectSize,sd=variance0^.5)
139+
test<- log_normal_mu_one_sample(x,mu0,alt)
140+
stats[i]<-test$statistic
141+
pvalues[i]<-test$p.value
142+
alts[i]<-test$alternative
143+
}
144+
temp<- tibble(test=testName,effectSize=muEffectSize,stat=stats,pvalue=pvalues,alt=alts)
145+
sim_results<-sim_results %>% bind_rows(temp)
146+
rm(stats,pvalues,alts,testName,temp,i)
147+
}
148+
}
149+
}
150+
151+
rm(alt,muEffectSize,x)
152+
153+
mu0<-0
154+
variance0<-15
155+
varianceEffectSizes<- seq(-5,5,1) %>%
156+
setdiff(0)
157+
158+
for (varianceEffectSizeinvarianceEffectSizes) {
159+
if (varianceEffectSize<0) {
160+
for (altin c("two.sided","less")) {
161+
stats<- vector(mode="numeric",length=B)
162+
pvalues<- vector(mode="numeric",length=B)
163+
alts<- vector(mode="character",length=B)
164+
testName<-"log_normal_variance_one_sample"
165+
for (iin1:B) {
166+
set.seed(i)
167+
x<- rlnorm(n=N,mean=mu0,sd= (variance0+varianceEffectSize)^.5)
168+
test<- log_normal_variance_one_sample(x,variance0,alt)
169+
stats[i]<-test$statistic
170+
pvalues[i]<-test$p.value
171+
alts[i]<-test$alternative
172+
}
173+
temp<- tibble(test=testName,effectSize=varianceEffectSize,stat=stats,pvalue=pvalues,alt=alts)
174+
sim_results<-sim_results %>% bind_rows(temp)
175+
rm(stats,pvalues,alts,testName,temp,i)
176+
}
177+
}else {
178+
for (altin c("two.sided","greater")) {
179+
stats<- vector(mode="numeric",length=B)
180+
pvalues<- vector(mode="numeric",length=B)
181+
alts<- vector(mode="character",length=B)
182+
testName<-"log_normal_variance_one_sample"
183+
for (iin1:B) {
184+
set.seed(i)
185+
x<- rlnorm(n=N,mean=mu0,sd= (variance0+varianceEffectSize)^.5)
186+
test<- log_normal_variance_one_sample(x,variance0,alt)
187+
stats[i]<-test$statistic
188+
pvalues[i]<-test$p.value
189+
alts[i]<-test$alternative
190+
}
191+
temp<- tibble(test=testName,effectSize=varianceEffectSize,stat=stats,pvalue=pvalues,alt=alts)
192+
sim_results<-sim_results %>% bind_rows(temp)
193+
rm(stats,pvalues,alts,testName,temp,i)
194+
}
195+
}
196+
}
197+
198+
# Check structure
199+
sim_results %>%
200+
distinct(test) %>%
201+
nrow()==2
202+
203+
sim_results %>%
204+
distinct(alt) %>%
205+
nrow()==3
206+
207+
sim_results %>%
208+
distinct(alt,test) %>%
209+
nrow()==6
210+
211+
sim_results %>%
212+
filter(test=="log_normal_mu_one_sample") %>%
213+
distinct(effectSize) %>%
214+
nrow()== length(muEffectSizes)
215+
216+
sim_results %>%
217+
filter(test=="log_normal_variance_one_sample") %>%
218+
distinct(effectSize) %>%
219+
nrow()== length(varianceEffectSizes)
220+
221+
sim_results %>%
222+
pull(pvalue) %>%
223+
min(na.rm=TRUE)>=0
224+
225+
sim_results %>%
226+
pull(pvalue) %>%
227+
max(na.rm=TRUE)<=1
228+
229+
# save
230+
sim_results %>%
231+
saveRDS("results/log_normal_type_two.rds")
232+
233+
rm(alt,varianceEffectSize,x,test)
234+
235+
rm(list= ls())

‎R Code/sampling distribution/check type I.R‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,6 +17,7 @@ load_df <- function(fn) {
1717

1818
fns<- c(
1919
"gaussian_type_one.rds",
20+
"log_normal_type_one.rds",
2021
"gamma_type_one_rate.rds",
2122
"gamma_type_one_scale.rds",
2223
"gamma_type_one_shape.rds",
@@ -46,7 +47,7 @@ typeI %>%
4647

4748
typeI %>%
4849
distinct(test) %>%
49-
nrow()==17
50+
nrow()==19
5051

5152
typeI %>%
5253
distinct(alt) %>%
@@ -145,6 +146,7 @@ load_df <- function(fn) {
145146

146147
fns<- c(
147148
"gaussian_type_one_one_way.rds",
149+
"log_normal_type_one_one_way.rds",
148150
"gamma_type_one_rate_one_way.rds",
149151
"gamma_type_one_scale_one_way.rds",
150152
"gamma_type_one_shape_one_way.rds",
@@ -169,7 +171,7 @@ typeI %>%
169171

170172
typeI %>%
171173
distinct(test) %>%
172-
nrow()==18
174+
nrow()==20
173175

174176
typeI %>%
175177
distinct(alt) %>%

‎R Code/sampling distribution/check type II.R‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,6 +17,7 @@ load_df <- function(fn) {
1717

1818
fns<- c(
1919
"gaussian_type_two.rds",
20+
"log_normal_type_two.rds",
2021
"gamma_type_two_rate.rds",
2122
"gamma_type_two_scale.rds",
2223
"gamma_type_two_shape.rds",
@@ -41,7 +42,7 @@ typeII %>%
4142

4243
typeII %>%
4344
distinct(test) %>%
44-
nrow()==18
45+
nrow()==20
4546

4647
typeII %>%
4748
distinct(alt) %>%
@@ -86,6 +87,7 @@ load_df <- function(fn) {
8687

8788
fns<- c(
8889
"gaussian_type_two_one_way.rds",
90+
"log_normal_type_two_one_way.rds",
8991
"gamma_type_two_rate_one_way.rds",
9092
"gamma_type_two_scale_one_way.rds",
9193
"gamma_type_two_shape_one_way.rds",
@@ -109,7 +111,7 @@ typeII %>%
109111

110112
typeII %>%
111113
distinct(test) %>%
112-
nrow()==18
114+
nrow()==20
113115

114116
typeII %>%
115117
distinct(alt) %>%

‎R Code/sampling distribution/sampling distribution.R‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,6 +17,7 @@ load_df <- function(fn) {
1717

1818
fns<- c(
1919
"gaussian_type_one.rds",
20+
"log_normal_type_one.rds",
2021
"gaussian_type_one_one_way.rds",
2122
"gamma_type_one_rate.rds",
2223
"gamma_type_one_rate_one_way.rds",
@@ -55,7 +56,7 @@ typeI %>%
5556

5657
typeI %>%
5758
distinct(test) %>%
58-
nrow()==36
59+
nrow()==38
5960

6061
typeI %>%
6162
distinct(alt) %>%

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