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recent updates to model formula

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mjgaughan 2024-04-23 09:55:37 -05:00
parent a0ab5720fa
commit 634f60b6a8
2 changed files with 68 additions and 67 deletions
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@ -1,69 +1,3 @@
names_to = "window",
values_to = "count") |>
unnest(count)
longer$observation_type <- gsub("^.*_", "", longer$window)
longer <- ddply(longer, "observation_type", transform, week=seq(from=0, by=1, length.out=length(observation_type)))
longer$count <- as.numeric(longer$count)
#longer <- longer[which(longer$observation_type == "all"),]
return(longer)
}
expanded_data <- expand_timeseries(readme_df[1,])
for (i in 2:nrow(readme_df)){
expanded_data <- rbind(expanded_data, expand_timeseries(readme_df[i,]))
}
View(expanded_data)
# this is the file with the lmer multi-level rddAnalysis
library(tidyverse)
library(plyr)
# 0 loading the readme data in
try(setwd(dirname(rstudioapi::getActiveDocumentContext()$path)))
readme_df <- read_csv("../final_data/deb_readme_did.csv")
# 1 preprocessing
#colnames(readme_df) <- c("upstream_vcs_link", "event_date", "event_hash", "before_all_ct", "before_mrg_ct", "after_all_ct", "after_mrg_ct", "before_auth_new", "after_commit_new", "after_auth_new", "before_commit_new")
col_order <- c("upstream_vcs_link", "age_of_project", "event_date", "event_hash", "before_all_ct", "after_all_ct", "before_mrg_ct", "after_mrg_ct", "before_auth_new", "after_auth_new", "before_commit_new", "after_commit_new")
readme_df <- readme_df[,col_order]
readme_df$ct_before_all <- str_split(gsub("[][]","", readme_df$before_all_ct), ", ")
readme_df$ct_after_all <- str_split(gsub("[][]","", readme_df$after_all_ct), ", ")
readme_df$ct_before_mrg <- str_split(gsub("[][]","", readme_df$before_mrg_ct), ", ")
readme_df$ct_after_mrg <- str_split(gsub("[][]","", readme_df$after_mrg_ct), ", ")
drop <- c("before_all_ct", "before_mrg_ct", "after_all_ct", "after_mrg_ct")
readme_df = readme_df[,!(names(readme_df) %in% drop)]
# 2 some expansion needs to happens for each project
expand_timeseries <- function(project_row) {
longer <- project_row |>
pivot_longer(cols = starts_with("ct"),
names_to = "window",
values_to = "count") |>
unnest(count)
longer$observation_type <- gsub("^.*_", "", longer$window)
longer <- ddply(longer, "observation_type", transform, week=seq(from=0, by=1, length.out=length(observation_type)))
longer$count <- as.numeric(longer$count)
#longer <- longer[which(longer$observation_type == "all"),]
return(longer)
}
expanded_data <- expand_timeseries(readme_df[1,])
for (i in 2:nrow(readme_df)){
expanded_data <- rbind(expanded_data, expand_timeseries(readme_df[i,]))
}
#filter out the windows of time that we're looking at
window_num <- 8
expanded_data <- expanded_data |>
filter(week >= (26 - window_num) & week <= (26 + window_num)) |>
mutate(D = ifelse(week > 26, 1, 0))
#separate out the cleaning
all_actions_data <- expanded_data[which(expanded_data$observation_type == "all"),]
mrg_actions_data <- expanded_data[which(expanded_data$observation_type == "mrg"),]
draft_all_model <- lmer(count ~ D * I(week - 26) + (1|upstream_vcs_link), REML=FALSE, data=all_actions_data)
summary(draft_all_model)
# 3 rdd in lmer analysis
# rdd: https://rpubs.com/phle/r_tutorial_regression_discontinuity_design
# lmer: https://www.youtube.com/watch?v=LzAwEKrn2Mc
library(lme4)
draft_all_model <- lmer(count ~ D * I(week - 26) + (1|upstream_vcs_link), REML=FALSE, data=all_actions_data)
summary(draft_all_model)
draft_all_model <- lmer(count ~ D * I(week - 26) + age_of_project + (1|upstream_vcs_link), REML=FALSE, data=all_actions_data)
summary(draft_all_model)
ICC(outcome="count", group="upstream_vcs_link", data=all_actions_data)
# need to calculate inter-class correlation coefficient?
library(merTools)
ICC(outcome="count", group="upstream_vcs_link", data=all_actions_data)
@ -510,3 +444,69 @@ poisson_mrg_model <- glmer(count ~ D + I(week - 26) + D:I(week - 26) + scaled_pr
summary(poisson_mrg_model)
poisson_mrg_residuals <- residuals(poisson_mrg_model)
qqnorm(poisson_mrg_residuals)
# this is the file with the lmer multi-level rddAnalysis
library(tidyverse)
library(plyr)
# 0 loading the readme data in
try(setwd(dirname(rstudioapi::getActiveDocumentContext()$path)))
readme_df <- read_csv("../final_data/deb_readme_did.csv")
# 1 preprocessing
#colnames(readme_df) <- c("upstream_vcs_link", "event_date", "event_hash", "before_all_ct", "before_mrg_ct", "after_all_ct", "after_mrg_ct", "before_auth_new", "after_commit_new", "after_auth_new", "before_commit_new")
col_order <- c("upstream_vcs_link", "age_of_project", "event_date", "event_hash", "before_all_ct", "after_all_ct", "before_mrg_ct", "after_mrg_ct", "before_auth_new", "after_auth_new", "before_commit_new", "after_commit_new")
readme_df <- readme_df[,col_order]
readme_df$ct_before_all <- str_split(gsub("[][]","", readme_df$before_all_ct), ", ")
readme_df$ct_after_all <- str_split(gsub("[][]","", readme_df$after_all_ct), ", ")
readme_df$ct_before_mrg <- str_split(gsub("[][]","", readme_df$before_mrg_ct), ", ")
readme_df$ct_after_mrg <- str_split(gsub("[][]","", readme_df$after_mrg_ct), ", ")
drop <- c("before_all_ct", "before_mrg_ct", "after_all_ct", "after_mrg_ct")
readme_df = readme_df[,!(names(readme_df) %in% drop)]
# 2 some expansion needs to happens for each project
expand_timeseries <- function(project_row) {
longer <- project_row |>
pivot_longer(cols = starts_with("ct"),
names_to = "window",
values_to = "count") |>
unnest(count)
longer$observation_type <- gsub("^.*_", "", longer$window)
longer <- ddply(longer, "observation_type", transform, week=seq(from=0, by=1, length.out=length(observation_type)))
longer$count <- as.numeric(longer$count)
#longer <- longer[which(longer$observation_type == "all"),]
return(longer)
}
expanded_data <- expand_timeseries(readme_df[1,])
for (i in 2:nrow(readme_df)){
expanded_data <- rbind(expanded_data, expand_timeseries(readme_df[i,]))
}
#filter out the windows of time that we're looking at
window_num <- 8
windowed_data <- expanded_data |>
filter(week >= (26 - window_num) & week <= (26 + window_num)) |>
mutate(D = ifelse(week > 26, 1, 0))
#scale the age numbers
windowed_data$scaled_project_age <- scale(windowed_data$age_of_project)
#separate out the cleaning d
all_actions_data <- windowed_data[which(windowed_data$observation_type == "all"),]
mrg_actions_data <- windowed_data[which(windowed_data$observation_type == "mrg"),]
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
# (1 |upstream_vcs_link) or (week | upstream_vcs_link)
poisson_all_model <- glmer(count ~ (D + I(week - 26) + D:I(week - 26) + scaled_project_age | upstream_vcs_link) + (1 |upstream_vcs_link), data=all_actions_data, family = poisson(link = "log"))
# 3 rdd in lmer analysis
# rdd: https://rpubs.com/phle/r_tutorial_regression_discontinuity_design
# lmer: https://www.youtube.com/watch?v=LzAwEKrn2Mc
library(lme4)
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
# (1 |upstream_vcs_link) or (week | upstream_vcs_link)
poisson_all_model <- glmer(count ~ (D + I(week - 26) + D:I(week - 26) + scaled_project_age | upstream_vcs_link) + (1 |upstream_vcs_link), data=all_actions_data, family = poisson(link = "log"))
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
# (1 |upstream_vcs_link) or (week | upstream_vcs_link)
poisson_all_model <- glmer(count ~ D + I(week - 26) + D:I(week - 26) + scaled_project_age + (D + I(week - 26) + D:I(week - 26) + scaled_project_age | upstream_vcs_link) + (1 |upstream_vcs_link), data=all_actions_data, family = poisson(link = "log"))
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
# (1 |upstream_vcs_link) or (week | upstream_vcs_link)
poisson_all_model <- glmer(count ~ D + I(week - 26) + D:I(week - 26) + scaled_project_age + (D | upstream_vcs_link) + (1 |upstream_vcs_link), data=all_actions_data, family = poisson(link = "log"))
summary(poisson_all_model)
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
# (D |upstream_vcs_link) or (week | upstream_vcs_link)
poisson_all_model <- glmer(count ~ D + I(week - 26) + D:I(week - 26) + scaled_project_age + (week | upstream_vcs_link) + (1 |upstream_vcs_link), data=all_actions_data, family = poisson(link = "log"))
summary(poisson_all_model)
poisson_residuals <- residuals(poisson_all_model)
qqnorm(poisson_residuals)

3
R/readmeRDDAnalysis.R
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@ -54,7 +54,8 @@ qqplot(all_actions_data$count, y)
# lmer: https://www.youtube.com/watch?v=LzAwEKrn2Mc
library(lme4)
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
poisson_all_model <- glmer(count ~ D + I(week - 26) + D:I(week - 26) + scaled_project_age + (week |upstream_vcs_link), data=all_actions_data, family = poisson(link = "log"))
# (D |upstream_vcs_link) or (week | upstream_vcs_link)
poisson_all_model <- glmer(count ~ D + I(week - 26) + D:I(week - 26) + scaled_project_age + (week || upstream_vcs_link), data=all_actions_data, family = poisson(link = "log"))
summary(poisson_all_model)
poisson_residuals <- residuals(poisson_all_model)
qqnorm(poisson_residuals)