updating rdd scripts w pop level
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mjgaughan
parent
1184069921
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R/.Rhistory
806
R/.Rhistory
@ -1,233 +1,11 @@
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filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
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library(ggplot2)
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mutate(D = ifelse(week > 27, 1, 0))
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data1 <- read_csv('../power_data_111023_mmt.csv',show_col_types = FALSE)
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windowed_sample_data$scaled_project_age <- scale(windowed_sample_data$age_of_project)
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data2 <- read_csv('../inst_all_packages_full_results.csv')
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windowed_sample_data$week_offset <- windowed_sample_data$week - 27
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data1 <- read_csv('../kk_final_expanded_data_final.csv',show_col_types = FALSE)
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all_actions_sample_data <- windowed_sample_data[which(windowed_sample_data$observation_type == "all"),]
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library(readr)
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#test model
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library(ggplot2)
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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library(tidyverse)
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summary(test_model)
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data1 <- read_csv('../kk_final_expanded_data_final.csv',show_col_types = FALSE)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model), group=upstream_vcs_link), show.legend = FALSE) +
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theme_bw()
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p
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# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
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#making some random data
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sampled_data <- readme_df[sample(nrow(readme_df), 220), ]
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expanded_sample_data <- expand_timeseries(sampled_data[1,])
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for (i in 2:nrow(sampled_data)){
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expanded_sample_data <- rbind(expanded_sample_data, expand_timeseries(sampled_data[i,]))
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}
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windowed_sample_data <- expanded_sample_data |>
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filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
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mutate(D = ifelse(week > 27, 1, 0))
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windowed_sample_data$scaled_project_age <- scale(windowed_sample_data$age_of_project)
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windowed_sample_data$week_offset <- windowed_sample_data$week - 27
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all_actions_sample_data <- windowed_sample_data[which(windowed_sample_data$observation_type == "all"),]
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model), group=upstream_vcs_link), show.legend = FALSE) +
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theme_bw()
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p
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (week_offset|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model), group=upstream_vcs_link), show.legend = FALSE) +
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theme_bw()
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p
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model), group=upstream_vcs_link), show.legend = FALSE) +
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theme_bw()
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p
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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# for visualization, may have to run model for each project and then identify top 5 projects for RDD graphs
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mrg_model <- lmer(count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=mrg_actions_data, REML=FALSE)
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summary(mrg_model)
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summary(all_model)
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)||upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
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#making some random data
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sampled_data <- readme_df[sample(nrow(readme_df), 220), ]
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expanded_sample_data <- expand_timeseries(sampled_data[1,])
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for (i in 2:nrow(sampled_data)){
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expanded_sample_data <- rbind(expanded_sample_data, expand_timeseries(sampled_data[i,]))
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}
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windowed_sample_data <- expanded_sample_data |>
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filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
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mutate(D = ifelse(week > 27, 1, 0))
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windowed_sample_data$scaled_project_age <- scale(windowed_sample_data$age_of_project)
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windowed_sample_data$week_offset <- windowed_sample_data$week - 27
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all_actions_sample_data <- windowed_sample_data[which(windowed_sample_data$observation_type == "all"),]
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=mean(predict(test_model)), show.legend = FALSE)) +
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theme_bw()
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p
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model), show.legend = FALSE)) +
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theme_bw()
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p
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=mean(predict(test_model))), show.legend = FALSE) +
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theme_bw()
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p
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=median(predict(test_model))), show.legend = FALSE) +
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theme_bw()
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p
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset) + scaled_project_age|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
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#making some random data
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sampled_data <- readme_df[sample(nrow(readme_df), 22), ]
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expanded_sample_data <- expand_timeseries(sampled_data[1,])
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for (i in 2:nrow(sampled_data)){
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expanded_sample_data <- rbind(expanded_sample_data, expand_timeseries(sampled_data[i,]))
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}
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windowed_sample_data <- expanded_sample_data |>
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filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
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mutate(D = ifelse(week > 27, 1, 0))
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windowed_sample_data$scaled_project_age <- scale(windowed_sample_data$age_of_project)
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windowed_sample_data$week_offset <- windowed_sample_data$week - 27
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all_actions_sample_data <- windowed_sample_data[which(windowed_sample_data$observation_type == "all"),]
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
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#making some random data
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sampled_data <- readme_df[sample(nrow(readme_df), 220), ]
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expanded_sample_data <- expand_timeseries(sampled_data[1,])
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for (i in 2:nrow(sampled_data)){
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expanded_sample_data <- rbind(expanded_sample_data, expand_timeseries(sampled_data[i,]))
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}
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windowed_sample_data <- expanded_sample_data |>
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filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
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mutate(D = ifelse(week > 27, 1, 0))
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windowed_sample_data$scaled_project_age <- scale(windowed_sample_data$age_of_project)
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windowed_sample_data$week_offset <- windowed_sample_data$week - 27
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all_actions_sample_data <- windowed_sample_data[which(windowed_sample_data$observation_type == "all"),]
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
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#making some random data
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sampled_data <- readme_df[sample(nrow(readme_df), 220), ]
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expanded_sample_data <- expand_timeseries(sampled_data[1,])
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for (i in 2:nrow(sampled_data)){
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expanded_sample_data <- rbind(expanded_sample_data, expand_timeseries(sampled_data[i,]))
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}
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windowed_sample_data <- expanded_sample_data |>
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filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
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mutate(D = ifelse(week > 27, 1, 0))
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windowed_sample_data$scaled_project_age <- scale(windowed_sample_data$age_of_project)
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windowed_sample_data$week_offset <- windowed_sample_data$week - 27
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all_actions_sample_data <- windowed_sample_data[which(windowed_sample_data$observation_type == "all"),]
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#test model
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test_model <- lmer(count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
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summary(test_model)
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#plot results
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p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
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geom_point(size=3, show.legend = FALSE) +
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geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
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theme_bw()
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p
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summary(all_model)
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all_residuals <- residuals(all_model)
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qqnorm(all_residuals)
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mrg_residuals <- residuals(mrg_model)
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qqnorm(mrg_residuals)
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summary(all_model)
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##end of the model testing and plotting section
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all_model <- lmer(count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=TRUE)
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summary(all_model)
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##end of the model testing and plotting section
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all_model <- lmer(count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
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summary(all_model)
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# this is the file with the lmer multi-level rddAnalysis
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# this is the file with the lmer multi-level rddAnalysis
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library(tidyverse)
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library(tidyverse)
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library(plyr)
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library(plyr)
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@ -272,155 +50,200 @@ windowed_data$week_offset <- windowed_data$week - 27
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#separate out the cleaning d
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#separate out the cleaning d
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all_actions_data <- windowed_data[which(windowed_data$observation_type == "all"),]
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all_actions_data <- windowed_data[which(windowed_data$observation_type == "all"),]
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mrg_actions_data <- windowed_data[which(windowed_data$observation_type == "mrg"),]
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mrg_actions_data <- windowed_data[which(windowed_data$observation_type == "mrg"),]
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#find some EDA to identify which types of models might be the best for this
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all_actions_data$log1p_count <- log1p(all_actions_data$count)
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hist(all_actions_data$count)
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#find some EDA to identify which types of models might be the best for this
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hist(log1p(all_actions_data$count))
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#find some EDA to identify which types of models might be the best for this
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hist(log(all_actions_data$count))
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# 3 rdd in lmer analysis
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# 3 rdd in lmer analysis
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# rdd: https://rpubs.com/phle/r_tutorial_regression_discontinuity_design
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# rdd: https://rpubs.com/phle/r_tutorial_regression_discontinuity_design
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# lmer: https://www.youtube.com/watch?v=LzAwEKrn2Mc
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# lmer: https://www.youtube.com/watch?v=LzAwEKrn2Mc
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library(lme4)
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library(lme4)
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##end of the model testing and plotting section
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all_model <- lmer(log(count) ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
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all_actions_data$logged_count <- log(all_actions_data$count)
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|
||||||
all_actions_data$log1p_count <- log1p(all_actions_data$count)
|
|
||||||
##end of the model testing and plotting section
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
|
|
||||||
summary(all_model)
|
|
||||||
all_residuals <- residuals(all_model)
|
|
||||||
qqnorm(all_residuals)
|
|
||||||
##end of the model testing and plotting section
|
|
||||||
all_model <- lmer(logged_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
|
|
||||||
##end of the model testing and plotting section
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
|
|
||||||
##end of the model testing and plotting section
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset| upstream_vcs_link), data=all_actions_data, REML=FALSE)
|
|
||||||
##end of the model testing and plotting section
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
|
|
||||||
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
|
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
|
||||||
#making some random data
|
library(optimx)
|
||||||
sampled_data <- readme_df[sample(nrow(readme_df), 220), ]
|
library(lattice)
|
||||||
expanded_sample_data <- expand_timeseries(sampled_data[1,])
|
|
||||||
for (i in 2:nrow(sampled_data)){
|
|
||||||
expanded_sample_data <- rbind(expanded_sample_data, expand_timeseries(sampled_data[i,]))
|
|
||||||
}
|
|
||||||
windowed_sample_data <- expanded_sample_data |>
|
|
||||||
filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
|
|
||||||
mutate(D = ifelse(week > 27, 1, 0))
|
|
||||||
windowed_sample_data$scaled_project_age <- scale(windowed_sample_data$age_of_project)
|
|
||||||
windowed_sample_data$week_offset <- windowed_sample_data$week - 27
|
|
||||||
all_actions_sample_data <- windowed_sample_data[which(windowed_sample_data$observation_type == "all"),]
|
|
||||||
#test model
|
|
||||||
test_model <- lmer(log1p_count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
|
|
||||||
all_actions_sample_data$log1p_count <- log1p(all_actions_sample_data$count)
|
|
||||||
#test model
|
|
||||||
test_model <- lmer(log1p_count ~ D * I(week_offset) + scaled_project_age + (D * I(week_offset)|upstream_vcs_link), data=all_actions_sample_data, REML=FALSE)
|
|
||||||
summary(test_model)
|
|
||||||
#plot results
|
|
||||||
p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
|
|
||||||
geom_point(size=3, show.legend = FALSE) +
|
|
||||||
geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
|
|
||||||
theme_bw()
|
|
||||||
p
|
|
||||||
#plot results
|
|
||||||
p <- ggplot(all_actions_sample_data, aes(x=week_offset, y=count, color=upstream_vcs_link), show.legend = FALSE) +
|
|
||||||
geom_point(size=3, show.legend = FALSE) +
|
|
||||||
geom_line(aes(y=predict(test_model)), show.legend = FALSE) +
|
|
||||||
theme_bw()
|
|
||||||
p
|
|
||||||
library(merTools)
|
|
||||||
ICC(outcome="count", group="week", data=all_actions_data)
|
|
||||||
ICC(outcome="count", group="upstream_vcs_link", data=all_actions_data)
|
|
||||||
ICC(outcome="count", group="week", data=all_actions_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
|
|
||||||
windowed_data <- expanded_data |>
|
|
||||||
filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
|
|
||||||
mutate(D = ifelse(week > 27, 1, 0))
|
|
||||||
#scale the age numbers
|
|
||||||
windowed_data$scaled_project_age <- scale(windowed_data$age_of_project)
|
|
||||||
windowed_data$week_offset <- windowed_data$week - 27
|
|
||||||
#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"),]
|
|
||||||
all_actions_data$logged_count <- log(all_actions_data$count)
|
|
||||||
all_actions_data$log1p_count <- log1p(all_actions_data$count)
|
|
||||||
# 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)
|
|
||||||
##end of the model testing and plotting section
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
|
|
||||||
summary(all_model)
|
|
||||||
(
|
|
||||||
##end of the model testing and plotting section
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead"))
|
|
||||||
##end of the model testing and plotting section
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead"))
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(optimizer="optimx",
|
|
||||||
optCtrl=list(method="nlminb")))
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
summary(all_model)
|
#identifying the quartiles of effect for D
|
||||||
all0_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
|
all_model_ranef <- as.data.frame(ranef(all_model, condVar=TRUE))
|
||||||
summary(all0_model)
|
View(all_model_ranef)
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
|
||||||
all_model.ranef <- ranef(all_model)
|
|
||||||
str(all_model.ranef)
|
|
||||||
head(all_model.ranef)
|
|
||||||
all_actions_data$D_effect_quart <- ntile(all_model.ranef$D, 4)
|
|
||||||
head(all_model.ranef)
|
|
||||||
all_model.ranef <- random.effects(all_model)
|
|
||||||
head(as.data.frame(all_model.ranef))
|
|
||||||
head(all_model_ranef)
|
|
||||||
all_model_ranef <- as.data.frame(ranef(all_model))
|
|
||||||
head(all_model_ranef)
|
|
||||||
d_effect_ranef_all <- subset(all_model_ranef, term="D")
|
|
||||||
d_effect_ranef_all <- all_model_ranef[all_model_ranef$term="D",]
|
|
||||||
d_effect_ranef_all <- all_model_ranef[all_model_ranef$term=="D",]
|
d_effect_ranef_all <- all_model_ranef[all_model_ranef$term=="D",]
|
||||||
|
#identifying the quartiles of effect for D
|
||||||
|
all_model_ranef <- ranef(all_model, condVar=TRUE)
|
||||||
|
d_effect_ranef_all <- all_model_ranef[all_model_ranef$term=="D",]
|
||||||
|
dotplot(all_model_ranef)
|
||||||
|
d_effect_ranef_all <- all_model_ranef['upstream_vcs_link']['D']
|
||||||
|
View(all_model_ranef)
|
||||||
|
d_effect_ranef_all <- all_model_ranef[upstream_vcs_link,2]
|
||||||
|
d_effect_ranef_all <- all_model_ranef['upstream_vcs_link',2]
|
||||||
|
d_effect_ranef_all <- all_model_ranef$upstream_vcs_link
|
||||||
View(d_effect_ranef_all)
|
View(d_effect_ranef_all)
|
||||||
d_effect_ranef_all$quartile <- ntile(d_effect_ranef_all$condval, 4)
|
dotplot(all_model_ranef)[["D"]]
|
||||||
View(d_effect_ranef_all)
|
dotplot(all_model_ranef)[["upstream_vcs_link"]]
|
||||||
# mrg behavior for this
|
dotplot(all_model_ranef)[["upstream_vcs_link"]["D"]]
|
||||||
mrg_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
dotplot(all_model_ranef)$D
|
||||||
|
View(all_model_ranef)
|
||||||
|
for (j in 1:nschool) {
|
||||||
|
jj <- order(all_model_ranef)[j]
|
||||||
|
lines (x=c(j,j),y=c(ranef.lower[jj],ranef.upper[jj]))
|
||||||
|
}
|
||||||
|
for (j in 1:upstream_vcs_link) {
|
||||||
|
jj <- order(all_model_ranef)[j]
|
||||||
|
lines (x=c(j,j),y=c(ranef.lower[jj],ranef.upper[jj]))
|
||||||
|
}
|
||||||
|
View(all_model_ranef)
|
||||||
|
df_ranefs <- as.data.frame(all_model_ranef)
|
||||||
|
View(df_ranefs)
|
||||||
|
#identifying the quartiles of effect for D
|
||||||
|
all_model_ranef <- ranef(all_model, condVar=TRUE)$upstream_vcs_link[[2]]
|
||||||
|
#identifying the quartiles of effect for D
|
||||||
|
all_model_ranef <- ranef(all_model, condVar=TRUE)$upstream_vcs_link
|
||||||
|
dotplot(all_model_ranef)
|
||||||
|
dotplot(all_model_ranef)
|
||||||
|
# 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 >= (27 - window_num) & week <= (27 + window_num)) |>
|
||||||
|
mutate(D = ifelse(week > 27, 1, 0))
|
||||||
|
#scale the age numbers
|
||||||
|
windowed_data$scaled_project_age <- scale(windowed_data$age_of_project)
|
||||||
|
windowed_data$week_offset <- windowed_data$week - 27
|
||||||
|
#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"),]
|
||||||
|
all_actions_data$log1p_count <- log1p(all_actions_data$count)
|
||||||
|
# 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
|
||||||
|
library(optimx)
|
||||||
|
library(lattice)
|
||||||
|
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
summary(mrg_model)
|
#identifying the quartiles of effect for D
|
||||||
|
all_model_ranef <- ranef(all_model, condVar=TRUE)
|
||||||
|
dotplot(all_model_ranef)$g[1]
|
||||||
|
re <- ranef(all_model,postVar = TRUE)
|
||||||
|
re$g$'(Intercept)' <- NULL
|
||||||
|
re$g$'D:I(week_offset)' <- NULL
|
||||||
|
re <- ranef(all_model, condVar=TRUE)
|
||||||
|
re$g$'(Intercept)' <- NULL
|
||||||
|
re$g$'D:I(week_offset)' <- NULL
|
||||||
|
dotplot(re)
|
||||||
|
dotplot(re)
|
||||||
|
re <- ranef(all_model, condVar=TRUE)
|
||||||
|
re$upstream_vcs_link$'(Intercept)' <- NULL
|
||||||
|
re$upstream_vcs_link$'D:I(week_offset)' <- NULL
|
||||||
|
View(re)
|
||||||
|
re$upstream_vcs_link$'I(week_offset)' <- NULL
|
||||||
|
dotplot(re)
|
||||||
|
View(re)
|
||||||
|
View(all_model_ranef)
|
||||||
|
dotplot(all_model_ranef)
|
||||||
|
#identifying the quartiles of effect for D
|
||||||
|
all_model_ranef <- ranef(all_model, condVar=TRUE)
|
||||||
|
dotplot(all_model_ranef)
|
||||||
|
#identifying the quartiles of effect for D
|
||||||
|
all_model_ranef <- ranef(all_model, condVar=TRUE)
|
||||||
|
dotplot(all_model_ranef)
|
||||||
|
re <- ranef(all_model, condVar=TRUE)
|
||||||
|
re$upstream_vcs_link$'(Intercept)' <- NULL
|
||||||
|
re$upstream_vcs_link$'D:I(week_offset)' <- NULL
|
||||||
|
re$upstream_vcs_link$'I(week_offset)' <- NULL
|
||||||
|
dotplot(re)
|
||||||
|
dotplot(all_model_ranef)
|
||||||
|
# this is the file with the lmer multi-level rddAnalysis
|
||||||
|
library(tidyverse)
|
||||||
|
library(plyr)
|
||||||
|
# 0 loading the readme data in
|
||||||
|
try(setwd(dirname(rstudioapi::getActiveDocumentContext()$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$observation_type == "all"),]
|
||||||
|
return(longer)
|
||||||
|
}
|
||||||
|
expanded_data <- expand_timeseries(readme_df[1,])
|
||||||
|
for (i in 2:nrow(readme_df)){
|
||||||
|
expanded_data <- rbind(expanded_data, expand_timeseries(readme_df[i,]))
|
||||||
|
}
|
||||||
|
#filter out the windows of time that we're looking at
|
||||||
|
window_num <- 8
|
||||||
|
windowed_data <- expanded_data |>
|
||||||
|
filter(week >= (27 - window_num) & week <= (27 + window_num)) |>
|
||||||
|
mutate(D = ifelse(week > 27, 1, 0))
|
||||||
|
#scale the age numbers
|
||||||
|
windowed_data$scaled_project_age <- scale(windowed_data$age_of_project)
|
||||||
|
windowed_data$week_offset <- windowed_data$week - 27
|
||||||
|
#separate out the cleaning d
|
||||||
|
all_actions_data <- windowed_data[which(windowed_data$observation_type == "all"),]
|
||||||
|
mrg_actions_data <- windowed_data[which(windowed_data$observation_type == "mrg"),]
|
||||||
|
all_actions_data$log1p_count <- log1p(all_actions_data$count)
|
||||||
|
# 3 rdd in lmer analysis
|
||||||
|
# rdd: https://rpubs.com/phle/r_tutorial_regression_discontinuity_design
|
||||||
|
# lmer: https://www.youtube.com/watch?v=LzAwEKrn2Mc
|
||||||
|
library(lme4)
|
||||||
|
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
|
||||||
|
library(optimx)
|
||||||
|
library(lattice)
|
||||||
|
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
||||||
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
|
summary(all_model)
|
||||||
|
#identifying the quartiles of effect for D
|
||||||
|
all_model_ranef <- ranef(all_model, condVar=TRUE)
|
||||||
|
dotplot(all_model_ranef)
|
||||||
|
df_ranefs <- as.data.frame(all_model_ranef)
|
||||||
|
View(df_ranefs)
|
||||||
|
D_df_ranef <- df_ranefs[term == "D"]
|
||||||
|
D_df_ranef <- df_ranefs[df_ranefs$term == "D"]
|
||||||
library(tidyverse)
|
library(tidyverse)
|
||||||
library(plyr)
|
library(plyr)
|
||||||
#get the contrib data instead
|
#get the contrib data instead
|
||||||
@ -464,49 +287,226 @@ windowed_data$week_offset <- windowed_data$week - 27
|
|||||||
all_actions_data <- windowed_data[which(windowed_data$observation_type == "all"),]
|
all_actions_data <- windowed_data[which(windowed_data$observation_type == "all"),]
|
||||||
mrg_actions_data <- windowed_data[which(windowed_data$observation_type == "mrg"),]
|
mrg_actions_data <- windowed_data[which(windowed_data$observation_type == "mrg"),]
|
||||||
#EDA?
|
#EDA?
|
||||||
|
hist(log(all_actions_data$count))
|
||||||
|
all_actions_data$logged_count <- log(all_actions_data$count)
|
||||||
|
all_actions_data$log1p_count <- log1p(all_actions_data$count)
|
||||||
|
# now for merge
|
||||||
|
mrg_actions_data$logged_count <- log(mrg_actions_data$count)
|
||||||
|
mrg_actions_data$log1p_count <- log1p(mrg_actions_data$count)
|
||||||
#TKTK ---------------------
|
#TKTK ---------------------
|
||||||
#imports for models
|
#imports for models
|
||||||
library(lme4)
|
library(lme4)
|
||||||
library(optimx)
|
library(optimx)
|
||||||
#models -- TKTK need to be fixed
|
library(lattice)
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
|
||||||
#EDA?
|
|
||||||
hist(log(all_actions_data$count))
|
|
||||||
all_actions_data$logged_count <- log(all_actions_data$count)
|
|
||||||
all_actions_data$log1p_count <- log1p(all_actions_data$count)
|
|
||||||
#models -- TKTK need to be fixed
|
|
||||||
all_model <- lmer(logged_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
|
||||||
#models -- TKTK need to be fixed
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
|
||||||
summary(all_model)
|
|
||||||
#models -- TKTK need to be fixed
|
#models -- TKTK need to be fixed
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
summary(all_model)
|
summary(all_model)
|
||||||
#models -- TKTK need to be fixed
|
#identifying the quartiles of effect for D
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE)
|
all_model_ranef <- as.data.frame(ranef(all_model))
|
||||||
week_offset
|
View(all_model_ranef)
|
||||||
#models -- TKTK need to be fixed
|
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
|
||||||
summary(all_model)
|
|
||||||
# mrg behavior for this
|
|
||||||
mrg_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
|
||||||
# mrg behavior for this
|
|
||||||
mrg_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset | upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
|
||||||
summary(mrg_model)
|
|
||||||
# mrg behavior for this
|
|
||||||
mrg_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset | upstream_vcs_link), data=mrg_actions_data, REML=FALSE, control = lmerControl(
|
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
|
||||||
# now for merge
|
|
||||||
mrg_actions_data$logged_count <- log(mrg_actions_data$count)
|
|
||||||
mrg_actions_data$log1p_count <- log1p(mrg_actions_data$count)
|
|
||||||
# mrg behavior for this
|
# mrg behavior for this
|
||||||
mrg_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset | upstream_vcs_link), data=mrg_actions_data, REML=FALSE, control = lmerControl(
|
mrg_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset | upstream_vcs_link), data=mrg_actions_data, REML=FALSE, control = lmerControl(
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
summary(mrg_model)
|
summary(mrg_model)
|
||||||
|
#identifying the quartiles of effect for D
|
||||||
|
mrg_model_ranef <- ranef(mrg_model)
|
||||||
|
View(mrg_model_ranef)
|
||||||
|
dotplot(mrg_model_ranef)
|
||||||
|
#load in data
|
||||||
|
contrib_df <- read_csv("../final_data/deb_contrib_pop_change.csv")
|
||||||
|
readme_df <- read_csv("../final_data/deb_readme_pop_change.csv")
|
||||||
|
View(readme_df)
|
||||||
|
#some expansion needs to happens for each project
|
||||||
|
expand_timeseries <- function(project_row) {
|
||||||
|
longer <- project_row |>
|
||||||
|
pivot_longer(cols = ends_with("new"),
|
||||||
|
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,])
|
||||||
|
View(expand_timeseries)
|
||||||
|
View(expanded_data)
|
||||||
|
longer <- project_row |>
|
||||||
|
pivot_longer(cols = ends_with("new"),
|
||||||
|
names_to = "window",
|
||||||
|
values_to = "count") |>
|
||||||
|
unnest(count) |>
|
||||||
|
mutate(after_doc = str_detect(window, "after"))
|
||||||
|
#some expansion needs to happens for each project
|
||||||
|
expand_timeseries <- function(project_row) {
|
||||||
|
longer <- project_row |>
|
||||||
|
pivot_longer(cols = ends_with("new"),
|
||||||
|
names_to = "window",
|
||||||
|
values_to = "count") |>
|
||||||
|
unnest(count) |>
|
||||||
|
mutate(after_doc = str_detect(window, "after"))
|
||||||
|
return(longer)
|
||||||
|
}
|
||||||
|
expanded_data <- expand_timeseries(readme_df[1,])
|
||||||
|
longer <- project_row |>
|
||||||
|
pivot_longer(cols = ends_with("new"),
|
||||||
|
names_to = "window",
|
||||||
|
values_to = "count") |>
|
||||||
|
unnest(count) |>
|
||||||
|
mutate(after_doc = as.numeric(str_detect(window, "after")))
|
||||||
|
return(longer)
|
||||||
|
#some expansion needs to happens for each project
|
||||||
|
expand_timeseries <- function(project_row) {
|
||||||
|
longer <- project_row |>
|
||||||
|
pivot_longer(cols = ends_with("new"),
|
||||||
|
names_to = "window",
|
||||||
|
values_to = "count") |>
|
||||||
|
unnest(count) |>
|
||||||
|
mutate(after_doc = as.numeric(str_detect(window, "after")))
|
||||||
|
return(longer)
|
||||||
|
}
|
||||||
|
expanded_data <- expand_timeseries(readme_df[1,])
|
||||||
|
#some expansion needs to happens for each project
|
||||||
|
expand_timeseries <- function(project_row) {
|
||||||
|
longer <- project_row |>
|
||||||
|
pivot_longer(cols = ends_with("new"),
|
||||||
|
names_to = "window",
|
||||||
|
values_to = "count") |>
|
||||||
|
unnest(count) |>
|
||||||
|
mutate(after_doc = as.numeric(str_detect(window, "after"))) |>
|
||||||
|
mutate(is_collab = as.numeric(str_detect(window, "collab")))
|
||||||
|
return(longer)
|
||||||
|
}
|
||||||
|
expanded_data <- expand_timeseries(readme_df[1,])
|
||||||
|
for (i in 2:nrow(readme_df)){
|
||||||
|
expanded_readme_data <- rbind(expanded_readme_data, expand_timeseries(readme_df[i,]))
|
||||||
|
}
|
||||||
|
expanded_readme_data <- expand_timeseries(readme_df[1,])
|
||||||
|
for (i in 2:nrow(readme_df)){
|
||||||
|
expanded_readme_data <- rbind(expanded_readme_data, expand_timeseries(readme_df[i,]))
|
||||||
|
}
|
||||||
|
expanded_contrib_data <- expand_timeseries(contrib_df[1,])
|
||||||
|
for (i in 2:nrow(contrib_df)){
|
||||||
|
expanded_contrib_data <- rbind(expanded_contrib_data, expand_timeseries(contrib_df[i,]))
|
||||||
|
}
|
||||||
|
View(expanded_contrib_data)
|
||||||
|
readme_model <- lmer(count ~ after_doc + (1| upstream_vcs_link), data=expanded_readme_data, REML=FALSE)
|
||||||
|
summary(readme_model)
|
||||||
|
readme_model <- lmer(count ~ after_doc + ( after_doc | upstream_vcs_link), data=expanded_readme_data, REML=FALSE)
|
||||||
|
summary(readme_model)
|
||||||
|
contrib_model <- lmer(count ~ after_doc + ( after_doc | upstream_vcs_link), data=expanded_contrib_data, REML=FALSE)
|
||||||
|
summary(contrib_model)
|
||||||
|
collab_readme_model <- lmer(count ~ after_doc + ( after_doc | upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
#breaking out the types of population counts
|
||||||
|
collab_pop_readme <- expanded_readme_data[which(expanded_readme_data$is_collab == 1),]
|
||||||
|
contrib_pop_readme <- expanded_readme_data[which(expanded_readme_data$is_collab == 0),]
|
||||||
|
collab_pop_contrib <- expanded_contrib_data[which(expanded_contrib_data$is_collab == 1),]
|
||||||
|
contrib_pop_contrib <- expanded_contrib_data[which(expanded_contrib_data$is_collab == 0),]
|
||||||
|
collab_readme_model <- lmer(count ~ after_doc + ( after_doc | upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
collab_readme_model <- lmer(count ~ after_doc + (1| upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
summary(collab_readme_model)
|
||||||
|
contrib_readme_model <- lmer(count ~ after_doc + ( 1| upstream_vcs_link), data=contrib_pop_readme, REML=FALSE)
|
||||||
|
summary(contrib_readme_model)
|
||||||
|
collab_readme_model <- lmer(count ~ after_doc + (after_doc| upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
collab_readme_model <- lmer(count ~ after_doc + (1| upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
summary(collab_readme_model)
|
||||||
|
contrib_readme_model <- lmer(count ~ after_doc + ( 1| upstream_vcs_link), data=contrib_pop_readme, REML=FALSE)
|
||||||
|
summary(contrib_readme_model)
|
||||||
|
collab_contrib_model <- lmer(count ~ after_doc + ( 1 | upstream_vcs_link), data=collab_pop_contrib, REML=FALSE)
|
||||||
|
summary(collab_contrib_model)
|
||||||
|
contrib_contrib_model <- lmer(count ~ after_doc + ( 1 | upstream_vcs_link), data=contrib_pop_contrib, REML=FALSE)
|
||||||
|
summary(contrib_contrib_model)
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = count, col = is_collab)) +
|
||||||
|
geom_point()
|
||||||
|
ggplot(aes(x = after_doc, y = count, col = as.factor(is_collab)) +
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = count, col = as.factor(is_collab))) +
|
||||||
|
geom_point()
|
||||||
|
expanded_readme_data |>
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = count, col = as.factor(is_collab))) +
|
||||||
|
geom_point()
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = as.factor(after_doc), y = count, col = as.factor(is_collab))) +
|
||||||
|
geom_point()
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = as.factor(after_doc), y = scale(count), col = as.factor(is_collab))) +
|
||||||
|
geom_point()
|
||||||
|
expanded_readme_data$log1pcount <- log1p(expanded_readme_data$count)
|
||||||
|
expanded_contrib_data$log1pcount <- log1p(expanded_contrib_data$count)
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = as.factor(after_doc), y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point()
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = as.factor(after_doc), y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F)
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F)
|
||||||
|
expanded_contrib_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F)
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = count, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
expanded_readme_data$logcount <- log(expanded_readme_data$count)
|
||||||
|
expanded_contrib_data$logcount <- log(expanded_contrib_data$count)
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = logcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
expanded_contrib_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F)
|
||||||
|
expanded_contrib_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
expanded_contrib_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = count, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = logcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
collab_readme_model <- lmer(logcount ~ after_doc + (1| upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
#breaking out the types of population counts
|
||||||
|
collab_pop_readme <- expanded_readme_data[which(expanded_readme_data$is_collab == 1),]
|
||||||
|
contrib_pop_readme <- expanded_readme_data[which(expanded_readme_data$is_collab == 0),]
|
||||||
|
collab_pop_contrib <- expanded_contrib_data[which(expanded_contrib_data$is_collab == 1),]
|
||||||
|
contrib_pop_contrib <- expanded_contrib_data[which(expanded_contrib_data$is_collab == 0),]
|
||||||
|
collab_readme_model <- lmer(logcount ~ after_doc + (1| upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
collab_readme_model <- lmer(log1pcount ~ after_doc + (1| upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
summary(collab_readme_model)
|
||||||
|
contrib_readme_model <- lmer(log1pcount ~ after_doc + ( 1| upstream_vcs_link), data=contrib_pop_readme, REML=FALSE)
|
||||||
|
summary(contrib_readme_model)
|
||||||
|
collab_contrib_model <- lmer(log1pcount ~ after_doc + ( 1 | upstream_vcs_link), data=collab_pop_contrib, REML=FALSE)
|
||||||
|
summary(collab_contrib_model)
|
||||||
|
contrib_contrib_model <- lmer(log1pcount ~ after_doc + ( 1 | upstream_vcs_link), data=contrib_pop_contrib, REML=FALSE)
|
||||||
|
summary(contrib_contrib_model)
|
||||||
|
library(ggplot2)
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = logcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
expanded_contrib_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = count, col = as.factor(is_collab))) +
|
||||||
|
geom_point() +
|
||||||
|
geom_smooth(method = 'lm', se = F) + geom_jitter()
|
||||||
|
|||||||
@ -51,12 +51,13 @@ mrg_actions_data$log1p_count <- log1p(mrg_actions_data$count)
|
|||||||
#imports for models
|
#imports for models
|
||||||
library(lme4)
|
library(lme4)
|
||||||
library(optimx)
|
library(optimx)
|
||||||
|
library(lattice)
|
||||||
#models -- TKTK need to be fixed
|
#models -- TKTK need to be fixed
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_offset| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
summary(all_model)
|
summary(all_model)
|
||||||
#identifying the quartiles of effect for D
|
#identifying the quartiles of effect for D
|
||||||
all_model_ranef <- as.data.frame(ranef(all_model))
|
all_model_ranef <- ranef(all_model)
|
||||||
d_effect_ranef_all <- all_model_ranef[all_model_ranef$term=="D",]
|
d_effect_ranef_all <- all_model_ranef[all_model_ranef$term=="D",]
|
||||||
d_effect_ranef_all$quartile <- ntile(d_effect_ranef_all$condval, 4)
|
d_effect_ranef_all$quartile <- ntile(d_effect_ranef_all$condval, 4)
|
||||||
#model residuals
|
#model residuals
|
||||||
@ -67,12 +68,10 @@ mrg_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (week_o
|
|||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
summary(mrg_model)
|
summary(mrg_model)
|
||||||
#identifying the quartiles of effect for D
|
#identifying the quartiles of effect for D
|
||||||
mrg_model_ranef <- as.data.frame(ranef(mrg_model))
|
mrg_model_ranef <- ranef(mrg_model)
|
||||||
|
dotplot(mrg_model_ranef)
|
||||||
d_effect_ranef_mrg <- mrg_model_ranef[mrg_model_ranef$term=="D",]
|
d_effect_ranef_mrg <- mrg_model_ranef[mrg_model_ranef$term=="D",]
|
||||||
d_effect_ranef_mrg$quartile <- ntile(d_effect_ranef_mrg$condval, 4)
|
d_effect_ranef_mrg$quartile <- ntile(d_effect_ranef_mrg$condval, 4)
|
||||||
#merge model residuals
|
#merge model residuals
|
||||||
mrg_residuals <- residuals(mrg_model)
|
mrg_residuals <- residuals(mrg_model)
|
||||||
qqnorm(mrg_residuals)
|
qqnorm(mrg_residuals)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
55
R/popRDDAnalyssis.R
Normal file
55
R/popRDDAnalyssis.R
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
library(tidyverse)
|
||||||
|
library(plyr)
|
||||||
|
library(stringr)
|
||||||
|
try(setwd(dirname(rstudioapi::getActiveDocumentContext()$path)))
|
||||||
|
#load in data
|
||||||
|
contrib_df <- read_csv("../final_data/deb_contrib_pop_change.csv")
|
||||||
|
readme_df <- read_csv("../final_data/deb_readme_pop_change.csv")
|
||||||
|
#some expansion needs to happens for each project
|
||||||
|
expand_timeseries <- function(project_row) {
|
||||||
|
longer <- project_row |>
|
||||||
|
pivot_longer(cols = ends_with("new"),
|
||||||
|
names_to = "window",
|
||||||
|
values_to = "count") |>
|
||||||
|
unnest(count) |>
|
||||||
|
mutate(after_doc = as.numeric(str_detect(window, "after"))) |>
|
||||||
|
mutate(is_collab = as.numeric(str_detect(window, "collab")))
|
||||||
|
return(longer)
|
||||||
|
}
|
||||||
|
expanded_readme_data <- expand_timeseries(readme_df[1,])
|
||||||
|
for (i in 2:nrow(readme_df)){
|
||||||
|
expanded_readme_data <- rbind(expanded_readme_data, expand_timeseries(readme_df[i,]))
|
||||||
|
}
|
||||||
|
expanded_contrib_data <- expand_timeseries(contrib_df[1,])
|
||||||
|
for (i in 2:nrow(contrib_df)){
|
||||||
|
expanded_contrib_data <- rbind(expanded_contrib_data, expand_timeseries(contrib_df[i,]))
|
||||||
|
}
|
||||||
|
expanded_readme_data$log1pcount <- log1p(expanded_readme_data$count)
|
||||||
|
expanded_contrib_data$log1pcount <- log1p(expanded_contrib_data$count)
|
||||||
|
expanded_readme_data$logcount <- log(expanded_readme_data$count)
|
||||||
|
expanded_contrib_data$logcount <- log(expanded_contrib_data$count)
|
||||||
|
#breaking out the types of population counts
|
||||||
|
collab_pop_readme <- expanded_readme_data[which(expanded_readme_data$is_collab == 1),]
|
||||||
|
contrib_pop_readme <- expanded_readme_data[which(expanded_readme_data$is_collab == 0),]
|
||||||
|
collab_pop_contrib <- expanded_contrib_data[which(expanded_contrib_data$is_collab == 1),]
|
||||||
|
contrib_pop_contrib <- expanded_contrib_data[which(expanded_contrib_data$is_collab == 0),]
|
||||||
|
#import models
|
||||||
|
library(lme4)
|
||||||
|
library(optimx)
|
||||||
|
collab_readme_model <- lmer(log1pcount ~ after_doc + (1| upstream_vcs_link), data=collab_pop_readme, REML=FALSE)
|
||||||
|
summary(collab_readme_model)
|
||||||
|
contrib_readme_model <- lmer(log1pcount ~ after_doc + ( 1| upstream_vcs_link), data=contrib_pop_readme, REML=FALSE)
|
||||||
|
summary(contrib_readme_model)
|
||||||
|
collab_contrib_model <- lmer(log1pcount ~ after_doc + ( 1 | upstream_vcs_link), data=collab_pop_contrib, REML=FALSE)
|
||||||
|
summary(collab_contrib_model)
|
||||||
|
contrib_contrib_model <- lmer(log1pcount ~ after_doc + ( 1 | upstream_vcs_link), data=contrib_pop_contrib, REML=FALSE)
|
||||||
|
summary(contrib_contrib_model)
|
||||||
|
|
||||||
|
library(ggplot2)
|
||||||
|
expanded_readme_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = log1pcount, col = as.factor(is_collab))) +
|
||||||
|
geom_point() + geom_jitter()
|
||||||
|
|
||||||
|
expanded_contrib_data |>
|
||||||
|
ggplot(aes(x = after_doc, y = count, col = as.factor(is_collab))) +
|
||||||
|
geom_point() + geom_jitter()
|
||||||
@ -58,13 +58,17 @@ all_actions_data$log1p_count <- log1p(all_actions_data$count)
|
|||||||
library(lme4)
|
library(lme4)
|
||||||
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
|
# https://www.bristol.ac.uk/cmm/learning/videos/random-intercepts.html#exvar
|
||||||
library(optimx)
|
library(optimx)
|
||||||
|
library(lattice)
|
||||||
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
|
||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
summary(all_model)
|
summary(all_model)
|
||||||
#identifying the quartiles of effect for D
|
#identifying the quartiles of effect for D
|
||||||
all_model_ranef <- as.data.frame(ranef(all_model))
|
all_model_ranef <- ranef(all_model, condVar=TRUE)
|
||||||
d_effect_ranef_all <- all_model_ranef[all_model_ranef$term=="D",]
|
dotplot(all_model_ranef)
|
||||||
d_effect_ranef_all$quartile <- ntile(d_effect_ranef_all$condval, 4)
|
df_ranefs <- as.data.frame(all_model_ranef)
|
||||||
|
#D_df_ranef <- df_ranefs[df_ranefs$term == "D"]
|
||||||
|
#d_effect_ranef_all <- all_model_ranef$upstream_vcs_link
|
||||||
|
#d_effect_ranef_all$quartile <- ntile(d_effect_ranef_all$condval, 4)
|
||||||
#model residuals
|
#model residuals
|
||||||
all_residuals <- residuals(all_model)
|
all_residuals <- residuals(all_model)
|
||||||
qqnorm(all_residuals)
|
qqnorm(all_residuals)
|
||||||
@ -73,12 +77,11 @@ mrg_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(
|
|||||||
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
|
||||||
summary(mrg_model)
|
summary(mrg_model)
|
||||||
#identifying the quartiles of effect for D
|
#identifying the quartiles of effect for D
|
||||||
mrg_model_ranef <- as.data.frame(ranef(mrg_model))
|
mrg_model_ranef <- ranef(mrg_model, condVar=TRUE)
|
||||||
|
dotplot(mrg_model_ranef)
|
||||||
d_effect_ranef_mrg <- mrg_model_ranef[mrg_model_ranef$term=="D",]
|
d_effect_ranef_mrg <- mrg_model_ranef[mrg_model_ranef$term=="D",]
|
||||||
d_effect_ranef_mrg$quartile <- ntile(d_effect_ranef_mrg$condval, 4)
|
d_effect_ranef_mrg$quartile <- ntile(d_effect_ranef_mrg$condval, 4)
|
||||||
#merge model residuals
|
#merge model residuals
|
||||||
mrg_residuals <- residuals(mrg_model)
|
mrg_residuals <- residuals(mrg_model)
|
||||||
qqnorm(mrg_residuals)
|
qqnorm(mrg_residuals)
|
||||||
# Performance:
|
# Performance:
|
||||||
|
|
||||||
|
|
||||||
Loading…
Reference in New Issue
Block a user