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- ---
- title: "Spacek et al., 2021, Figure 1-Supplement 5"
- output: pdf_document
- ---
- ```{r setup, include=FALSE}
- knitr::opts_chunk$set(echo = TRUE)
- library(arm)
- library(lmerTest)
- library(tidyverse)
- source('get_data.R')
- ```
- ```{r read_data_1_S5_c-f, include=FALSE}
- tib = get_data("../csv/fig1S5mvi.csv")
- ```
- ```{r tidy_for_1_S5cd, include = FALSE}
- # Turn feedback into a binary variable
- tb <- tib %>% mutate(feedback = ifelse(opto == TRUE, 0, 1))
- ```
- # Figure 1-Supplement 5c
- ## Effect of suppression on firing rate - movies
- ```{r fit_model_1_S5c}
- # Random intercept for neurons - including random slope gives singular fit
- lmer.1_S5c = lmer(rates ~ feedback + (1 | uid),
- data = tb %>% drop_na(rates))
- display(lmer.1_S5c)
- anova(lmer.1_S5c)
- ```
- ```{r get_predicted_average_effect_1_S5c, include=F}
- mSuppr = fixef(lmer.1_S5c)[1]
- diffRate = fixef(lmer.1_S5c)[2]
- mActive = fixef(lmer.1_S5c)[1] + diffRate
- ```
- Feedback: `r format(mActive, digits=2, nsmall=2)` spikes/s \newline
- Suppression: `r format(mSuppr, digits=2, nsmall=2)` spikes/s \newline
- n = `r nrow(tb %>% drop_na(rates) %>% count(uid))` neurons from `r nrow(tb %>% drop_na(rates) %>% count(mid))` mouse
- \newpage
- # Figure 1-Supplement 5d
- ## Effect of suppression on burst ratio - movies
- ```{r fit_model_1_S5d}
- # Random intercept for neurons, including random slope gives singular fits
- lmer.1_S5d = lmer(burstratios ~ feedback + (1 | uid),
- data = tb %>% drop_na(burstratios))
- display(lmer.1_S5d)
- anova(lmer.1_S5d)
- ```
- ```{r get_predicted_average_effect_1_S5d, include=F}
- mSuppr = fixef(lmer.1_S5d)[1]
- diffRate = fixef(lmer.1_S5d)[2]
- mActive = fixef(lmer.1_S5d)[1] + diffRate
- ```
- Feedback: `r format(mActive, digits=2, nsmall=2)` \newline
- Suppression: `r format(mSuppr, digits=2, nsmall=2)` \newline
- n = `r nrow(tb %>% drop_na(burstratios) %>% count(uid))` neurons from `r nrow(tb %>% drop_na(burstratios) %>% count(mid))` mouse
- ```{r read_data_1_S5_h-i, include=FALSE}
- tib = get_data("../csv/fig1S5grt.csv")
- ```
- ```{r tidy_for_1_S5_h-i, include = FALSE}
- # Turn feedback into a binary variable
- tb <- tib %>% mutate(feedback = ifelse(opto == TRUE, 0, 1))
- ```
- \newpage
- # Figure 1-Supplement 5h
- ## Effect of suppression on firing rates - gratings
- ```{r fit_model_1_S5h}
- # Random intercept for neurons
- lmer.1_S5h = lmer(rates ~ feedback + (1 | uid),
- data = tb %>% drop_na(rates))
- display(lmer.1_S5h)
- anova(lmer.1_S5h)
- ```
- ```{r get_predicted_average_effect_1_S5h, include=F}
- mSuppr = fixef(lmer.1_S5h)[1]
- diffRate = fixef(lmer.1_S5h)[2]
- mActive = fixef(lmer.1_S5h)[1] + diffRate
- ```
- Feedback: `r format(mActive, digits=2, nsmall=2)` spikes/s \newline
- Suppression: `r format(mSuppr, digits=2, nsmall=2)` spikes/s \newline
- n = `r nrow(tb %>% drop_na(rates) %>% count(uid))` neurons from `r nrow(tb %>% drop_na(rates) %>% count(mid))` mouse
- \newpage
- # Figure 1-Supplement 5i
- ## Effect of suppression on burst ratio - gratings
- ```{r fit_model_1_S5i}
- # Random intercept for neurons
- lmer.1_S5i = lmer(burstratios ~ feedback + (1 | uid),
- data = tb %>% drop_na(burstratios))
- display(lmer.1_S5i)
- anova(lmer.1_S5i)
- ```
- ```{r predicted_average_effect_1_S5i, include=F}
- mSuppr = fixef(lmer.1_S5i)[1]
- diffRate = fixef(lmer.1_S5i)[2]
- mActive = fixef(lmer.1_S5i)[1] + diffRate
- ```
- Feedback: `r format(mActive, digits=2, nsmall=2)` \newline
- Suppression: `r format(mSuppr, digits=2, nsmall=2)` \newline
- n = `r nrow(tb %>% drop_na(burstratios) %>% count(uid))` neurons from `r nrow(tb %>% drop_na(burstratios) %>% count(mid))` mouse
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