natfeedback_code_eLife/R/figure_1_S5.Rmd

---
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