Organic Chemistry Survey: Classroom Norms (Class/Own Beliefs)

Prepare Data

Import surveys, combine into single data frame, delete identifying information, assign IDs, and separate out by scale for item examination.

# https://hansjoerg.me/2018/04/23/rasch-in-r-tutorial/

knitr::knit_hooks$set(
   error = function(x, options) {
     paste('\n\n<div class="alert alert-danger">',
           gsub('##', '\n', gsub('^##\ Error', '**Error**', x)),
           '</div>', sep = '\n')
   },
   warning = function(x, options) {
     paste('\n\n<div class="alert alert-warning">',
           gsub('##', '\n', gsub('^##\ Warning:', '**Warning**', x)),
           '</div>', sep = '\n')
   },
   message = function(x, options) {
     paste('\n\n<div class="alert alert-info">',
           gsub('##', '\n', x),
           '</div>', sep = '\n')
   }
)

# load libraries ----------------------------------------------------------
library(stringi)
library(psych)
library(DT)
library(naniar)
library(UpSetR)
library(nFactors)
library(lavaan)
library(corrplot)
library(tidyr)

library(ggplot2)
library(dplyr)
library("eRm")
library("ltm")
library("difR")
library("psych")

# load data ---------------------------------------------------------------
# alt <- read.csv(file="UBelong Post-Survey Pitt OChem Spring 2022 Alternative Scales_April 28, 2022_12.34.csv", header=T)
# alt <- alt[-c(1,2),]
# alt$scale <- "alt"
# 
# orig <- read.csv(file="UBelong Post-Survey Pitt OChem Spring 2022 Original Scales_April 28, 2022_12.35.csv", header=T)
# orig <- orig[-c(1,2),]
# orig$scale <- "orig"
# 
# df <- rbind.data.frame(alt, orig)
# df <- subset(df, select = -c(1:19))
# names(df)
# myFun <- function(n) {
#   a <- do.call(paste0, replicate(5, sample(LETTERS, n, TRUE), FALSE))
#   paste0(a, sprintf("%04d", sample(9999, n, TRUE)), sample(LETTERS, n, TRUE))
# }
# df$id <- myFun(nrow(df))
# write.csv(df, file="imported_anonymized.csv", row.names = F)

df <- read.csv(file="imported_anonymized.csv", header=T)

# extract items -----------------------------------------------------------
# new items
EEochem <- subset(df, select=c(scale,grep("EEochem", colnames(df)))) # entry expectations
CCdisc <- subset(df, select=c(scale,grep("CCdisc", colnames(df)))) # classroom climate
IDochem <- cbind.data.frame(subset(df, select=c(scale,grep("IDochem", colnames(df)))), subset(df, select=grep("FASochem", colnames(df)))) # identity
CSochem <- subset(df, select=grep("CSochem", colnames(df))) # career satisfaction

# established scales
MSchem <- subset(df, select=c(scale,grep("MSchem", colnames(df)))) # discipline growth mindset (chemistry)
IPchem <- subset(df, select=c(scale,grep("IPchem", colnames(df)))) # instructor growth mindset (chemistry)
SEchem <- subset(df, select=c(scale, grep("SEchem", colnames(df)))) # disciplinary self-efficacy (chemistry)
MSochem <- subset(df, select=c(scale, grep("MSochem", colnames(df)))) # disciplinary growth mindset (organic chemistry)
IPochem <- subset(df, select=grep("IPochem", colnames(df))) # instructor growth mindset (organic chemistry)
SEochem <- subset(df, select=grep("SEochem", colnames(df))) # disciplinary self-efficacy (organic chemistry)
CNEBochem <- subset(df, select=c(scale, grep("CNEBochem", colnames(df)))) # entity norms and beliefs
CNHSochem_others <- cbind.data.frame(subset(subset(df, select=grep("CNHSochem", colnames(df))), select=c(1:3))) # help seeking
CNHSochem_self <- cbind.data.frame(subset(subset(df, select=grep("CNHSochem", colnames(df))), select=c(4:6))) # help seeking
CNSWochem <- subset(df, select=grep("CNSWochem", colnames(df))) # help seeking
FCochem <- subset(df, select=grep("FCochem", colnames(df))) # faculty caring

CNEBochem$CNEBochem03_rc[CNEBochem$CNEBochem03 == 1] <- 4
CNEBochem$CNEBochem03_rc[CNEBochem$CNEBochem03 == 2] <- 3
CNEBochem$CNEBochem03_rc[CNEBochem$CNEBochem03 == 3] <- 2
CNEBochem$CNEBochem03_rc[CNEBochem$CNEBochem03 == 4] <- 1
CNEBochem$CNEBochem06_rc[CNEBochem$CNEBochem06 == 1] <- 4
CNEBochem$CNEBochem06_rc[CNEBochem$CNEBochem06 == 2] <- 3
CNEBochem$CNEBochem06_rc[CNEBochem$CNEBochem06 == 3] <- 2
CNEBochem$CNEBochem06_rc[CNEBochem$CNEBochem06 == 4] <- 1
CNEBochem$CNEBochem03 <- CNEBochem$CNEBochem03_rc
CNEBochem$CNEBochem06 <- CNEBochem$CNEBochem06_rc
CNEBochem <- subset(CNEBochem, select=-c(CNEBochem03_rc, CNEBochem06_rc))

Classroom Norms

Items

Class Beliefs

Imagine students who scored low on the first exam in this class. What did most students in this class think about the low scoring students?

…low scoring students were not smart enough to truly understand [organic chemistry]
…not everyone has the natural ability to get an ‘A’ in [organic chemistry]
…with enough hard work, low scoring students could have been getting an ‘A’ in [organic chemistry]

Own Beliefs

What did you think about the low scoring students? I thought…

…low scoring students were not smart enough to truly understand [organic chemistry]
…not everyone has the natural ability to get an ‘A’ in [organic chemistry]
…with enough hard work, low scoring students could have been getting an ‘A’ in [organic chemistry]

Stats - Original

Univariate Stats

d <- subset(CNEBochem, scale == "orig", select=-c(scale))
CNEBchem_desc <- data.frame(describe(d))
datatable(subset(CNEBchem_desc, select=-c(n, trimmed, mad))) %>%
  formatRound(1:10) %>%
  formatStyle(8:9, color = styleInterval(c(-2, 2), c('red', 'black', 'red')))

Missingness

vis_miss(d)

# gg_miss_upset(EEochem)

Histograms

ggplot(gather(d), aes(value)) + 
  geom_histogram(bins = 4) + 
  facet_wrap(~key)

Warning Removed 2 rows containing non-finite values (stat_bin).

Item Correlations

corr <- corr.test(d, adjust = "holm")

rval <- corr$r
rval[lower.tri(corr$r, diag = T)] <- NA

datatable(rval) %>%
  formatRound(1:ncol(rval)) %>%
  formatStyle(1:ncol(rval), color = styleInterval(c(-.7, .7), c('red', 'black', 'red')))

corrplot(corr$r)

EFA (1Fac)

d <- na.omit(d)
ev <- eigen(cor(d))
ap <- parallel(subject=nrow(d),var=ncol(d),rep=100,cent=.05)
nS <- nScree(x=ev$values, aparallel=ap$eigen$qevpea)
plotnScree(nS)

EFA <- factanal(d, factors = 1, rotation = "promax")
print(EFA, digits=3, cutoff=.0, sort=TRUE)

## 
## Call:
## factanal(x = d, factors = 1, rotation = "promax")
## 
## Uniquenesses:
## CNEBochem01 CNEBochem02 CNEBochem03 CNEBochem04 CNEBochem05 CNEBochem06 
##       0.890       0.411       0.658       0.760       0.285       0.753 
## 
## Loadings:
## [1] 0.767 0.585 0.845 0.331 0.489 0.497
## 
##                Factor1
## SS loadings      2.242
## Proportion Var   0.374
## 
## Test of the hypothesis that 1 factor is sufficient.
## The chi square statistic is 38.45 on 9 degrees of freedom.
## The p-value is 1.45e-05

EFA (2Fac)

d <- na.omit(d)
ev <- eigen(cor(d))
ap <- parallel(subject=nrow(d),var=ncol(d),rep=100,cent=.05)
nS <- nScree(x=ev$values, aparallel=ap$eigen$qevpea)
plotnScree(nS)

EFA <- factanal(d, factors = 2, rotation = "promax")
print(EFA, digits=3, cutoff=.25, sort=TRUE)

## 
## Call:
## factanal(x = d, factors = 2, rotation = "promax")
## 
## Uniquenesses:
## CNEBochem01 CNEBochem02 CNEBochem03 CNEBochem04 CNEBochem05 CNEBochem06 
##       0.882       0.489       0.613       0.748       0.086       0.005 
## 
## Loadings:
##             Factor1 Factor2
## CNEBochem02  0.687         
## CNEBochem04  0.554         
## CNEBochem05  1.014         
## CNEBochem06          1.072 
## CNEBochem01          0.290 
## CNEBochem03  0.304   0.398 
## 
##                Factor1 Factor2
## SS loadings      1.927   1.417
## Proportion Var   0.321   0.236
## Cumulative Var   0.321   0.557
## 
## Factor Correlations:
##         Factor1 Factor2
## Factor1   1.000  -0.565
## Factor2  -0.565   1.000
## 
## Test of the hypothesis that 2 factors are sufficient.
## The chi square statistic is 20.99 on 4 degrees of freedom.
## The p-value is 0.000318

EFA (3Fac)

d <- na.omit(d)
ev <- eigen(cor(d))
ap <- parallel(subject=nrow(d),var=ncol(d),rep=100,cent=.05)
nS <- nScree(x=ev$values, aparallel=ap$eigen$qevpea)
plotnScree(nS)

EFA <- factanal(d, factors = 3, rotation = "promax", cutoff = 0.3)
print(EFA, digits=3, cutoff=.3, sort=TRUE)

## 
## Call:
## factanal(x = d, factors = 3, rotation = "promax", cutoff = 0.3)
## 
## Uniquenesses:
## CNEBochem01 CNEBochem02 CNEBochem03 CNEBochem04 CNEBochem05 CNEBochem06 
##       0.005       0.488       0.548       0.670       0.005       0.249 
## 
## Loadings:
##             Factor1 Factor2 Factor3
## CNEBochem02  0.597                 
## CNEBochem05  1.074                 
## CNEBochem01          1.030         
## CNEBochem03                  0.559 
## CNEBochem06                  0.900 
## CNEBochem04  0.482                 
## 
##                Factor1 Factor2 Factor3
## SS loadings      1.829   1.184   1.163
## Proportion Var   0.305   0.197   0.194
## Cumulative Var   0.305   0.502   0.696
## 
## Factor Correlations:
##         Factor1 Factor2 Factor3
## Factor1    1.00   0.410   0.560
## Factor2    0.41   1.000   0.294
## Factor3    0.56   0.294   1.000
## 
## The degrees of freedom for the model is 0 and the fit was 0.0894

Stats - Alternative

Univariate Stats

d <- subset(CNEBochem, scale == "alt", select=-c(scale))
CNEBchem_desc <- data.frame(describe(d))
datatable(subset(CNEBchem_desc, select=-c(n, trimmed, mad))) %>%
  formatRound(1:10) %>%
  formatStyle(8:9, color = styleInterval(c(-2, 2), c('red', 'black', 'red')))

Missingness

vis_miss(d)

# gg_miss_upset(EEochem)

Histograms

ggplot(gather(d), aes(value)) + 
  geom_histogram(bins = 4) + 
  facet_wrap(~key)

Warning Removed 6 rows containing non-finite values (stat_bin).

Item Correlations

corr <- corr.test(d, adjust = "holm")

rval <- corr$r
rval[lower.tri(corr$r, diag = T)] <- NA

datatable(rval) %>%
  formatRound(1:ncol(rval)) %>%
  formatStyle(1:ncol(rval), color = styleInterval(c(-.7, .7), c('red', 'black', 'red')))

corrplot(corr$r)

EFA (1Fac)

d <- na.omit(d)
ev <- eigen(cor(d))
ap <- parallel(subject=nrow(d),var=ncol(d),rep=100,cent=.05)
nS <- nScree(x=ev$values, aparallel=ap$eigen$qevpea)
plotnScree(nS)

EFA <- factanal(d, factors = 1, rotation = "promax", cutoff = 0.3)
print(EFA, digits=3, cutoff=.0, sort=TRUE)

## 
## Call:
## factanal(x = d, factors = 1, rotation = "promax", cutoff = 0.3)
## 
## Uniquenesses:
## CNEBochem01 CNEBochem02 CNEBochem03 CNEBochem04 CNEBochem05 CNEBochem06 
##       0.916       0.511       0.718       0.893       0.313       0.699 
## 
## Loadings:
## [1] 0.700 0.531 0.829 0.548 0.289 0.327
## 
##                Factor1
## SS loadings      1.950
## Proportion Var   0.325
## 
## Test of the hypothesis that 1 factor is sufficient.
## The chi square statistic is 64.32 on 9 degrees of freedom.
## The p-value is 1.96e-10

EFA (2Fac)

d <- na.omit(d)
ev <- eigen(cor(d))
ap <- parallel(subject=nrow(d),var=ncol(d),rep=100,cent=.05)
nS <- nScree(x=ev$values, aparallel=ap$eigen$qevpea)
plotnScree(nS)

EFA <- factanal(d, factors = 2, rotation = "promax", cutoff = 0.3)
print(EFA, digits=3, cutoff=.4, sort=TRUE)

## 
## Call:
## factanal(x = d, factors = 2, rotation = "promax", cutoff = 0.3)
## 
## Uniquenesses:
## CNEBochem01 CNEBochem02 CNEBochem03 CNEBochem04 CNEBochem05 CNEBochem06 
##       0.005       0.473       0.719       0.748       0.211       0.723 
## 
## Loadings:
##             Factor1 Factor2
## CNEBochem02  0.617         
## CNEBochem03  0.570         
## CNEBochem05  0.925         
## CNEBochem06  0.523         
## CNEBochem01          1.036 
## CNEBochem04          0.432 
## 
##                Factor1 Factor2
## SS loadings      1.868   1.347
## Proportion Var   0.311   0.225
## Cumulative Var   0.311   0.536
## 
## Factor Correlations:
##         Factor1 Factor2
## Factor1   1.000  -0.379
## Factor2  -0.379   1.000
## 
## Test of the hypothesis that 2 factors are sufficient.
## The chi square statistic is 31.11 on 4 degrees of freedom.
## The p-value is 2.9e-06

EFA (3Fac)

d <- na.omit(d)
ev <- eigen(cor(d))
ap <- parallel(subject=nrow(d),var=ncol(d),rep=100,cent=.05)
nS <- nScree(x=ev$values, aparallel=ap$eigen$qevpea)
plotnScree(nS)

EFA <- factanal(d, factors = 3, rotation = "promax", cutoff = 0.3)
print(EFA, digits=3, cutoff=.4, sort=TRUE)

## 
## Call:
## factanal(x = d, factors = 3, rotation = "promax", cutoff = 0.3)
## 
## Uniquenesses:
## CNEBochem01 CNEBochem02 CNEBochem03 CNEBochem04 CNEBochem05 CNEBochem06 
##       0.005       0.005       0.484       0.733       0.448       0.304 
## 
## Loadings:
##             Factor1 Factor2 Factor3
## CNEBochem03  0.715                 
## CNEBochem06  0.906                 
## CNEBochem02          1.041         
## CNEBochem05          0.507         
## CNEBochem01                  0.983 
## CNEBochem04                  0.444 
## 
##                Factor1 Factor2 Factor3
## SS loadings      1.533   1.380   1.198
## Proportion Var   0.256   0.230   0.200
## Cumulative Var   0.256   0.485   0.685
## 
## Factor Correlations:
##         Factor1 Factor2 Factor3
## Factor1   1.000  -0.258   0.178
## Factor2  -0.258   1.000  -0.535
## Factor3   0.178  -0.535   1.000
## 
## The degrees of freedom for the model is 0 and the fit was 0.0264

1PL Model - Orig (1F)

Summary & Fit

d <- subset(CNEBochem, scale == "orig", select=-c(scale))
d <- d %>%
  mutate_at(vars(1:ncol(d)), recode, `1` = 0, `2` = 0, `3` = 1, `4` = 1)

mod2 <- rasch(d)

Warning in rasch(d): Hessian matrix at convergence is not positive definite; unstable solution.

summary(mod2)

Warning in sqrt(diag(new.covar)): NaNs produced

Warning in sqrt(Var[n.ind + 1, n.ind + 1]): NaNs produced

## 
## Call:
## rasch(data = d)
## 
## Model Summary:
##    log.Lik      AIC      BIC
##  -296.9734 607.9467 624.7079
## 
## Coefficients:
##                      value std.err  z.vals
## Dffclt.CNEBochem01  1.2834  0.1461  8.7844
## Dffclt.CNEBochem02 -0.6834  0.2578 -2.6507
## Dffclt.CNEBochem03  0.4333  0.2756  1.5718
## Dffclt.CNEBochem04  2.0903     NaN     NaN
## Dffclt.CNEBochem05 -0.0131  0.2904 -0.0452
## Dffclt.CNEBochem06 -0.1212  0.2881 -0.4207
## Dscrmn              0.8960     NaN     NaN
## 
## Integration:
## method: Gauss-Hermite
## quadrature points: 21 
## 
## Optimization:
## Convergence: 0 
## max(|grad|): 10 
## quasi-Newton: BFGS

item.fit(mod2, simulate.p.value=T)

Warning in rasch(data = X.new): Hessian matrix at convergence is not positive definite; unstable solution.

## 
## Item-Fit Statistics and P-values
## 
## Call:
## rasch(data = d)
## 
## Alternative: Items do not fit the model
## Ability Categories: 10
## Monte Carlo samples: 100 
## 
##                 X^2 Pr(>X^2)
## CNEBochem01 13.0366   0.1881
## CNEBochem02 10.8825   0.5248
## CNEBochem03  3.9446   0.9208
## CNEBochem04 12.8103   0.1386
## CNEBochem05  9.3885   0.6139
## CNEBochem06  7.5899   0.7624

ICC

plot(mod2, type = 'ICC', auto.key = FALSE)

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

IIC

plot(mod2, type = 'IIC', auto.key = FALSE)

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Individual ICC Plots

items <- colnames(d)
n <- 1
for (i in 1:ncol(d)) {
  plot(mod2, type = 'ICC', auto.key = FALSE, items = n, main = items[n], annot = F)
  n <- n + 1
}

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Individual IIC Plots

items <- colnames(d)
n <- 1
for (i in 1:ncol(d)) {
  plot(mod2, type = 'IIC', auto.key = FALSE, items = n, main = items[n], annot = F)
  n <- n + 1
}

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Test Information Function

plot(mod2, type=c("IIC"), items=c(0), ylim=c(0,5))

1PL Model - Alt (1F)

Summary & Fit

d <- subset(CNEBochem, scale == "alt", select=-c(scale))
d <- d %>%
  mutate_at(vars(1:ncol(d)), recode, `1` = 0, `2` = 0, `3` = 1, `4` = 1)

d1 <- subset(d, select=c(CNEBochem03, CNEBochem06))
d2 <- subset(d, select=c(CNEBochem02, CNEBochem05))
d3 <- subset(d, select=c(CNEBochem01, CNEBochem04))

d <- d1

mod2 <- rasch(d)
summary(mod2)

## 
## Call:
## rasch(data = d)
## 
## Model Summary:
##    log.Lik      AIC      BIC
##  -123.0712 252.1424 260.0174
## 
## Coefficients:
##                     value std.err z.vals
## Dffclt.CNEBochem03 0.0145  0.1448 0.1001
## Dffclt.CNEBochem06 0.3371  0.1509 2.2341
## Dscrmn             2.9261  0.7238 4.0427
## 
## Integration:
## method: Gauss-Hermite
## quadrature points: 21 
## 
## Optimization:
## Convergence: 0 
## max(|grad|): 0.0029 
## quasi-Newton: BFGS

item.fit(mod2, simulate.p.value=T)

Warning in rasch(data = X.new): Hessian matrix at convergence is not positive definite; unstable solution.

## 
## Item-Fit Statistics and P-values
## 
## Call:
## rasch(data = d)
## 
## Alternative: Items do not fit the model
## Ability Categories: 10
## Monte Carlo samples: 100 
## 
##                 X^2 Pr(>X^2)
## CNEBochem03 12.0698    0.505
## CNEBochem06 11.3033   0.5149

ICC

plot(mod2, type = 'ICC', auto.key = FALSE)

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

IIC

plot(mod2, type = 'IIC', auto.key = FALSE)

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Individual ICC Plots

items <- colnames(d)
n <- 1
for (i in 1:ncol(d)) {
  plot(mod2, type = 'ICC', auto.key = FALSE, items = n, main = items[n], annot = F)
  n <- n + 1
}

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Individual IIC Plots

items <- colnames(d)
n <- 1
for (i in 1:ncol(d)) {
  plot(mod2, type = 'IIC', auto.key = FALSE, items = n, main = items[n], annot = F)
  n <- n + 1
}

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Test Information Function

plot(mod2, type=c("IIC"), items=c(0), ylim=c(0,5))

1PL Model - Alt (2F)

Summary & Fit

d <- d2

mod2 <- rasch(d)
summary(mod2)

## 
## Call:
## rasch(data = d)
## 
## Model Summary:
##    log.Lik      AIC      BIC
##  -109.1146 224.2293 232.1042
## 
## Coefficients:
##                      value std.err  z.vals
## Dffclt.CNEBochem02 -0.7694  0.1609 -4.7804
## Dffclt.CNEBochem05 -0.3257  0.1448 -2.2497
## Dscrmn              3.3902  0.9066  3.7396
## 
## Integration:
## method: Gauss-Hermite
## quadrature points: 21 
## 
## Optimization:
## Convergence: 0 
## max(|grad|): 3.3e-06 
## quasi-Newton: BFGS

item.fit(mod2, simulate.p.value=T)

## 
## Item-Fit Statistics and P-values
## 
## Call:
## rasch(data = d)
## 
## Alternative: Items do not fit the model
## Ability Categories: 10
## Monte Carlo samples: 100 
## 
##                 X^2 Pr(>X^2)
## CNEBochem02  8.9556   0.4455
## CNEBochem05 11.1753   0.3861

ICC

plot(mod2, type = 'ICC', auto.key = FALSE)

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

IIC

plot(mod2, type = 'IIC', auto.key = FALSE)

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Individual ICC Plots

items <- colnames(d)
n <- 1
for (i in 1:ncol(d)) {
  plot(mod2, type = 'ICC', auto.key = FALSE, items = n, main = items[n], annot = F)
  n <- n + 1
}

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Individual IIC Plots

items <- colnames(d)
n <- 1
for (i in 1:ncol(d)) {
  plot(mod2, type = 'IIC', auto.key = FALSE, items = n, main = items[n], annot = F)
  n <- n + 1
}

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Test Information Function

plot(mod2, type=c("IIC"), items=c(0), ylim=c(0,5))

1PL Model - Alt (3F)

Summary & Fit

d <- d3

mod2 <- rasch(d)
summary(mod2)

## 
## Call:
## rasch(data = d)
## 
## Model Summary:
##    log.Lik      AIC      BIC
##  -89.47386 184.9477 192.8226
## 
## Coefficients:
##                     value std.err z.vals
## Dffclt.CNEBochem01 1.0326  0.2536 4.0712
## Dffclt.CNEBochem04 1.5773  0.3469 4.5473
## Dscrmn             1.8010  0.6069 2.9675
## 
## Integration:
## method: Gauss-Hermite
## quadrature points: 21 
## 
## Optimization:
## Convergence: 0 
## max(|grad|): 0.00068 
## quasi-Newton: BFGS

item.fit(mod2, simulate.p.value=T)

Warning in rasch(data = X.new): Hessian matrix at convergence is not positive definite; unstable solution.

## 
## Item-Fit Statistics and P-values
## 
## Call:
## rasch(data = d)
## 
## Alternative: Items do not fit the model
## Ability Categories: 10
## Monte Carlo samples: 100 
## 
##                 X^2 Pr(>X^2)
## CNEBochem01 21.3531   0.4356
## CNEBochem04 11.7735   0.5248

ICC

plot(mod2, type = 'ICC', auto.key = FALSE)

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

IIC

plot(mod2, type = 'IIC', auto.key = FALSE)

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in text.default(z[pos[it]], pr[pos[it], itms[it]], labels = nams[it], :

“auto.key” is not a graphical parameter

Individual ICC Plots

items <- colnames(d)
n <- 1
for (i in 1:ncol(d)) {
  plot(mod2, type = 'ICC', auto.key = FALSE, items = n, main = items[n], annot = F)
  n <- n + 1
}

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Individual IIC Plots

items <- colnames(d)
n <- 1
for (i in 1:ncol(d)) {
  plot(mod2, type = 'IIC', auto.key = FALSE, items = n, main = items[n], annot = F)
  n <- n + 1
}

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Warning in plot.window(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy, type, …): “auto.key” is not a graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in axis(side = side, at = at, labels = labels, …): “auto.key” is not a

graphical parameter

Warning in box(…): “auto.key” is not a graphical parameter

Warning in title(…): “auto.key” is not a graphical parameter

Warning in plot.xy(xy.coords(x, y), type = type, …): “auto.key” is not a

graphical parameter

Test Information Function

plot(mod2, type=c("IIC"), items=c(0), ylim=c(0,5))

Organic Chemistry Survey: Classroom Norms (Class/Own Beliefs)

Heather Perkins

5/13/2022

Prepare Data

Classroom Norms

Items

Class Beliefs

Own Beliefs

Stats - Original

Univariate Stats

Missingness

Histograms

Item Correlations

EFA (1Fac)

EFA (2Fac)

EFA (3Fac)

Stats - Alternative

Univariate Stats

Missingness

Histograms

Item Correlations

EFA (1Fac)

EFA (2Fac)

EFA (3Fac)

1PL Model - Orig (1F)

Summary & Fit

ICC

IIC

Individual ICC Plots

Individual IIC Plots

Test Information Function

1PL Model - Alt (1F)

Summary & Fit

ICC

IIC

Individual ICC Plots

Individual IIC Plots

Test Information Function

1PL Model - Alt (2F)

Summary & Fit

ICC

IIC

Individual ICC Plots

Individual IIC Plots

Test Information Function

1PL Model - Alt (3F)

Summary & Fit

ICC

IIC

Individual ICC Plots

Individual IIC Plots

Test Information Function