Here's the code I$\text{'}$m trying to set for an R project.

These are the directions:

Twelve E$.$ coli populations are cultivated in parallel in a reduced glucose medium that also contains citrate since $1988.$ Important is that only glucose can be used as carbon source under the experimental conditions. After many thousands of generations, scientists of the Lenski lab found that one population can suddenly metabolize citrate due to a mutations $($see attached paper$).$ Your assignment is now to analyze an additional data set that they generated and published $2023.$ I will distribute the paper after you all submitted your assignments.

The data table shows changes of the citrate concentrations in the culture medium of $4$ different E$.$ coli populations $($A$,$B$,$C$,$D$)$ during a $24$h window. Samples are taken at time point: $0,1,2,3,4,6,9,24.$ The scientist repeated the experiment $5$ times $-->5$ replicates. They measured the changes in the citrate concentration as changes of OD$420($Optical Density at $420$ nm$).$ The E$.$ coli population A$-$D represent different generations of the population that developed the mutation$/$mutations to metabolize citrate.: A$=30,000$ ; B$=32,000$; C$=34,000$; D$=40,000$ generations from start.

Your assignment:

Write an R program to analyze the data: calculate the mean plus standard deviation for each data point, plot the data with time $[$hours$]$ on the x$-$axis and citrate concentration $[$OD$420]$ on the y$-$axis. Submit your R script. $($You may need to reorganize the spreadsheet and remember to read the data into a variable$)$

Attached to this is an image of the data and below is my code.

setwd$("$C:$/$Users$/$Drake$/$Downloads$")$ # Install required packages if not already installed if $(!$requireNamespace$("$readr$",$ quietly $=$ TRUE$))\{$ install.packages$("$readr$")\}$ if $(!$requireNamespace$("$dplyr$",$ quietly $=$ TRUE$))\{$ install.packages$("$dplyr$")\}$ if $(!$requireNamespace$("$ggplot$2",$ quietly $=$ TRUE$))\{$ install.packages$("$ggplot$2")\}$ if $(!$requireNamespace$("$tidyr$",$ quietly $=$ TRUE$))\{$ install.packages$("$tidyr$")\}$ # Load libraries library$($readr$)$ library$($dplyr$)$ library$($ggplot$2)$ library$($tidyr$)$ data read.table$($file$=$'Data$\_$Citrate$\_$concentrations.csv$\text{'},$ header$=$TRUE, sep $=",")$ head$($data$)$ data$\_$long data $\%>\%$ pivot$\_$longer$($cols $=-$Time, names$\_$to $=$ "Population", values$\_$to $="$OD$420")$ summary$\_$stats data$\_$long $\%>\%$ group$\_$by$($Time$,$ Population$)\%>\%$ summarise$($ mean$\_$OD$420=$ mean$($OD$420,$ na$.$rm $=$ TRUE$),$ sd$\_$OD$420=$ sd$($OD$420,$ na$.$rm $=$ TRUE$),.$groups $=$ 'drop' $)$ print$($summary$\_$stats$)$ plot ggplot$($summary$\_$stats, aes$($x $=$ Time, y $=$ mean$\_$OD$420,$ color $=$ Population$))+$ geom$\_$line$($size $=1)+$ geom$\_$point$($size $=2)+$ geom$\_$errorbar$($aes$($ymin $=$ mean$\_$OD$420-$ sd$\_$OD$420,$ ymax $=$ mean$\_$OD$420+$ sd$\_$OD$420),$ width $=0\mathrm{.}2)+$ labs$($ title $=$ "Citrate Concentration Over Time", x $=$ "Time $($hours$)",$ y $=$ "Citrate Concentration $($OD$420)",$ color $=$ "Population" $)+$ theme$\_$minimal$()+$ theme$($text $=$ element$\_$text$($size $=12))$ ggsave$("$citrate$\_$concentration$\_$plot.png$",$ plot$)$

Below are my errors:

$[$Workspace loaded from ~$/.$RData$]>$ library$($ggplot$2)>$ library$($tidyr$)>$ data read.table$($file$=$'Data$\_$Citrate$\_$concentrations.csv$\text{'},$ header$=$TRUE, sep $=",")$ Error in file$($file$,"$rt$")$ : cannot open the connection In addition: Warning message: In file$($file$,"$rt$")$ : cannot open file 'Data$\_$Citrate$\_$concentrations.csv$\text{'}$: No such file or directory $>$ head$($data$)1$ function $(...,$ list $=$ character$(),$ package $=$ NULL, lib.loc $=$ NULL, $2$ verbose $=$ getOption$("$verbose$"),$ envir $=.$GlobalEnv, overwrite $=$ TRUE$)3\{4$ fileExt function$($x$)\{5$ db grepl$("\backslash \backslash \backslash \backslash .[^.]+\backslash \backslash \backslash \backslash .($gz$|$bz$2|$xz$)$$$",$ x$)6$ ans sub$(".*\backslash \backslash \backslash \backslash .","",$ x$)>$ data$\_$long data $\%>\%+$ pivot$\_$longer$($cols $=-$Time, names$\_$to $=$ "Population", values$\_$to $="$OD$420")$ Error in UseMethod$("$pivot$\_$longer"$)$ : no applicable method for 'pivot$\_$longer' applied to an object of class "function" $>$ summary$\_$stats data$\_$long $\%>\%+$ group$\_$by$($Time$,$ Population$)\%>\%+$ summarise$(+$ mean$\_$OD$420=$ mean$($OD$420,$ na$.$rm $=$ TRUE$),+$ sd$\_$OD$420=$ sd$($OD$420,$ na$.$rm $=$ TRUE$),+.$groups $=$ 'drop' $+)$ Error in summarise$(.,$ mean$\_$OD$420=$ mean$($OD$420,$ na$.$rm $=$ TRUE$),$ sd$\_$OD$420=$ sd$($OD$420,$ : could not find function "summarise" $>$ print$($summary$\_$stats$)$ Error: object 'summary$\_$stats' not found $>$ plot ggplot$($summary$\_$stats, aes$($x $=$ Time, y $=$ mean$\_$OD$420,$ color $=$ Population$))++$ geom$\_$line$($size $=1)++$ geom$\_$point$($size $=2)++$ geom$\_$errorbar$($aes$($ymin $=$ mean$\_$OD$420-$ sd$\_$OD$420,$ ymax $=$ mean$\_$OD$420+$ sd$\_$OD$420),$ width $=0\mathrm{.}2)++$ labs$(+$ title $=$ "Citrate Concentration Over Time", $+$ x $=$ "Time $($hours$)",+$ y $=$ "Citrate Concentration $($OD$420)",+$ color $=$ "Population" $+)++$ theme$\_$minimal$()++$ theme$($text $=$ element$\_$text$($size $=12))$ Error: object 'summary$\_$stats' not found $>$ ggsave$("$citrate$\_$concentration$\_$plot.png$",$ plot$)$ Saving $7$ x $7$ in image Error in x$theme : object of type 'closure' is not subsettable

I would appreciate the assistance