LIBNAME myFolder "P:\QAC\QAC201\Studies and Codebooks\StudyName\Data";
data new; set myFolder.filename;
R
load ("/path/to/file.Rdata")
myData_orig <- objectName
# If calling in from a text file:
myData_orig <- read.table(file = "/path/to/file.txt", sep = "\t", header = TRUE)
Selecting Variables
SPSS
* put this as a subordinate of the SAVE OUTFILE command; the outfile will only contain that specified variables.
/KEEP VAR1 VAR2 VAR3 VAR4 VAR5 VAR6 VAR7 VAR8.
STATA
use VAR1 VAR2 VAR3 VAR4 VAR5 VAR6 VAR7 VAR8 ///
using "P:\QAC\qac201\Studies and Codebooks\StudyName\Data\filename", clear
SAS
* put this code inside a data step;
KEEP VAR1 VAR2 VAR3 VAR4 VAR5 VAR6 VAR7 VAR8;
Selecting Observations When using large data sets, it is often necessary to subset the data so that you are including only those observations that can assist in answering your particular research question. In these cases, you may want to select your own sample from within the survey’s sampling frame. For example, if you are interested in identifying demographic predictors of depression among Type II diabetes patients, you would plan to subset the data to subjects endorsing Type II Diabetes.
SPSS
*must be added as a command option.
/SELECT=diabetes2 EQ 1
STATA
// create a subset from the data
if diabetes2==1
// if running a procedure on a subset of the data (format: procedure [arguments] if [condition]). for example,
reg height weight if diabetes2==1
SAS
* inside the data step;
if diabetes2=1;
R
# create a subset of the data
myDataSubset <- myData[myData$diabetes2 == 1, ]
Missing Data Often, you must define the response categories that represent missing data. For example, if the number 9 is used to represent a missing value, you must either designate in your program that this value represents missingness or else you must recode the variable into a missing data character that your statistical software recognizes. If you do not, the 9 will be treated as a real/meaningful value and will be included in each of your analyses.
SPSS
RECODE VAR1 (9=SYSMIS).
STATA
replace VAR1=. if VAR1==9
SAS
* inside the data step;
if VAR1=9 then VAR1=.;
R
myData$VAR1[myData$VAR1 == 9 ] <- NA
Converting String to Numeric Variable It is important when preparing to run statistical analyses in most software packages, that all variables have response categories that are numeric rather than “string” or “character” (i.e. response categories are actual strings of characters and/or symbols). All variables with string responses must therefore be recoded into numeric values. These numeric values are known as dummy codes in that they carry no direct numeric meaning.
SPSS
RECODE TREE ('Maple'=1) ('Oak'=2) INTO TREE_N.
STATA
generate TREE_N=.
replace TREE_N=1 if TREE=="Maple"
replace TREE_N=2 if TREE=="Oak"
// OR
encode TREE, gen(TREE_N)
SAS
* inside the data step;
if TREE='Maple' then TREE_N=1;
else if TREE= 'Oak' then TREE_N=2;
R
# Usually not necessary in R.
Collapsing Responses within a Variable If a variable has many response categories, it can be difficult to interpret the statistical analyses in which it is used. Alternatively, there may be too few subjects or observations identified by one or more response categories to allow for a successful analysis. In these cases, you would need to collapse across categories. For example, if you have the following categories for geographic region, you may want to collapse some of these categories:
Region: New England=1, Middle Atlantic=2, East North Central=3, West North Central=4, South Atlantic=5, East South Central=6, West South Central=7, Mountain=8, Pacific=9.
New_Region: East=1, West=2.
SPSS
COMPUTE new_region=2.
IF (region=1|region=2|region=3|region=5|region=6) new_region=1.
STATA
generate new_region =2
replace new_region=1 if region==1|region==2|region==3|region==5|region==6
// OR
recode region (1/3 5 6=2), gen(new_region)
SAS
* inside the data step;
if region=1 or region=2 or region=3 or region=5 or region=6 then new_region=1;
else if region=4 or region=7 or region=8 or region=9 then new_region=2;
Collapsing Responses Across Variables In many cases, you will want to combine multiple variables into one. For example, while NESARC assesses several individual anxiety disorders, I may be interested in anxiety more generally. In this case I would create a general anxiety variable in which those individuals who received a diagnosis of social phobia, generalized anxiety disorder, specific phobia, panic disorder, agoraphobia, or obsessive compulsive disorder would be coded “yes” and those who were free from all of these diagnoses would be coded “no”.
SPSS
IF (socphob=1|gad=1|specphob=1|panic=1|agora=1|ocd=1) anxiety=1.
RECODE anxiety (SYSMIS=0).
STATA
gen anxiety=1 if socphob==1|gad==1|specphob==1|panic==1|agora==1|ocd==1
replace anxiety=0 if anxiety==.
SAS
* inside the data step;
if socphob=1 or gad=1 or specphob=1 or panic=1 or agora=1 or ocd=1 then anxiety=1;
else anxiety=0;
Creating Index or Score If you are working with a number of items that represent a single construct, it may be useful to create a composite variable/score. For example, I want to use a list of nicotine dependence symptoms meant to address the presence or absence of nicotine dependence (e.g. tolerance, withdrawal, craving, etc.). Rather than using a dichotomous variable (i.e. nicotine dependence present/absent), I want to examine the construct as a dimensional scale (i.e. number of nicotine dependence symptoms). In this case, I would want to recode each symptom variable so that yes=1 and no=0 and then sum the items so that they represent one composite score.
Labeling Variables Given the often cryptic names that variables are given, it can sometimes be useful to label them.
SPSS
VARIABLE LABELS VAR1 'label'.
STATA
label variable VAR1 "label"
SAS
* inside the data step;
LABEL VAR1='label';
R
# no built-in label tags for variables
Renaming Variables Given the often cryptic names that variables are given, it can sometimes be useful to give a variable a new name (something that is easier for you to remember or recognize).
SPSS
* no actual rename function, this will create a copy of the variable with the desired name.
COMPUTE newvarname=VAR1.
Labeling Variable Responses/Values Given that nominal and ordinal variables have, or are given numeric response values (i.e. dummy codes), it can be useful to label those values so that the labels are displayed in your output.
* Set up format before the data step;
proc format; VALUE FORMATNAME 0="value0label" 1="value1label" 2="value2label" 3="value3label";
data myData; set myData;
* other data management procedures;
format VAR1 FORMATNAME.
run;
R
# get order of the values
levels(myData$VAR1)
# input the labels in the same order as how the values were printed above
levels(myData$VAR1) <- c("value0label", "value1label", "value2label", "value3label")
// visualization to show frequencies ssc install catplot catplot CategResponseVar CategExplanatoryVar
// visualization to show percents from overall total ssc install catplot catplot CategResponseVar CategExplanatoryVar, percent
// visualization to show percents within group – best to use when // response variable is more than 2 levels graph hbar (percent), over(CategResponseVar) over(CategExplanatoryVar) percent stack asyvars
// visualization to show percents within group – can only be used // when response variable has 2 levels. // Requires data management that has response variable coded as a binary 0/1 graph bar BinaryCategoricalResponseVar, over(CategExplanatoryVar)
# visualization - Assumes response variable is coded as 0/1
ggplot(data=graph_data) + stat_summary(aes(x=CategExplanatoryVar, y=BinaryResponseVar), fun=”mean”, geom=”bar”) + ylab(“Proportion of Subjects at each Response Level within each group”) + ggtitle(“Informative Title Here”)
Quantitative-Categorial (means by group)
SPSS
* numbers.
MEANS TABLES= CategExplanatoryVar by QuantResponseVar
/CELLS MEAN COUNT STDDEV.
* visualization: use GUI point-and-click.
\\Option 1: Boxplot
graph box QuantResponseVar, over(CategExplanatoryVar)\\Option 2: Bar Chart to show means graph bar QuantResponseVar, over(CategExplanatoryVar)
// visualization to show frequencies ssc install catplot catplot CategResponseVar CategExplanatoryVar// visualization to show percents from overall total ssc install catplot catplot CategResponseVar CategExplanatoryVar, percent
// visualization to show percents within group – best to use when // response variable is more than 2 levels graph hbar (percent), over(CategResponseVar) over(CategExplanatoryVar) percent stack asyvars
// visualization to show percents within group – can only be used // when response variable has 2 levels. // Requires data management that has response variable coded as a binary 0/1 graph bar BinaryCategoricalResponseVar, over(CategExplanatoryVar)
myChi <- chisq.test(myData$CategResponseVar, myData$CategExplanatoryVar)
myChi
myChi$observed # for actual, observed cell counts
prop.table(myChi$observed, 2) # for column percentages
prop.table(myChi$observed, 1) # for row percentages
## Post-hoc test of which explanatory levels vary. source(“https://raw.githubusercontent.com/PassionDrivenStatistics/R/master/ChiSquarePostHoc.R”) myChi<-chisq.test(myData$CategResponseVar, myData$CategExplantoryVar) Observed_table<-myChi$observed chisq.post.hoc(observed_table, popsInRows=FALSE, control=”bonferroni”)
## Or check Pearson Residuals myChi$residuals
Quantitative-Categorial (anova)
SPSS
UNIANOVA QuantResponseVar BY CategExplanatoryVar.
* for post-hoc test add the following options to the UNIANOVA command.
UNIANOVA QuantResponseVar BY CategExplanatoryVar.
/POSTHOC=CategExplanatoryVar (TUKEY)
/PRINT=ETASQ DESCRIPTIVE.
STATA
oneway QuantResponseVar CategExplanatoryVar, tabulate
// for post-hoc test add the `sidak` option to oneway command
oneway QuantResponseVar CategExplanatoryVar, tabulate sidak
SAS
proc anova; class CategExplanatoryVar;
model QuantResponseVar = CategExplanatoryVar; means CategExplanatoryVar;
* for post-hoc test add the `duncan` option to proc anova command;
proc anova; class CategExplanatoryVar;
model QuantResponseVar = CategExplanatoryVar; means CategExplanatoryVar /duncan;
R
myAnovaResults <- aov(QuantResponseVar ~ CategExplanatoryVar, data = myData)
summary(myAnovaResults)
# for post-hoc test
myAnovaResults <- aov(QuantResponseVar ~ CategExplanatoryVar, data = myData)
TukeyHSD(myAnovaResults)
proc sort; by CategThirdVar;
proc anova; class CategExplanatoryVar;
model QuantResponseVar=CategExplanatoryVar;
means CategExplanatoryVar;
by CategThirdVar /duncan;
R
by(myData,
myData$CategThirdVar,
function(x) list(aov(QuantResponseVar ~ CategExplanatoryVar, data = x), summary(aov( QuantResponseVar ~ CategExplanatoryVar, data = x))))
Quantitative-Quantitative (pearson correlation)
SPSS
SORT CASES BY CategThirdVar.
SPLIT FILE LAYERED BY CategThirdVar.
CORRELATIONS
/VARIABLES= QuantResponseVar QuantExplanatoryVar
/STATISTICS DESCRIPTIVES.
SPLIT FILE OFF.
* note if explanatory var is categorical, make sure that the variable is type `nominal`.
REGRESSION
/DEPENDENT QuantResponseVar
/METHOD ENTER ExplanatoryVar.
STATA
//if explanatory var is quantitative
reg QuantResponseVar c.QuantExplanatoryVar
//if explanatory var is categorical
reg QuantResponseVar i.CategExplanatoryVar
SAS
* if explanatory var is quantitative;
proc glm;
model QuantResponseVar=QuantExplanatoryVar /solution;
* if explanatory var is categorical;
proc glm; class CategExplanatoryVar;
model QuantResponseVar=CategExplanatoryVar /solution;
R
# if explanatory var is quantitative
my.lm <- lm(QuantResponseVar ~ QuantExplanatoryVar, data = myData)
summary(my.lm)
# if explanatory var is categorical
my.lm <- lm(QuantResponseVar ~ factor(CategExplanatoryVar), data = myData)
summary(my.lm)
Logistic
SPSS
* note if explanatory var is categorical, make sure that the variable is type `nominal`.
LOGISTIC REGRESSION BinaryResponseVar with ExplanatoryVar ThirdVar1 ThirdVar2.
STATA
// for all quantitative predictors, add `c.` before the variable name (e.g. c.height)
// for all categorical predictors, add `i.` before the variabe name (e.g. i.race)
logistic BinaryResponseVar ExplanatoryVar ThirdVar1 ThirdVar2
SAS
* list all categorical variables in the model under the class subcommand (e.g. CategThirdVar);
proc logistic;
class BinaryResponseVar(ref="referenceGroup") CategThirdVar;
model BinaryResponseVar = ExplanatoryVar CategThirdVar QuantThirdVar;
R
# if categorical variable is encoded as numeric, wrap it around with the factor() function (e.g. factor(ExplanatoryVar) )
my.logreg <- glm(BinaryResponseVar ~ ExplanatoryVar, data = myData, family = "binomial")
summary(my.logreg) # for p-values
exp(my.logreg$coefficients) # for odds ratios
exp(confint(my.logreg)) # for confidence intervals on the odds ratios
# If you have many explanatory variables, you can just continue to add them in
my.logreg <- glm(BinaryResponseVar ~ ExplanatoryVar + ExplanatoryVar2, data = myData, family = "binomial")
summary(my.logreg) # for p-values
exp(my.logreg$coefficients) # for odds ratios
exp(confint(my.logreg)) # for confidence intervals on the odds ratios
Multiple regression
SPSS
* note if explanatory var is categorical, make sure that the variable is type `nominal`.
REGRESSION
/DEPENDENT QuantResponseVar
/METHOD ENTER ExplanatoryVar ExtraVar1 ExtraVar2.
STATA
//if a predictor var is quantitative, add `c.`. if a predictor var is categorical, add `i.`.
reg QuantResponseVar i.CategExplanatoryVar i.CategExtraVar1 c.QuantExtraVar2
SAS
* if a predictor var is categorical, add to `class`;
proc glm;
class CategExplanatoryVar;
model QuantResponseVar=CategExplanatoryVar ExtraVar1 /solution;
R
# if a predictor var is categorical, wrap the var with factor() (e.g. factor(CategExtraVar) )
my.lm <- lm(QuantResponseVar ~ QuantExplanatoryVar + factor(CategExtraVar), data = myData)
summary(my.lm)
Regression with Interaction Term
Incorporating interaction term when response is Quantitative (Multiple Linear Regression)
SPSS
* note if explanatory var is categorical, make sure that the variable is type `nominal`. REGRESSION /DEPENDENT QuantResponseVar /METHOD ENTER ExplanatoryVar ExtraVar1 ExtraVar2.
STATA
//to incorporate a moderator (statistical interaction term) in your model add `#` between the two terms // add `i.` for categorical terms in the interaction and `c.` for quantitative terms in the interaction.reg QuantResponseVar QuantExplanatoryVar i.CategoricalModeratingVar i.CategoricalModeratingVar#c.QuantExplanatoryVar
SAS
* if a predictor var is categorical, add to `class`; proc glm; class CategoricalModeratingVar; model QuantResponseVar=ExplanatoryVar|CategoricalModeratingVar /solution;
R
# to incorporate a statistical interaction between two of your explanatory variables my.lm <- lm(QuantResponseVar ~ ExplanatoryVar + CategoricalModeratingVar + ExplanatoryVar*CategoricalModeratingVar, data = myData) summary(my.lm)
Incorporating interaction term when response is Categorical (Logistic)
SPSS
* note if explanatory var is categorical, make sure that the variable is type `nominal`. LOGISTIC REGRESSION BinaryResponseVar with ExplanatoryVar ThirdVar1 ThirdVar2.
STATA
// for all categorical predictors, add `i.` before the variabe name (e.g. i.race) and `c.` before quantitative variables logistic BinaryResponseVar QuantExplanatoryVar i.CategoricalModeratingVar i.CategoricalModeratingVar#c.QuantExplanatoryVar
SAS
* list all categorical variables in the model under the class subcommand (e.g. CategThirdVar); proc logistic; class BinaryResponseVar(ref="referenceGroup") CategoricalModeratingVar; model BinaryResponseVar = ExplanatoryVar|CategoricalModeratingVar;
R
# if categorical variable is encoded as numeric, wrap it around with the factor() function (e.g. factor(ExplanatoryVar3) ) my.logreg <- glm(BinaryResponseVar ~ ExplanatoryVar + CategoricalModeratingVar + ExplanatoryVar*CategoricalModeratingVar, data = myData, family = "binomial") summary(my.logreg) # for p-values exp(my.logreg$coefficients) # for odds ratios exp(confint(my.logreg)) # for confidence intervals on the odds ratios