kuekawa – My Statistical tools

#What works clearinghouse version of standardized program difference
#Hedges's g and Cox Index
#See page 15 and 16
#https://ies.ed.gov/ncee/wwc/Docs/referenceresources/WWC_Procedures_Handbook_V4_1_Draft.pdf
#Kaz has the web-based calculator -- to use for QC'ing my results here
#https://www.estat.us/file/calc_t_test1.php

CCC<-filter(match.data1,treat==0)
TTT<-filter(match.data1,treat==1)

#These are for raw database
#raw data
#CCC<-filter(studydata3,treatment==0)
#TTT<-filter(studydata3,treatment==1)
#CCC<-filter(psmdata,treat==0)
#TTT<-filter(psmdata,treat==1)

###############################################################################
#What works clearinghouse version of standardized program difference
#Hedges's g and Cox Index
#See page 15 and 16
#https://ies.ed.gov/ncee/wwc/Docs/referenceresources/WWC_Procedures_Handbook_V4_1_Draft.pdf
#Kaz has the web-based calculator -- to use for QC'ing my results here
#https://www.estat.us/file/calc_t_test1.php

#Hedges' g for continuous variables
#Kaz added the correct, sample size adjusted version of this while meeting with Samara for transition
kaz_macro_lin<-function(kaz1){
col_name <- deparse(substitute(kaz1))
C_mean<-mean(CCC[[col_name]])
T_mean<-mean(TTT[[col_name]])
C_sd<-sd(CCC[[col_name]])
T_sd<-sd(TTT[[col_name]])
C_n<-length(CCC[[col_name]])
T_n<-length(TTT[[col_name]])
total_n<-C_n+T_n
#linear
simple_gap=T_mean-C_mean
g1<- ((T_n-1)*(T_sd*T_sd))+((C_n-1)*(C_sd*C_sd))
g2= T_n + C_n -2
g3= sqrt(g1/g2)
wwc_effect= simple_gap/g3

#I didn't adjust for sample size
omega<-(1-3/( 4*total_n -9))
wwc_effect_n_adjusted= (omega*simple_gap)/g3
print(T_n)
print(C_n)
print(total_n)
print(T_mean)
print(C_mean)
print(T_sd)
print(C_sd)
print ("Hedges'g without sample size adjustment")
print(wwc_effect)
print ("Hedges'g with sample size adjustment (Use this)")
print(wwc_effect_n_adjusted)
print ("FYI: Adjustment factor")
print(omega)
}

#Cox Index
#Kaz added the correct, sample size adjusted version of this while meeting with Samara for transition
kaz_macro_bin<-function(kaz1){
col_name <- deparse(substitute(kaz1))
C_mean<-mean(CCC[[col_name]])
T_mean<-mean(TTT[[col_name]])
C_sd<-sd(CCC[[col_name]])
T_sd<-sd(TTT[[col_name]])
C_n<-length(CCC[[col_name]])
T_n<-length(TTT[[col_name]])

#binary
Odds_C<-(C_mean/(1-C_mean))
Odds_T<-(T_mean/(1-T_mean))

Odds_ratio<-Odds_T/Odds_C

LN_C<-log(Odds_C)
LN_T<-log(Odds_T)
LN_DIF<-LN_T-LN_C

# WWC_effect=(round(LN_DIF/1.65,0.001))
WWC_effect_binary<-(LN_DIF/1.65)

#sample size adjustment (Kaz is adding this on December 30 2022)
#I didn't use this for writing the report draft
total_n<-C_n+T_n
omega<-(1-3/( 4*total_n -9))
WWC_binary_effect_n_adjusted=(omega*LN_DIF)/1.65;
print(T_n)
print(C_n)
print(total_n)
print(T_mean)
print(C_mean)
print("Cox Index without sample size adjustment")
print(WWC_effect_binary)
print("Cox Index with sample size adjustment -- Use this")
print(WWC_binary_effect_n_adjusted)
print ("FYI: Adjustment factor")
print(omega)
}

###############################################################################
table(psmdata$treat)

kaz_macro_bin(male)
kaz_macro_bin(minority)
kaz_macro_bin(disadv)
kaz_macro_bin(binary_dualcredit)

kaz_macro_lin(GPA_12_GRADE)
kaz_macro_lin(SAT_TOTAL)

#Sam asked me to check this
kaz_macro_lin(TOTAL_DUALCREDIT)

kaz_macro_bin(enroll_FR_spring)
kaz_macro_bin(enroll_SP_fall)
kaz_macro_bin(enroll_SP_spring)

December 28, 2022

PHP syntax for calculating WWC standardized group difference (Hedges' g and Cox Index)

<?php

function compute()

{

$Tmean = $_POST['Tmean'];

$Cmean = $_POST['Cmean'];

$TSD = $_POST['TSD'];

$CSD = $_POST['CSD'];

$TN = $_POST['TN'];

$CN = $_POST['CN'];

$mean_dif=$Tmean-$Cmean;

$SE=sqrt(

(($TSD*$TSD) / $TN)+(($CSD*$CSD) / $CN)

);

$T=$mean_dif/$SE;

$DF=$TN+$CN-2;

$P="Under Development (Still working on this)";

/*$P=stats_dens_normal($T, 0,1);*/

/*$P=stats_dens_gamma(float $X, float $shape, float $scale);*/

/*$P= $T / 100 ;*/

/*Hedges g*/

/*g numerator*/

$g_numerator=($Tmean-$Cmean)*(1-3/((4*($TN+$CN))-9));

/*g demnominator*/

$g_denominator=SQRT(((($TN-1)* ($TSD**2) )+(($CN-1)* ($CSD**2) ))/($TN+$CN-2));

$hedges_d=$g_numerator/$g_denominator;

$hedges_d_abs=abs($hedges_d);

/*if binary variabels*/

$T_Odds=$Tmean/(1-$Tmean);

$C_Odds=$Cmean/(1-$Cmean);

$Odds_ratio=$T_Odds/$C_Odds;

$Tstep1=log($T_Odds);

$Cstep1=log($C_Odds);

$step2=$Tstep1-$Cstep1;

$WWC_binary_effect=$step2/1.65;

/*Use omega factor to adjust for data size*/

$total_num=$TN + $CN;

$omega=(1-3/( 4*$total_num -9));

$WWC_binary_effect_omega=($omega*$step2)/1.65;

if ($hedges_d >= 0.2) echo "Small Effect (Cohen)";

if ($hedges_d >= 0.5) echo "Medium Effect (Cohen)";

if ($hedges_d >= 0.8) echo "Large Effect (Cohen)";

echo " ";

echo "WWC group comparison of continuous variables";

echo " ";

echo "Values you entered:";

echo " ";

echo "Treatment N:" .$TN;

echo " ";

echo "Treatment mean:" .$Tmean;

echo " ";

echo "Treatment SD:" .$TSD;

echo " ";

echo "Comparison N:" .$CN;

echo " ";

echo "Comparison mean:" .$Cmean;

echo " ";

echo "Comparison SD:" .$CSD;

echo " ";

echo "The group mean difference:".round($mean_dif,2);

echo " ";

echo "without rounding:".round($mean_dif,5);

echo " ";

/*echo "Probability " .round($P,2);*/

echo "Probability: " .$P;

echo " ";

$abs_T=abs($T);

echo "T-score is: " .round($T,2);

echo " ";

echo "without rounding: " .round($T,5);

echo " ";

if($abs_T < 1.96 ) {

echo "Not significant at alpha 0.05 (two tail test;I used a z-test and ignored degree of freedom; threshold 1.96)";

}elseif($abs_T >=1.96){

echo "Significant at alpha 0.05 (two tail test;I used a z-test and ignored degree freedom; threshold 1.96)";

}

echo " ";

echo "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";echo " ";

echo "If a variable is an interval scale:";

echo " ";

echo "Hedges g " .round($hedges_d,2);

echo " ";

echo "without rounding: " .round($hedges_d,5);

echo " ";

echo "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";echo " ";

echo " ";

echo "Hedges g description";

echo " ";

echo "Page 16 of https://ies.ed.gov/ncee/wwc/Docs/referenceresources/WWC_Procedures_Handbook_V4_1_Draft.pdf";

echo " ";

echo "For continuous outcomes, the WWC has adopted the most commonly used effect size";

echo " ";

echo "index, the standardized mean difference known as Hedges’ g, with an adjustment for small";

echo " ";

echo "sample bias. For group design studies, this effect size is defined as the difference between the";

echo " ";

echo "mean outcome for the intervention group and the mean outcome for the comparison group, ";

echo " ";

echo "divided by the pooled within-group standard deviation of the outcome measure. Defining yi and ";

echo " ";

echo "yc as the means of the outcome for students in the intervention and comparison groups, ni and nc";

echo " ";

echo "as the student sample sizes, si and sc as the student-level standard deviations, given by ....";

echo " ";

echo "In addition, we define as the small sample size correction the effect size (Hedges 1981), which is given by ";

echo " ";

/*cohen's rule of thumb*/

echo "Cohen's rule of thumb";echo " ";

echo "if d >= 0.2 small effect -- if d >= 0.5 medium effect if --- d >= 0.8 large effect";echo " ";

if($hedges_d_abs < 0.2) {

echo "Close to zero and Not even small Effect (Cohen)";

}elseif($hedges_d_abs>=0.2 and $hedges_d_abs < 0.5){

echo "Small effect (Cohen)";

}elseif($hedges_d_abs>=0.5 and $hedges_d_abs < 0.8){

echo "Medium effect (Cohen)";

}elseif($hedges_d_abs>=0.8){

echo "Large effect (Cohen)";

}else {

echo "others";

}

echo " ";

echo "If a variable is obviously a continuous variable (e.g., MAX is greater than 1), ignore the result below (It says NAN)";

echo " ";

echo "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";echo " ";

echo "If the variable is a binary variable (0 or 1), the Cox index value is " .round($WWC_binary_effect,2);

echo " ";

echo "with a lot of digits without rounding " .round($WWC_binary_effect,5);echo " ";

echo "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";echo " ";

echo " ";

echo "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";echo " ";

echo "Omega adjusted (data size taken into consideration) " .round($WWC_binary_effect_omega,2);

echo " ";

echo "with a lot of digits without rounding " .round($WWC_binary_effect_omega,5);

echo " ";

echo "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";echo " ";

echo " ";

echo "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";echo " ";

echo "Odds ratio:" .round($Odds_ratio,2);

echo " ";

echo "without rounding " .round($Odds_ratio,5);

echo " ";

echo "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";echo " ";

echo " ";

echo "Cox Index description";

echo " ";

echo "Page 16 of https://ies.ed.gov/ncee/wwc/Docs/referenceresources/WWC_Procedures_Handbook_V4_1_Draft.pdf";

echo " ";

echo "For dichotomous outcomes, the difference in group means is calculated as the difference in";

echo " ";

echo "the probability of the occurrence of an event. The effect size measure of choice for dichotomous ";

echo " ";

echo "outcomes is the Cox index, which yields effect size values similar to the values of Hedges’ g that";

echo " ";

echo "one would obtain if group means, standard deviations, and sample sizes were available, assuming";

echo " ";

echo "the dichotomous outcome measure is based on an underlying logistic similar to a normal";

echo " ";

echo "distribution. Defining pi and pc as the probability of an outcome for students in the intervention";

echo " ";

echo "and comparison groups, the effect size is given by";

echo " ";

echo "";

echo " ";

}

/*echo "The result is: " . compute();*/

compute();

REFERENCE

Cohen's rule of thumb about effect sizes:

<li>If greater than 02, Small Effect

<li>If greater than 0.5, Medium Effect

<li>If greater 0.8 then Large Effect

Cohen, J. Statistical power for the behavioral sciences (2nd ed.). Hillsdale, NJ: Erlbaum (1988).

<ahref="https://wmich.edu/sites/default/files/attachments/u58/2015/Effect_Size_Substantive_Interpretation_Guidelines.pdf">

Effect Size Substantive Interpretation Guidelines: Issues in the Interpretation of Effect Sizes Jeff Valentine and Harris Cooper, Duke University(see page. 5)</a>

WWC related info:

<a href="https://ies.ed.gov/ncee/wwc/Docs/ReferenceResources/wwc_procedures_handbook_v4_draft.pdf">WWC procedures handbook (see page. 14)</a>

<a href="https://ies.ed.gov/ncee/wwc/Docs/OnlineTraining/wwc_training_m3.pdf">WWC standards slides (Definition of small sample size correction, slide 14)</a>

WWC considers the effect size greater than .25 substnatively important.

<a href="https://ies.ed.gov/ncee/wwc/Docs/referenceresources/wwc_procedures_handbook_v4.pdf">P.22 of WWC standards</a>

<a href="calc_t_test1.php">Back to the calculcator </a>

<a href="https://www.estat.us">My website</a>

Look at calc process t..1

November 30, 2022November 30, 2022

Odds ratio in SAS PROC LOGISTIC

Odds ratio in SAS PROC LOGISTICS are just

exp(coefficient)

This is obvious for binary variables.

Even for continuous variables, it's just

exp(coefficient)

..which means that I think it is mot counterintuitive to standardize continuous variables.

So one easy way to get odds ratios is to run PROC LOGISTICS with continuous variables standardized and use exp(X) in Excel.

November 29, 2022

SAS Proc logistic and WWC effect size

ods trace on;
proc logistic data=final DESCENDING;
model YA01_3_bin =
treat
male
age_log
CH_compass
/*R_compass*/
white
black
/*other_race*/;
ods output ParameterEstimates=kaz1;
run;

data kaz1b;
set kaz1;
if Variable="Intercept" or Variable="treat";
keep Variable Estimate;
run;
proc transpose data=kaz1b out=kaz1bt;
id Variable;
run;

data kaz1bt2;
set kaz1bt;
C_LOGIT=intercept;
T_LOGIT=intercept+treat;
C_EXP=exp(C_LOGIT)/(1+exp(C_LOGIT));
C_ODDS=C_EXP/(1-C_EXP);
C_STEP1=log(C_ODDS);

T_EXP=exp(T_LOGIT)/(1+exp(T_LOGIT));
T_ODDS=T_EXP/(1-T_EXP);
T_STEP1=log(T_ODDS);

STEP2=T_STEP1-C_STEP1;
wwc_effect_size=STEP2/1.65;
odds_ratio=T_ODDS/C_ODDS;
run;

November 27, 2022November 27, 2022

Python for Everybody - Full University Python Course

November 25, 2022November 26, 2022

WWC effect size omega factor (to adjust for n) and R sample

https://ies.ed.gov/ncee/wwc/Docs/referenceresources/WWC_Procedures_Handbook_V4_1_Draft.pdf

See Page 16.

two_values<-view1b[3:4]
num<-view1b[2]

omega<-(1-3/(4*num-9))

C_LOGIT<-two_values[1]
C_EXP<-exp(C_LOGIT)/(1+exp(C_LOGIT))
C_ODDS<-C_EXP/(1-C_EXP)
C_STEP1<-log(C_ODDS)
T_LOGIT<-two_values[1]+two_values[2]
T_EXP<-exp(T_LOGIT)/(1+exp(T_LOGIT))
T_ODDS<-T_EXP/(1-T_EXP)
T_STEP1<-log(T_ODDS)
STEP2<-T_STEP1-C_STEP1
wwc_effect_size<-STEP2/1.65

wwc_effect_size_omega<-(omega*STEP2)/1.65

odds_ratio<-T_ODDS/C_ODDS

Author: kuekawa

R packages not installing

Standard Maritime Communication Phrases

How to detach Paypal on Kajabi.

401K Websites

R code for deriving Hedge's g (or Cox Index)

PHP syntax for calculating WWC standardized group difference (Hedges' g and Cox Index)

Odds ratio in SAS PROC LOGISTIC

SAS Proc logistic and WWC effect size

Python for Everybody - Full University Python Course

WWC effect size omega factor (to adjust for n) and R sample