Producing different p value each time I 'Knit HTML'
<p>I have embedded some code in my Rmd file to perform t.test on a set of data. But weirdly, each time I click on 'Knit HTML', I see different outputs for p-value in the HTML file. But the same doesn't happen if I am running code in the console. Can somebody please help understand why it must be happening and how I can avoid it?
Below is that piece of code:</p>

<pre><code>```{r, echo=TRUE}
tresults &lt;- matrix(nrow = 4, ncol = 3)
for (i in 1:4){
options(scipen = 999) #Force are to not use exponential notation
tresult &lt;- t.test(years[[i]][,11], years[[i]][,21], var.equal = T, alternative = "greater")
tresults[i,] &lt;- as.numeric(c(tresult[[1]], tresult[[2]], tresult[[3]]))}
tresults &lt;- format(round(tresults, 3), nsmall = 3) #round off to 3 decimal points
tresults &lt;- cbind(c("2004-05", "2005-06", "2006-07", "2007-08"), tresults)
colnames(tresults) &lt;- c("years", "t", "df", "p-value")
print(tresults)
```
</code></pre>

<p>Edit:
'years' is basically a list that contains data-frame corresponding to each year - </p>

<pre><code>#List the datasets
years &lt;- list(prod_data_0405, prod_data_0506, prod_data_0607, prod_data_0708)
</code></pre>

<p>I have created a sample of this list, converted it to data-frame for the convenience of sharing using following command:</p>

<pre><code>years_sample &lt;- as.data.frame(do.call(rbind, years_sample))
</code></pre>

<p>and saved it on <a href="https://drive.google.com/open?id=0B0G1sKUlyodjYUtRV2F3SDBRQnc" rel="nofollow">this link</a>. Please use it to test the code and let me know.</p>

<p><strong>Edit 2</strong>
Here is the sample that I have created using dput(years)</p>

<pre><code>list(structure(list(ID = c(1, 2, 3, 4, 5, 6), Area..acres. = c(4, 
1, 2, 3, 1, 1), Cotton = c(2, 2.5, 2, 5, 3, 0), Pigeon.pea = c(0.33, 
NaN, 0.5, 0.21, NaN, 0), Soyabean = c(4, NaN, NaN, 6, NaN, NaN
), Sorghum = c("", "", "", "6", "", ""), Other = c(NaN, NaN, 
NaN, 1.6, NaN, NaN), Total.yield..Quintal. = c(6.33, 2.5, 5, 
23.56, 3, 0), Gross.Income..Rs. = c(4695, 4750, 4612.5, 11531.67, 
5700, 3800), Total.Expenditure..Rs. = c(1955, 1700, 2237, 3296.67, 
1520, 2900), Net.Income..Rs. = c(2740, 3050, 2366.5, 235, 4180, 
0), Area..acres..1 = c(1, 8, 2, 3, 5, 5), Cotton.1 = c("", "4.6", 
"5", "", "2.33", "0"), Pigeon.pea.1 = c(NaN, 0.4, 0.5, 0.33, 
0.2, 0), Soyabean.1 = c(NaN, 2, NaN, 0.23, 3, NaN), Sorghum.1 = c(4, 
11, NaN, NaN, 4.5, 0), Other.1 = c(NaN, NaN, NaN, NaN, NaN, NaN
), Total.yield..Quintal..1 = c(4, 40, 11, 1.7, 15.1, 0), Gross.Income..Rs..1 = c(3200, 
7603.12, 7612.5, 1013.33, 4705, 5980), Total.Expenditure..Rs..1 = c(1950, 
3042.7, 2850, 1193.33, 2060, 4050), Net.Income..Rs..1 = c(1250, 
4560.72, 4762.5, -150, 2645, 2852.5)), .Names = c("ID", "Area..acres.", 
"Cotton", "Pigeon.pea", "Soyabean", "Sorghum", "Other", "Total.yield..Quintal.", 
"Gross.Income..Rs.", "Total.Expenditure..Rs.", "Net.Income..Rs.", 
"Area..acres..1", "Cotton.1", "Pigeon.pea.1", "Soyabean.1", "Sorghum.1", 
"Other.1", "Total.yield..Quintal..1", "Gross.Income..Rs..1", 
"Total.Expenditure..Rs..1", "Net.Income..Rs..1"), row.names = c(NA, 
6L), class = "data.frame"), structure(list(ID = c(1, 2, 3, 4, 
5, 6), Area..acres. = c(2, 1, 2, 6, 1, 1), Cotton = c(NaN, 6, 
2, 1.75, NaN, NaN), Pigeon.pea = c(0.75, 2, NaN, 1, NaN, NaN), 
    Soyabean = c(4, NaN, 1.5, 2.75, 3, 3), Sorghum = c(1, NaN, 
    2, 1, NaN, NaN), Other = c(0.25, 0.1, NaN, NaN, NaN, NaN), 
    Total.yield..Quintal. = c(12, 8.1, 11, 18.5, 3, 3), Gross.Income..Rs. = c(6525, 
    3000, 5575, 4666.67, 3240, 3800), Total.Expenditure..Rs. = c(3785, 
    2290, 2270, 2450, 1950, 2900), Net.Income..Rs. = c(2740, 
    710, 3305, 2216.67, 1290, 900), Area..acres..1 = c(3, 2, 
    2, 5, 4, 5), Cotton.1 = c(2, 2.5, 2, NaN, 0.83, 3), Pigeon.pea.1 = c(0.75, 
    0.25, 1, NaN, 1, 0.62), Soyabean.1 = c("", "", "", "", "", 
    ""), Sorghum.1 = c(4, 0.1, 4, 1.5, 2, 3), Other.1 = c(NaN, 
    0.1, NaN, NaN, NaN, NaN), Total.yield..Quintal..1 = c(9.5, 
    5.7, 7, 3, 7.5, 17.5), Gross.Income..Rs..1 = c(4433.33, 3500, 
    4275, 1275, 2900, 5980), Total.Expenditure..Rs..1 = c(3823.33, 
    3270, 2660, 2075, 2262.5, 3560), Net.Income..Rs..1 = c(610, 
    230, 1615, 800, 637.5, 2420)), .Names = c("ID", "Area..acres.", 
"Cotton", "Pigeon.pea", "Soyabean", "Sorghum", "Other", "Total.yield..Quintal.", 
"Gross.Income..Rs.", "Total.Expenditure..Rs.", "Net.Income..Rs.", 
"Area..acres..1", "Cotton.1", "Pigeon.pea.1", "Soyabean.1", "Sorghum.1", 
"Other.1", "Total.yield..Quintal..1", "Gross.Income..Rs..1", 
"Total.Expenditure..Rs..1", "Net.Income..Rs..1"), row.names = c(NA, 
6L), class = "data.frame"), structure(list(ID = c(1, 2, 3, 4, 
5, 6), Area..acres. = c(2, 1.5, 2, 3, 2, 3), Cotton = c(NaN, 
2, NaN, 2.66, NaN, NaN), Pigeon.pea = c(NaN, 0.33, 0.4, 0.53, 
0.5, NaN), Soyabean = c(3.5, NaN, 2, NaN, 3, 2.66), Sorghum = c(NaN, 
NaN, NaN, 0.25, 2, NaN), Other = c(NaN, NaN, NaN, 0.19, NaN, 
NaN), Total.yield..Quintal. = c(NaN, 3.5, 4.8, 10.02, 11, 8), 
    Gross.Income..Rs. = c(4200, 4646.66, 5389, 6507.33, 6600, 
    3200), Total.Expenditure..Rs. = c("1670", "2060", "2385", 
    "2528.33", "3006.5", "1426.66"), Net.Income..Rs. = c(2530, 
    2586.66, 3004, 3979, 3592.5, 1773.34), Area..acres..1 = c(2, 
    1.5, 2, 7, 1.5, 7.5), Cotton.1 = c(2, 3.33, 3, 2.16, 2, 0.93
    ), Pigeon.pea.1 = c(1, 0.33, 0.4, 0.33, 0.26, 0.2), Soyabean.1 = c(NaN, 
    NaN, NaN, NaN, NaN, NaN), Sorghum.1 = c(NaN, NaN, NaN, 5, 
    NaN, 6), Other.1 = c(NaN, NaN, NaN, NaN, NaN, NaN), Total.yield..Quintal..1 = c(6, 
    5.5, 6.8, 20, 3.4, 14.5), Gross.Income..Rs..1 = c(5930, 7500, 
    6920, 5100, 4666, 2822.66), Total.Expenditure..Rs..1 = c(3225, 
    3400, 3610, 3654.28, 5600, 1754.66), Net.Income..Rs..1 = c(2705, 
    4100, 3310, 1445.72, -934, 1068)), .Names = c("ID", "Area..acres.", 
"Cotton", "Pigeon.pea", "Soyabean", "Sorghum", "Other", "Total.yield..Quintal.", 
"Gross.Income..Rs.", "Total.Expenditure..Rs.", "Net.Income..Rs.", 
"Area..acres..1", "Cotton.1", "Pigeon.pea.1", "Soyabean.1", "Sorghum.1", 
"Other.1", "Total.yield..Quintal..1", "Gross.Income..Rs..1", 
"Total.Expenditure..Rs..1", "Net.Income..Rs..1"), row.names = c(NA, 
6L), class = "data.frame"), structure(list(ID = c(1, 2, 3, 4, 
5, 6), Area..acres. = c(2, 2, 2, 3, 2, 1), Cotton = c(NaN, 3, 
2, NaN, NaN, 4), Pigeon.pea = c(NaN, NaN, 0.5, 0.5, 1.5, 1), 
    Soyabean = c(3.66, NaN, NaN, 3, 1, NaN), Sorghum = c(2, NaN, 
    NaN, 1, 2.5, NaN), Other = c(22, NaN, NaN, 0.17, NaN, NaN
    ), Total.yield..Quintal. = c(12.3, 6, 5, 14.3, 10, 5), Gross.Income..Rs. = c(6030, 
    6420, 5562, 8183.33, 7780, 11800), Total.Expenditure..Rs. = c(3192, 
    4080, 3350, 20530, 3240, 5130), Net.Income..Rs. = c(2838, 
    2340, 2212, 5653.33, 4540, 6670), Area..acres..1 = c(2, 1, 
    2, 8, 1, 5), Cotton.1 = c(2, 4, 2.5, 3, 5.8, 5), Pigeon.pea.1 = c(3, 
    NaN, 0.5, 0.7, NaN, 0.25), Soyabean.1 = c(1, NaN, NaN, NaN, 
    NaN, NaN), Sorghum.1 = c(NaN, NaN, NaN, 3.7, NaN, 2), Other.1 = c(NaN, 
    NaN, NaN, NaN, NaN, NaN), Total.yield..Quintal..1 = c(0, 
    4, 6, 28, 5.8, 23), Gross.Income..Rs..1 = c(8675, 9760, 6677.5, 
    7417.7, 13050, 10860), Total.Expenditure..Rs..1 = c(7700, 
    6750, 5425, 4112.5, 6300, 4870), Net.Income..Rs..1 = c(975, 
    3010, 1252.5, 3305.7, 4750, 5990)), .Names = c("ID", "Area..acres.", 
"Cotton", "Pigeon.pea", "Soyabean", "Sorghum", "Other", "Total.yield..Quintal.", 
"Gross.Income..Rs.", "Total.Expenditure..Rs.", "Net.Income..Rs.", 
"Area..acres..1", "Cotton.1", "Pigeon.pea.1", "Soyabean.1", "Sorghum.1", 
"Other.1", "Total.yield..Quintal..1", "Gross.Income..Rs..1", 
"Total.Expenditure..Rs..1", "Net.Income..Rs..1"), row.names = c(NA, 
6L), class = "data.frame"))
</code></pre>